1
|
Frando A, Grundner C. More than two components: complexities in bacterial phosphosignaling. mSystems 2024; 9:e0028924. [PMID: 38591891 PMCID: PMC11097640 DOI: 10.1128/msystems.00289-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
For over 40 years, the two-component systems (TCSs) have taken front and center in our thinking about the signaling mechanisms by which bacteria sense and respond to their environment. In contrast, phosphorylation on Ser/Thr and Tyr (O-phosphorylation) was long thought to be mostly restricted to eukaryotes and a somewhat accessory signaling mechanism in bacteria. Several recent studies exploring systems aspects of bacterial O-phosphorylation, however, now show that it is in fact pervasive, with some bacterial proteomes as highly phosphorylated as those of eukaryotes. Labile, non-canonical protein phosphorylation sites on Asp, Arg, and His are now also being identified in large numbers in bacteria and first cellular functions are discovered. Other phosphomodifications on Cys, Glu, and Lys remain largely unexplored. The surprising breadth and complexity of bacterial phosphosignaling reveals a vast signaling capacity, the full scope of which we may only now be beginning to understand but whose functions are likely to affect all aspects of bacterial physiology and pathogenesis.
Collapse
Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| |
Collapse
|
2
|
Djorić D, Atkinson SN, Kristich CJ. Reciprocal regulation of enterococcal cephalosporin resistance by products of the autoregulated yvcJ-glmR-yvcL operon enhances fitness during cephalosporin exposure. PLoS Genet 2024; 20:e1011215. [PMID: 38512984 PMCID: PMC10986989 DOI: 10.1371/journal.pgen.1011215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/02/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Enterococci are commensal members of the gastrointestinal tract and also major nosocomial pathogens. They possess both intrinsic and acquired resistance to many antibiotics, including intrinsic resistance to cephalosporins that target bacterial cell wall synthesis. These antimicrobial resistance traits make enterococcal infections challenging to treat. Moreover, prior therapy with antibiotics, including broad-spectrum cephalosporins, promotes enterococcal proliferation in the gut, resulting in dissemination to other sites of the body and subsequent infection. As a result, a better understanding of mechanisms of cephalosporin resistance is needed to enable development of new therapies to treat or prevent enterococcal infections. We previously reported that flow of metabolites through the peptidoglycan biosynthesis pathway is one determinant of enterococcal cephalosporin resistance. One factor that has been implicated in regulating flow of metabolites into cell wall biosynthesis pathways of other Gram-positive bacteria is GlmR. In enterococci, GlmR is encoded as the middle gene of a predicted 3-gene operon along with YvcJ and YvcL, whose functions are poorly understood. Here we use genetics and biochemistry to investigate the function of the enterococcal yvcJ-glmR-yvcL gene cluster. Our results reveal that YvcL is a DNA-binding protein that regulates expression of the yvcJ-glmR-yvcL operon in response to cell wall stress. YvcJ and GlmR bind UDP-GlcNAc and reciprocally regulate cephalosporin resistance in E. faecalis, and binding of UDP-GlcNAc by YvcJ appears essential for its activity. Reciprocal regulation by YvcJ/GlmR is essential for fitness during exposure to cephalosporin stress. Additionally, our results indicate that enterococcal GlmR likely acts by a different mechanism than the previously studied GlmR of Bacillus subtilis, suggesting that the YvcJ/GlmR regulatory module has evolved unique targets in different species of bacteria.
Collapse
Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Samantha N. Atkinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| |
Collapse
|
3
|
Frando A, Boradia V, Grundner C. Regulatory Intersection of Two-component System and Ser/Thr Protein Kinase Signaling in Mycobacterium tuberculosis. J Mol Biol 2024; 436:168379. [PMID: 38043732 DOI: 10.1016/j.jmb.2023.168379] [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: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Phosphosignaling in bacteria is mediated by two distinct systems, the two-component systems (TCSs) and the protein Ser/Thr/Tyr, or O-phosphorylation systems. These two arms of phosphosignaling are currently thought to be largely independent from one another. We mined a deep Mycobacterium tuberculosis (Mtb) phosphoproteome and identified over 170 O-phosphorylation sites on histidine kinases and response regulators of TCSs, suggesting that the two signaling pathways extensively intersect. Several TCSs were phosphorylated on multiple sites, and many by multiple Ser/Thr protein kinases, suggesting convergent and cooperative regulatory interactions. To test in which way these O-phosphorylation sites affect TCS activity, we reconstituted the NarSL phosphorelay in vitro. The Ser/Thr protein kinase PknL phosphorylated the histidine kinase NarS and activated its autophosphorylating activity. A phosphoablative mutation at the PknL phosphorylation site Thr380 resulted in low autophosphorylating activity, whereas a phosphomimetic mutation strongly activated autophosphorylation. The phosphomimetic mutation also resulted in more efficient phosphotransfer from NarS to the response regulator NarL and suppression of gene expression. These data show control of NarSL signaling by STPKs through a phosphoswitch and point to extensive, functional crosstalk between TCSs and O-phosphorylation.
