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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [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: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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2
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Chrenková A, Bisiak F, Brodersen DE. Breaking bad nucleotides: understanding the regulatory mechanisms of bacterial small alarmone hydrolases. Trends Microbiol 2024; 32:769-780. [PMID: 38262803 DOI: 10.1016/j.tim.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Guanosine tetra- and pentaphosphate nucleotides, (p)ppGpp, function as central secondary messengers and alarmones in bacterial cell biology, signalling a range of stress conditions, including nutrient starvation and exposure to cell-wall-targeting antibiotics, and are critical for survival. While activation of the stringent response and alarmone synthesis on starved ribosomes by members of the RSH (Rel) class of proteins is well understood, much less is known about how single-domain small alarmone synthetases (SASs) and their corresponding alarmone hydrolases, the small alarmone hydrolases (SAHs), are regulated and contribute to (p)ppGpp homeostasis. The substrate spectrum of these enzymes has recently been expanded to include hyperphosphorylated adenosine nucleotides, suggesting that they take part in a highly complex and interconnected signalling network. In this review, we provide an overview of our understanding of the SAHs and discuss their structure, function, regulation, and phylogeny.
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Affiliation(s)
- Adriana Chrenková
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Francesco Bisiak
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark.
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3
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Barbuti MD, Lambert E, Myrbråten IS, Ducret A, Stamsås GA, Wilhelm L, Liu X, Salehian Z, Veening JW, Straume D, Grangeasse C, Perez C, Kjos M. The function of CozE proteins is linked to lipoteichoic acid biosynthesis in Staphylococcus aureus. mBio 2024; 15:e0115724. [PMID: 38757970 PMCID: PMC11237490 DOI: 10.1128/mbio.01157-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024] Open
Abstract
Coordinated membrane and cell wall synthesis is vital for maintaining cell integrity and facilitating cell division in bacteria. However, the molecular mechanisms that underpin such coordination are poorly understood. Here we uncover the pivotal roles of the staphylococcal proteins CozEa and CozEb, members of a conserved family of membrane proteins previously implicated in bacterial cell division, in the biosynthesis of lipoteichoic acids (LTA) and maintenance of membrane homeostasis in Staphylococcus aureus. We establish that there is a synthetic lethal relationship between CozE and UgtP, the enzyme synthesizing the LTA glycolipid anchor Glc2DAG. By contrast, in cells lacking LtaA, the flippase of Glc2DAG, the essentiality of CozE proteins was alleviated, suggesting that the function of CozE proteins is linked to the synthesis and flipping of the glycolipid anchor. CozE proteins were indeed found to modulate the flipping activity of LtaA in vitro. Furthermore, CozEb was shown to control LTA polymer length and stability. Together, these findings establish CozE proteins as novel players in membrane homeostasis and LTA biosynthesis in S. aureus.IMPORTANCELipoteichoic acids are major constituents of the cell wall of Gram-positive bacteria. These anionic polymers are important virulence factors and modulators of antibiotic susceptibility in the important pathogen Staphylococcus aureus. They are also critical for maintaining cell integrity and facilitating proper cell division. In this work, we discover that a family of membrane proteins named CozE is involved in the biosynthesis of lipoteichoic acids (LTAs) in S. aureus. CozE proteins have previously been shown to affect bacterial cell division, but we here show that these proteins affect LTA length and stability, as well as the flipping of glycolipids between membrane leaflets. This new mechanism of LTA control may thus have implications for the virulence and antibiotic susceptibility of S. aureus.
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Affiliation(s)
- Maria Disen Barbuti
- 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
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UM 5086, Université de Lyon, Lyon, France
| | - Gro Anita Stamsås
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Linus Wilhelm
- Molecular Microbiology and Structural Biochemistry, CNRS UM 5086, Université de Lyon, Lyon, France
| | - Xue Liu
- Department of Pathogen, Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Zhian Salehian
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UM 5086, Université de Lyon, Lyon, France
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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4
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Li J, Wang R, Liu Y, Miao X. Role of ERA protein in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in Synechococcus elongatus PCC 7942. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159431. [PMID: 37977490 DOI: 10.1016/j.bbalip.2023.159431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Glyceroglycolipids are the primary thylakoid membrane lipids in cyanobacteria. Their diverse bioactivities have led to extensive utilization in the biomedical industry. In this study, we elucidated the role of ERA (E. coli Ras-like protein) in augmenting glyceroglycolipid synthesis and bolstering stress resilience in Synechococcus elongatus PCC 7942 during phosphate starvation. Notably, the ERA overexpression strain (ERA OE) outperformed the wild-type (WT) strain under phosphate-starved conditions, displaying an average 13.9 % increase in biomass over WT during the entire growth period, peaking at 0.185 g L-1 of dry cell weight on day 6. Lipidomic analysis using UHPLC-MS/MS techniques revealed that ERA OE exhibited a higher total glyceroglycolipid content compared to WT under phosphate starvation, representing a 7.95 % increase over WT and constituting a maximum of 5.07 % of dry cell weight on day 6. Transcriptomic analysis identified a significant up-regulation of the gldA gene (encoding glycerol dehydrogenase) involved in glycerolipid metabolism due to overexpression of ERA during phosphate starvation. These findings suggest a potential mechanism by which ERA regulates glyceroglycolipid synthesis through the up-regulation of GldA, thereby enhancing phosphate starvation tolerance in S. elongatus PCC 7942. Furthermore, lipidomic analysis revealed that ERA facilitated the production of glyceroglycolipid molecules containing C16:1 and C18:1 fatty acids. Additionally, ERA redirected lipid flux and promoted glyceroglycolipid accumulation while attenuating triacylglycerol production under phosphate starvation. This study represents the first demonstration of pivotal role of ERA in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in cyanobacteria, offering new insights into the effective utilization of glyceroglycolipids in various applications.