Collapse
Affiliation(s)
- Andrew Frando
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Vishant Boradia
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Christoph Grundner
- Seattle Children's Research Institute, Seattle, WA, United States; Department of Pediatrics, University of Washington, Seattle, WA, United States; Department of Global Health, United States.
| |
Collapse
|
4
|
Cho J, Manna AC, Snelling HS, Cheung AL. GraS signaling in Staphylococcus aureus is regulated by a single D35 residue in the extracellular loop. Microbiol Spectr 2023; 11:e0198223. [PMID: 37728380 PMCID: PMC10581149 DOI: 10.1128/spectrum.01982-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023] Open
Abstract
Bacterial two-component systems are crucial features of bacterial pathogens such as methicillin-resistant Staphylococcus aureus to overcome environmental and antimicrobial stresses by activating regulons to interfere with the bactericidal mechanisms. GraRS is a unique subset of two-component systems belonging to the intramembrane-sensing histidine kinase family (IM-HK) and is responsible for resistance to cationic host defense peptides. However, the precise manner by which the short 9-residue extracellular loop of the membrane sensor GraS detects the antimicrobial peptides and transduces the signal is not comprehensively understood. Here, we show that a single point mutation (D35A) in the extracellular loop of GraS blocked activation of GraRS, but this effect was also abrogated with graS mutations in the N-terminal transmembrane segments without any accompanying effect on GraS protein expression. Additionally, mutations in H120 and T172 in the dimerization/histidine phosphotransfer (DHp) domain of GraS increased activation without any accompanying enhancement in dimerization, likely due to disruption of the H120-T172 interaction that restricts rotational movements of the DHp helices since swapping H120 and T172 did not alter GraS activation. Notably, the enhancing effects of H120 and T172 mutations were abolished with a D35 mutation, highlighting the pivotal role of D35 in the 9-residue extracellular loop of GraS in GraR phosphorylation. In summary, our study delivers the significance of the D35 in the extracellular loop of GraS and ensuing changes in the N-terminal transmembrane helices as a model to illustrate signaling in the IM-HK subset of two-component regulatory systems. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen capable of infecting skin, blood, internal organs, and artificial medical devices. Generally, personal hygiene and a robust immune system can limit the spread of this pathogen; however, MRSA possesses an assortment of phenotypic tools to survive the hostile host environment including host defense peptides. More specifically, S. aureus utilizes two-component systems to sense noxious environmental cues to respond to harmful environmental elements. Our study focused on a two-component system called GraRS that S. aureus deploys against host defense peptides. We showed that one single residue in the extracellular loop of GraS and the adjacent membrane segment controlled the activation of GraRS, indicating the importance of a well-tuned-charged residue in the extracellular loop of GraS for sensing activity.
Collapse
Affiliation(s)
- Junho Cho
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Helah S. Snelling
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Ambrose L. Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| |
Collapse
|
5
|
VanZeeland NE, Schultz KM, Klug CS, Kristich CJ. Multisite Phosphorylation Regulates GpsB Function in Cephalosporin Resistance of Enterococcus faecalis. J Mol Biol 2023; 435:168216. [PMID: 37517789 PMCID: PMC10528945 DOI: 10.1016/j.jmb.2023.168216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Enterococci are normal human commensals and major causes of hospital-acquired infections. Enterococcal infections can be difficult to treat because enterococci harbor intrinsic and acquired antibiotic resistance, such as resistance to cephalosporins. In Enterococcus faecalis, the transmembrane kinase IreK, a member of the bacterial PASTA kinase family, is essential for cephalosporin resistance. The activity of IreK is boosted by the cytoplasmic protein GpsB, which promotes IreK autophosphorylation and signaling to drive cephalosporin resistance. A previous phosphoproteomics study identified eight putative IreK-dependent phosphorylation sites on GpsB, but the functional importance of GpsB phosphorylation was unknown. Here we used genetic and biochemical approaches to define three sites of phosphorylation on GpsB that functionally impact IreK activity and cephalosporin resistance. Phosphorylation at two sites (S80 and T84) serves to impair the ability of GpsB to activate IreK in vivo, suggesting phosphorylation of these sites acts as a means of negative feedback for IreK. The third site of phosphorylation (T133) occurs in a segment of GpsB termed the C-terminal extension that is unique to enterococcal GpsB homologs. The C-terminal extension is highly mobile in solution, suggesting it is largely unstructured, and phosphorylation of T133 appears to enable efficient phosphorylation at S80 / T84. Overall our results are consistent with a model in which multisite phosphorylation of GpsB impairs its ability to activate IreK, thereby diminishing signal transduction through the IreK-dependent pathway and modulating phenotypic cephalosporin resistance.
Collapse
Affiliation(s)
- Nicole E VanZeeland
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Kathryn M Schultz
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA.
| |
Collapse
|
6
|
GpsB Promotes PASTA Kinase Signaling and Cephalosporin Resistance in Enterococcus faecalis. J Bacteriol 2022; 204:e0030422. [PMID: 36094306 PMCID: PMC9578390 DOI: 10.1128/jb.00304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Enterococci are opportunistic pathogens that can cause severe bacterial infections. Treatment of these infections is challenging because enterococci possess intrinsic and acquired mechanisms of resistance to commonly used antibiotics, including cephalosporins. The transmembrane serine/threonine PASTA kinase, IreK, is an important determinant of enterococcal cephalosporin resistance. Upon exposure to cephalosporins, IreK becomes autophosphorylated, which stimulates its kinase activity to phosphorylate downstream substrates and drive cephalosporin resistance. However, the molecular mechanisms that modulate IreK autophosphorylation in response to cell wall stress, such as that induced by cephalosporins, remain unknown. A cytoplasmic protein, GpsB, promotes signaling by PASTA kinase homologs in other bacterial species, but the function of enterococcal GpsB has not been previously investigated. We used in vitro and in vivo approaches to test the hypothesis that enterococcal GpsB promotes IreK signaling in response to cephalosporins to drive cephalosporin resistance. We found that GpsB promotes IreK activity both in vivo and in vitro. This effect is required for cephalosporins to trigger IreK autophosphorylation and activation of an IreK-dependent signaling pathway, and thereby is also required for enterococcal intrinsic cephalosporin resistance. Moreover, analyses of GpsB mutants and a ΔireK gpsB double mutant suggest that GpsB has an additional function, beyond regulation of IreK activity, which is required for optimal growth and full cephalosporin resistance. Collectively, our data provide new insights into the mechanism of signal transduction by the PASTA kinase IreK and the mechanism of enterococcal intrinsic cephalosporin resistance. IMPORTANCE Enterococci are opportunistic pathogens that can cause severe bacterial infections. Treatment of these infections is challenging because enterococci possess intrinsic and acquired resistance to commonly used antibiotics. In particular, enterococci are intrinsically resistant to cephalosporin antibiotics, a trait that requires the activity of a transmembrane serine/threonine kinase, IreK, which belongs to the bacterial PASTA kinase family. The mechanisms by which PASTA kinases are regulated in cells are poorly understood. Here, we report that the cytoplasmic protein GpsB directly promotes IreK signaling in enterococci to drive cephalosporin resistance. Thus, we provide new insights into PASTA kinase regulation and control of enterococcal cephalosporin resistance, and suggest that GpsB could be a promising target for new therapeutics to disable cephalosporin resistance.