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Affiliation(s)
- Junhao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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5
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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [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: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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Chen E, Shaffer MG, Bilodeau RE, West RE, Oberly PJ, Nolin TD, Culyba MJ. Clinical rel mutations in Staphylococcus aureus prime pathogen expansion under nutrient stress. mSphere 2023; 8:e0024923. [PMID: 37750686 PMCID: PMC10597345 DOI: 10.1128/msphere.00249-23] [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: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 09/27/2023] Open
Abstract
Persistent infection by Staphylococcus aureus has been linked to the bacterial stringent response (SR), a conserved stress response pathway regulated by the Rel protein. Rel synthesizes (p)ppGpp "alarmones" in response to amino acid starvation, which enables adaptation to stress by modulating bacterial growth and virulence. We previously identified five novel protein-altering mutations in rel that arose in patients with persistent methicillin-resistant S. aureus bacteremia. The mutations mapped to both the enzymatic and regulatory protein domains of Rel. Here, we set out to characterize the phenotype of these mutations to understand how they may have been selected in vivo. After introducing each mutation into S. aureus strain JE2, we analyzed growth, fitness, and antibiotic profiles. Despite being located in different protein domains, we found that all of the mutations converged on the same phenotype. Each shortened the time of lag phase growth and imparted a fitness advantage in nutritionally depleted conditions. Through quantification of intracellular (p)ppGpp, we link this phenotype to increased SR activation, specifically during the stationary phase of growth. In contrast to two previously identified clinical rel mutations, we find that our rel mutations do not cause antibiotic tolerance. Instead, our findings suggest that in vivo selection was due to an augmented SR that primes cells for growth in nutrient-poor conditions, which may be a strategy for evading host-imposed nutritional immunity. Importance Host and pathogen compete for available nutrition during infection. For bacteria, the stringent response (SR) regulator Rel responds to amino acid deprivation by signaling the cell to modulate its growth rate, metabolism, and virulence. In this report, we characterize five rel mutations that arose during cases of persistent methicillin-resistant Staphylococcus aureus bacteremia. We find that all of the mutations augmented SR signaling specifically under nutrient-poor conditions, enabling the cell to more readily grow and survive. Our findings reveal a strategy used by bacterial pathogens to evade the nutritional immunity imposed by host tissues during infection.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert E. Bilodeau
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Raymond E. West
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Patrick J. Oberly
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Thomas D. Nolin
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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7
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Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
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Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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8
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Comparative Genomics Identifies Novel Genetic Changes Associated with Oxacillin, Vancomycin and Daptomycin Susceptibility in ST100 Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2023; 12:antibiotics12020372. [PMID: 36830286 PMCID: PMC9952151 DOI: 10.3390/antibiotics12020372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Infections due to vancomycin-intermediate S. aureus (VISA) and heterogeneous VISA (hVISA) represent a serious concern due to their association with vancomycin treatment failure. However, the underlying molecular mechanism responsible for the hVISA/VISA phenotype is complex and not yet fully understood. We have previously characterized two ST100-MRSA-hVISA clinical isolates recovered before and after 40 days of vancomycin treatment (D1 and D2, respectively) and two in vitro VISA derivatives (D23C9 and D2P11), selected independently from D2 in the presence of vancomycin. This follow-up study was aimed at further characterizing these isogenic strains and obtaining their whole genome sequences to unravel changes associated with antibiotic resistance. It is interesting to note that none of these isogenic strains carry SNPs in the regulatory operons vraUTSR, walKR and/or graXRS. Nonetheless, genetic changes including SNPs, INDELs and IS256 genomic insertions/rearrangements were found both in in vivo and in vitro vancomycin-selected strains. Some were found in the downstream target genes of the aforementioned regulatory operons, which are involved in cell wall and phosphate metabolism, staphylococcal growth and biofilm formation. Some of the genetic changes reported herein have not been previously associated with vancomycin, daptomycin and/or oxacillin resistance in S. aureus.