Collapse
|
7
|
Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
Collapse
Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
8
|
Abstract
Enterococcus faecalis is an opportunistic pathogen and a major cause of severe nosocomial infections. Treatment options against enterococcal infections are declining due to the resistance of enterococci to numerous antibiotics. A key risk factor for developing enterococcal infections is treatment with cephalosporin antibiotics, to which enterococci are intrinsically resistant. For susceptible organisms, cephalosporins inhibit bacterial growth by acylating the active site of penicillin-binding proteins (PBPs), key enzymes that catalyze peptidoglycan cross-linking. Two specific PBPs of enterococci, Pbp4(5) and PbpA(2b), exhibit low reactivity toward cephalosporins, allowing these PBPs to cross-link peptidoglycan in the presence of cephalosporins to drive resistance in enterococci, but the mechanisms by which these PBPs are regulated are poorly understood. The CroS/R two-component signal transduction system (TCS) is also required for cephalosporin resistance. Activation of CroS/R by cephalosporins leads to CroR-dependent changes in gene expression. However, the specific genes regulated by CroS/R that are responsible for cephalosporin resistance remain largely unknown. In this study, we characterized CroR-dependent transcriptome remodeling by RNA-seq, identifying pbp4(5) as a CroR regulon member in multiple, diverse lineages of E. faecalis. Through genetic analysis of the pbp4(5) and croR promoters, we uncovered a CroR-dependent regulatory motif. Mutations in this motif to disrupt CroR-dependent upregulation of pbp4(5) in the presence of cell wall stress resulted in a reduction of resistance to cephalosporins in E. faecalis, demonstrating that enhanced production of Pbp4(5) and likely other proteins involved in peptidoglycan biogenesis by the CroS/R system drives enterococcal cephalosporin resistance.
Collapse
|
9
|
Antimicrobial tolerance and its role in the development of resistance: Lessons from enterococci. Adv Microb Physiol 2022; 81:25-65. [PMID: 36167442 DOI: 10.1016/bs.ampbs.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria have developed resistance against every antimicrobial in clinical use at an alarming rate. There is a critical need for more effective use of antimicrobials to both extend their shelf life and prevent resistance from arising. Significantly, antimicrobial tolerance, i.e., the ability to survive but not proliferate during antimicrobial exposure, has been shown to precede the development of bona fide antimicrobial resistance (AMR), sparking a renewed and rapidly increasing interest in this field. As a consequence, problematic infections for the first time are now being investigated for antimicrobial tolerance, with increasing reports demonstrating in-host evolution of antimicrobial tolerance. Tolerance has been identified in a wide array of bacterial species to all bactericidal antimicrobials. Of particular interest are enterococci, which contain the opportunistic bacterial pathogens Enterococcus faecalis and Enterococcus faecium. Enterococci are one of the leading causes of hospital-acquired infection and possess intrinsic tolerance to a number of antimicrobial classes. Persistence of these infections in the clinic is of growing concern, particularly for the immunocompromised. Here, we review current known mechanisms of antimicrobial tolerance, and include an in-depth analysis of those identified in enterococci with implications for both the development and prevention of AMR.
Collapse
|
10
|
Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
Collapse
|
11
|
Ulrych A, Fabrik I, Kupčík R, Vajrychová M, Doubravová L, Branny P. Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation. J Mol Biol 2021; 433:167319. [PMID: 34688688 DOI: 10.1016/j.jmb.2021.167319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that encodes a single eukaryotic-type Ser/Thr protein kinase StkP and its functional counterpart, the protein phosphatase PhpP. These signaling enzymes play critical roles in coordinating cell division and growth in pneumococci. In this study, we determined the proteome and phosphoproteome profiles of relevant mutants. Comparison of those with the wild-type provided a representative dataset of novel phosphoacceptor sites and StkP-dependent substrates. StkP phosphorylates key proteins involved in cell division and cell wall biosynthesis in both the unencapsulated laboratory strain Rx1 and the encapsulated virulent strain D39. Furthermore, we show that StkP plays an important role in triggering an adaptive response induced by a cell wall-directed antibiotic. Phosphorylation of the sensor histidine kinase WalK and downregulation of proteins of the WalRK core regulon suggest crosstalk between StkP and the WalRK two-component system. Analysis of proteomic profiles led to the identification of gene clusters regulated by catabolite control mechanisms, indicating a tight coupling of carbon metabolism and cell wall homeostasis. The imbalance of steady-state protein phosphorylation in the mutants as well as after antibiotic treatment is accompanied by an accumulation of the global Spx regulator, indicating a Spx-mediated envelope stress response. In summary, StkP relays the perceived signal of cell wall status to key cell division and regulatory proteins, controlling the cell cycle and cell wall homeostasis.
Collapse
Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Rudolf Kupčík
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| |
Collapse
|
12
|
King A, Blackledge MS. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem Biol Drug Des 2021; 98:1038-1064. [PMID: 34581492 PMCID: PMC8616828 DOI: 10.1111/cbdd.13962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a global and pressing concern. Our current therapeutic arsenal is increasingly limited as bacteria are developing resistance at a rate that far outpaces our ability to create new treatments. Novel approaches to treating and curing bacterial infections are urgently needed. Bacterial kinases have been increasingly explored as novel drug targets and are poised for development into novel therapeutic agents to combat bacterial infections. This review describes several general classes of bacterial kinases that play important roles in bacterial growth, antibiotic resistance, and biofilm formation. General features of these kinase classes are discussed and areas of particular interest for the development of inhibitors will be highlighted. Small molecule kinase inhibitors are described and organized by phenotypic effect, spotlighting particularly interesting inhibitors with novel functions and potential therapeutic benefit. Finally, we provide our perspective on the future of bacterial kinase inhibition as a viable strategy to combat bacterial infections and overcome the pressures of increasing antibiotic resistance.
Collapse
Affiliation(s)
- Ashley King
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| | - Meghan S. Blackledge
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| |
Collapse
|
13
|
Nagarajan SN, Lenoir C, Grangeasse C. Recent advances in bacterial signaling by serine/threonine protein kinases. Trends Microbiol 2021; 30:553-566. [PMID: 34836791 DOI: 10.1016/j.tim.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been nearly three decades since the discovery of the first bacterial serine/threonine protein kinase (STPK). Since then, a blend of technological advances has led to the characterization of a multitude of STPKs and phosphorylation substrates in several bacterial species that finely regulate intricate signaling cascades. Years of intense research from several laboratories have demonstrated unexpected roles for serine/threonine phosphorylation, regulating not only bacterial growth and cell division but also antibiotic persistence, virulence and infection, metabolism, chromosomal biology, and cellular differentiation. This review aims to provide an account of the most recent and significant developments in this up and growing field in microbiology.
Collapse
Affiliation(s)
- Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
| |
Collapse
|
14
|
Iannetta AA, Minton NE, Uitenbroek AA, Little JL, Stanton CR, Kristich CJ, Hicks LM. IreK-Mediated, Cell Wall-Protective Phosphorylation in Enterococcus faecalis. J Proteome Res 2021; 20:5131-5144. [PMID: 34672600 PMCID: PMC10037947 DOI: 10.1021/acs.jproteome.1c00635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Enterococcus faecalis is a Gram-positive bacterium that is a major cause of hospital-acquired infections due, in part, to its intrinsic resistance to cell wall-active antimicrobials. One critical determinant of this resistance is the transmembrane kinase IreK, which belongs to the penicillin-binding protein and serine/threonine kinase-associated kinase family of bacterial signaling proteins involved with the regulation of cell wall homeostasis. The activity of IreK is enhanced in response to cell wall stress, but direct substrates of IreK phosphorylation, leading to antimicrobial resistance, are largely unknown. To better understand stress-modulated phosphorylation events contributing to antimicrobial resistance, wild type E. faecalis cells treated with cell wall-active antimicrobials, chlorhexidine or ceftriaxone, were examined via phosphoproteomics. Among the most prominent changes was increased phosphorylation of divisome components after both treatments, suggesting that E. faecalis modulates cell division in response to cell wall stress. Phosphorylation mediated by IreK was then determined via a similar analysis with a E. faecalis ΔireK mutant strain, revealing potential IreK substrates involved with the regulation of peptidoglycan biosynthesis and within the E. faecalis CroS/R two-component system, another signal transduction pathway that promotes antimicrobial resistance. These results reveal critical insights into the biological functions of IreK.
Collapse
Affiliation(s)
- Anthony A. Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicole E. Minton
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Alexis A. Uitenbroek
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Jaime L. Little
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Caroline R. Stanton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
15
|
Ramos Y, Sansone S, Morales DK. Sugarcoating it: Enterococcal polysaccharides as key modulators of host-pathogen interactions. PLoS Pathog 2021; 17:e1009822. [PMID: 34499702 PMCID: PMC8428557 DOI: 10.1371/journal.ppat.1009822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
| | - Stephanie Sansone
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- Department of Urology, Weill Cornell Medicine, New York, New York, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
16
|
Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
Collapse
Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| |
Collapse
|
17
|
Chatterjee A, Willett JLE, Dunny GM, Duerkop BA. Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PLoS Genet 2021; 17:e1009204. [PMID: 33411815 PMCID: PMC7790226 DOI: 10.1371/journal.pgen.1009204] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are being considered as alternative therapeutics for the treatment of multidrug resistant bacterial infections. Considering phages have narrow host-ranges, it is generally accepted that therapeutic phages will have a marginal impact on non-target bacteria. We have discovered that lytic phage infection induces transcription of type VIIb secretion system (T7SS) genes in the pathobiont Enterococcus faecalis. Membrane damage during phage infection induces T7SS gene expression resulting in cell contact dependent antagonism of different Gram positive bystander bacteria. Deletion of essB, a T7SS structural component, abrogates phage-mediated killing of bystanders. A predicted immunity gene confers protection against T7SS mediated inhibition, and disruption of its upstream LXG toxin gene rescues growth of E. faecalis and Staphylococcus aureus bystanders. Phage induction of T7SS gene expression and bystander inhibition requires IreK, a serine/threonine kinase, and OG1RF_11099, a predicted GntR-family transcription factor. Additionally, sub-lethal doses of membrane targeting and DNA damaging antibiotics activated T7SS expression independent of phage infection, triggering T7SS antibacterial activity against bystander bacteria. Our findings highlight how phage infection and antibiotic exposure of a target bacterium can affect non-target bystander bacteria and implies that therapies beyond antibiotics, such as phage therapy, could impose collateral damage to polymicrobial communities. Renewed interest in phages as alternative therapeutics to combat multi-drug resistant bacterial infections, highlights the importance of understanding the consequences of phage-bacteria interactions in the context of microbial communities. Although it is well established that phages are highly specific for their host bacterium, there is no clear consensus on whether or not phage infection (and thus phage therapy) would impose collateral damage to non-target bacteria in polymicrobial communities. Here we provide direct evidence of how phage infection of a clinically relevant pathogen triggers an intrinsic type VII secretion system (T7SS) antibacterial response that consequently restricts the growth of neighboring bacterial cells that are not susceptible to phage infection. Phage induction of T7SS activity is a stress response and in addition to phages, T7SS antagonism can be induced using sub-inhibitory concentrations of antibiotics that facilitate membrane or DNA damage. Together these data show that a bacterial pathogen responds to diverse stressors to induce T7SS activity which manifests through the antagonism of neighboring non-kin bystander bacterial cells.
Collapse
Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Julia L. E. Willett
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail:
| |
Collapse
|
18
|
Affiliation(s)
- Felicity Alcock
- Microbes in Health and Disease Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
19
|
Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis. mBio 2020; 11:mBio.02962-20. [PMID: 33234689 PMCID: PMC7701990 DOI: 10.1128/mbio.02962-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enterococci are leading causes of antibiotic-resistant infection transmitted in hospitals. The intrinsic hardiness of these organisms allows them to survive disinfection practices and then proliferate in the gastrointestinal tracts of antibiotic-treated patients. The objective of this study was to identify the underlying genetic basis for its unusual hardiness. Using a functional genomic approach, we identified traits and pathways of general importance for enterococcal survival and growth that distinguish them from closely related pathogens as well as ancestrally related species. We further identified unique traits that enable them to survive antibiotic challenge, revealing a large set of genes that contribute to intrinsic antibiotic resistance and a smaller set of uniquely important genes that are rare outside enterococci. The enterococci, which are among the leading causes of multidrug-resistant (MDR) hospital infection, are notable for their environmental ruggedness, which extends to intrinsic antibiotic resistance. To identify genes that confer this unique property, we used Tn-seq to comprehensively explore the genome of MDR Enterococcus faecalis strain MMH594 for genes important for growth in nutrient-containing medium and with low-level antibiotic challenge. As expected, a large core of genes for DNA replication, expression, and central metabolism, shared with other bacteria, are intolerant to transposon disruption. However, genes were identified that are important to E. faecalis that are either absent from or unimportant for Staphylococcus aureus and Streptococcus pneumoniae fitness when similarly tested. Further, 217 genes were identified that when challenged by sub-MIC antibiotic levels exhibited reduced tolerance to transposon disruption, including those previously shown to contribute to intrinsic resistance, and others not previously ascribed this role. E. faecalis is one of the few Gram-positive bacteria experimentally shown to possess a functional Entner-Doudoroff pathway for carbon metabolism, a pathway that contributes to stress tolerance in other microbes. Through functional genomics and network analysis we defined the unusual structure of this pathway in E. faecalis and assessed its importance. These approaches also identified toxin-antitoxin and related systems that are unique and active in E. faecalis. Finally, we identified genes that are absent in the closest nonenterococcal relatives, the vagococci, and that contribute importantly to fitness with and without antibiotic selection, advancing an understanding of the unique biology of enterococci.
Collapse
|
20
|
Djorić D, Minton NE, Kristich CJ. The enterococcal PASTA kinase: A sentinel for cell envelope stress. Mol Oral Microbiol 2020; 36:132-144. [PMID: 32945615 DOI: 10.1111/omi.12313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Enterococci are Gram-positive, opportunistic pathogens that reside throughout the gastrointestinal tracts of most terrestrial organisms. Enterococci are resistant to many antibiotics, which makes enterococcal infections difficult to treat. Enterococci are also particularly hardy bacteria that can tolerate a variety of environmental stressors. Understanding how enterococci sense and respond to the extracellular environment to enact adaptive biological responses may identify new targets that can be exploited for development of treatments for enterococcal infections. Bacterial eukaryotic-like serine/threonine kinases (eSTKs) and cognate phosphatases (STPs) are important signaling systems that mediate biological responses to extracellular stimuli. Some bacterial eSTKs are transmembrane proteins that contain a series of extracellular repeats of the penicillin-binding and Ser/Thr kinase-associated (PASTA) domain, leading to their designation as "PASTA kinases." Enterococcal genomes encode a single PASTA kinase and its cognate phosphatase. Investigations of the enterococcal PASTA kinase revealed its importance in resistance to antibiotics and other cell wall stresses, in enterococcal colonization of the mammalian gut, clues about its mechanism of signal transduction, and its integration with other enterococcal signal transduction systems. In this review, we describe the current state of knowledge of PASTA kinase signaling in enterococci and describe important gaps that still need to be addressed to provide a better understanding of this important signaling system.
Collapse
Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicole E Minton
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
| |
Collapse
|
21
|
Regulation of virulence and antibiotic resistance in Gram-positive microbes in response to cell wall-active antibiotics. Curr Opin Infect Dis 2020; 32:217-222. [PMID: 31021953 DOI: 10.1097/qco.0000000000000542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Antibiotic stress can evoke considerable genotypic and phenotypic changes in Gram-positive bacteria. Here, we review recent studies describing altered virulence expression in response to cell wall-acting antibiotics and discuss mechanisms that coordinate regulation of the antibiotic response. RECENT FINDINGS Pleiotropic effects induced by antibiotic exposure include alterations to bacterial metabolism, cell wall structure and antibiotic resistance. In addition, subinhibitory concentrations of cell wall-active (CWA) antibiotics have increasingly been shown to induce the production of exotoxins and biofilm formation that may influence virulence. Remarkably, phenotypes associated with comparable antibiotic stresses can vary considerably, emphasizing the need to better understand the response to CWA antibiotics. Recent studies support both direct antibiotic recognition and recognition of antibiotic-induced stress to the bacterial cell wall. Specifically, bacterial two-component systems, penicillin-binding protein and serine/threonine kinase-associated kinases and conserved oxidative-stress sensors each contribute to modulating the antibiotic stress response. SUMMARY Bacterial sensory systems and global regulators coordinate signaling in response to CWA antibiotics. Regulation of the antibiotic response is complex and involves integration of signals from multiple response pathways. A better definition of the antibiotic stress response among Gram-positive pathogens may yield novel therapeutic targets to counter antibiotic resistance and virulence factor expression.
Collapse
|
22
|
Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
Collapse
Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
23
|
Maltas J, Wood KB. Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance. PLoS Biol 2019; 17:e3000515. [PMID: 31652256 PMCID: PMC6834293 DOI: 10.1371/journal.pbio.3000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/06/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Evolved resistance to one antibiotic may be associated with "collateral" sensitivity to other drugs. Here, we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict because independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. Although phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in a four-drug uniform cycle.
Collapse
Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
24
|
Role of epaQ, a Previously Uncharacterized Enterococcus faecalis Gene, in Biofilm Development and Antimicrobial Resistance. J Bacteriol 2019; 201:JB.00078-19. [PMID: 30910809 DOI: 10.1128/jb.00078-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/15/2019] [Indexed: 12/31/2022] Open
Abstract
Enterococcus faecalis is a commensal of the human gastrointestinal tract; it is also an opportunistic pathogen and one of the leading causes of hospital-acquired infections. E. faecalis produces biofilms that are highly resistant to antibiotics, and it has been previously reported that certain genes of the epa operon contribute to biofilm-associated antibiotic resistance. Despite several studies examining the epa operon, many gene products of this operon remain annotated as hypothetical proteins. Here, we further explore the epa operon; we identified epaQ, currently annotated as encoding a hypothetical membrane protein, as being important for biofilm formation in the presence of the antibiotic daptomycin. Mutants with disruptions of epaQ were more susceptible to daptomycin relative to the wild type, suggesting its importance in biofilm-associated antibiotic resistance. Furthermore, the ΔepaQ mutant exhibited an altered biofilm architectural arrangement and formed small aggregates in liquid cultures. Our cumulative data show that epa mutations result in altered polysaccharide content, increased cell surface hydrophobicity, and decreased membrane potential. Surprisingly, several epa mutations significantly increased resistance to the antibiotic ceftriaxone, indicating that the way in which the epa operon impacts antibiotic resistance is antibiotic dependent. These results further define the key role of epa in antibiotic resistance in biofilms and in biofilm architecture.IMPORTANCE E. faecalis is a common cause of nosocomial infection, has a high level of antibiotic resistance, and forms robust biofilms. Biofilm formation is associated with increased antibiotic resistance. Therefore, a thorough understanding of biofilm-associated antibiotic resistance is important for combating resistance. Several genes from the epa operon have previously been implicated in biofilm-associated antibiotic resistance, pathogenesis, and competitive fitness in the GI tract, but most genes in this locus remain uncharacterized. Here, we examine epaQ, which has not been characterized functionally. We show that the ΔepaQ mutant exhibits reduced biofilm formation in the presence of daptomycin, altered biofilm architecture, and increased resistance to ceftriaxone, further expanding our understanding of the contribution of this operon to intrinsic enterococcal antibiotic resistance and biofilm growth.
Collapse
|
25
|
Cleverley RM, Rutter ZJ, Rismondo J, Corona F, Tsui HCT, Alatawi FA, Daniel RA, Halbedel S, Massidda O, Winkler ME, Lewis RJ. The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes. Nat Commun 2019; 10:261. [PMID: 30651563 PMCID: PMC6335420 DOI: 10.1038/s41467-018-08056-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/07/2018] [Indexed: 01/01/2023] Open
Abstract
Bacterial growth and cell division requires precise spatiotemporal regulation of the synthesis and remodelling of the peptidoglycan layer that surrounds the cytoplasmic membrane. GpsB is a cytosolic protein that affects cell wall synthesis by binding cytoplasmic mini-domains of peptidoglycan synthases to ensure their correct subcellular localisation. Here, we describe critical structural features for the interaction of GpsB with peptidoglycan synthases from three bacterial species (Bacillus subtilis, Listeria monocytogenes and Streptococcus pneumoniae) and suggest their importance for cell wall growth and viability in L. monocytogenes and S. pneumoniae. We use these structural motifs to identify novel partners of GpsB in B. subtilis and extend the members of the GpsB interactome in all three bacterial species. Our results support that GpsB functions as an adaptor protein that mediates the interaction between membrane proteins, scaffolding proteins, signalling proteins and enzymes to generate larger protein complexes at specific sites in a bacterial cell cycle-dependent manner.
Collapse
Affiliation(s)
- Robert M Cleverley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Zoe J Rutter
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Jeanine Rismondo
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2DD, UK
| | - Federico Corona
- Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cagliari, 09100, Italy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Fuad A Alatawi
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4AX, UK
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4AX, UK
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
| | - Orietta Massidda
- Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cagliari, 09100, Italy
- Department CIBIO, University of Trento, via Sommarive 9, 38123, Povo, Italy
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, 47405, USA
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|