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9
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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase. PLoS Genet 2023; 19:e1010618. [PMID: 36735730 PMCID: PMC9931155 DOI: 10.1371/journal.pgen.1010618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 01/14/2023] [Indexed: 02/04/2023] Open
Abstract
Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb_rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase.
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10
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Abstract
Since Jacques Monod's foundational work in the 1940s, investigators studying bacterial physiology have largely (but not exclusively) focused on the exponential phase of bacterial cultures, which is characterized by rapid growth and high biosynthesis activity in the presence of excess nutrients. However, this is not the predominant state of bacterial life. In nature, most bacteria experience nutrient limitation most of the time. In fact, investigators even prior to Monod had identified other aspects of bacterial growth, including what is now known as the stationary phase, when nutrients become limiting. This review will discuss how bacteria transition to growth arrest in response to nutrient limitation through changes in transcription, translation, and metabolism. We will then examine how these changes facilitate survival during potentially extended periods of nutrient limitation, with particular attention to the metabolic strategies that underpin bacterial longevity in this state.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA;
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11
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Agarwal N, Sharma S, Pal P, Kaushal PS, Kumar N. Era, a GTPase-like protein of the Ras family, does not control ribosome assembly in Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35917161 DOI: 10.1099/mic.0.001200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Era GTPase is universally present in microbes including Mycobacterium tuberculosis (Mtb) complex bacteria. While Era is known to regulate ribosomal assembly in Escherichia coli and predicted to be essential for in vitro growth, its function in mycobacteria remains obscured. Herein, we show that Era ortholog in the attenuated Mtb H37Ra strain, MRA_2388 (annotated as EraMT) is a cell envelope localized protein harbouring critical GTP-binding domains, which interacts with several envelope proteins of Mtb. The purified Era from M. smegmatis (annotated as EraMS) exhibiting ~90 % sequence similarity with EraMT, exists in monomeric conformation. While it is co-purified with RNA upon overexpression in E. coli, the presence of RNA does not modulate the GTPase activity of the EraMS as against its counterpart from other organisms. CRISPRi silencing of eraMT does not show any substantial effect on the in vitro growth of Mtb H37Ra, which suggests a redundant function of Era in mycobacteria. Notably, no effect on ribosome assembly, protein synthesis or bacterial susceptibility to protein synthesis inhibitors was observed upon depletion of EraMT in Mtb H37Ra, further indicating a divergent role of Era GTPase in mycobacteria.
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Affiliation(s)
- Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Shivani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Pramila Pal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India.,Jawaharlal Nehru University, New Mehrauli Road, New Delhi- 110067 (Delhi), India
| | - Prem S Kaushal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Naresh Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
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12
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How to save a bacterial ribosome in times of stress. Semin Cell Dev Biol 2022; 136:3-12. [PMID: 35331628 DOI: 10.1016/j.semcdb.2022.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
Abstract
Biogenesis of ribosomes is one of the most cost- and resource-intensive processes in all living cells. In bacteria, ribosome biogenesis is rate-limiting for growth and must be tightly coordinated to yield maximum fitness of the cells. Since bacteria are continuously facing environmental changes and stress conditions, they have developed sophisticated systems to sense and regulate their nutritional status. Amino acid starvation leads to the synthesis and accumulation of the nucleotide-based second messengers ppGpp and pppGpp [(p)ppGpp], which in turn function as central players of a pleiotropic metabolic adaptation mechanism named the stringent response. Here, we review our current knowledge on the multiple roles of (p)ppGpp in the stress-related modulation of the prokaryotic protein biosynthesis machinery with the ribosome as its core constituent. The alarmones ppGpp/pppGpp act as competitors of their GDP/GTP counterparts, to affect a multitude of ribosome-associated P-loop GTPases involved in the translation cycle, ribosome biogenesis and hibernation. A similar mode of inhibition has been found for the GTPases of the proteins involved in the SRP-dependent membrane-targeting machinery present in the periphery of the ribosome. In this sense, during stringent conditions, binding of (p)ppGpp restricts the membrane insertion and secretion of proteins. Altogether, we highlight the enormously resource-intensive stages of ribosome biogenesis as a critical regulatory hub of the stringent response that ultimately tunes the protein synthesis capacity and consequently the survival of the cell.
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Hemeg HA. Combatting persisted and biofilm antimicrobial resistant bacterial by using nanoparticles. Z NATURFORSCH C 2022; 77:365-378. [PMID: 35234019 DOI: 10.1515/znc-2021-0296] [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: 11/24/2021] [Accepted: 02/04/2022] [Indexed: 11/15/2022]
Abstract
Some bacteria can withstand the existence of an antibiotic without undergoing any genetic changes. They are neither cysts nor spores and are one of the causes of disease recurrence, accounting for about 1% of the biofilm. There are numerous approaches to eradication and combating biofilm-forming organisms. Nanotechnology is one of them, and it has shown promising results against persister cells. In the review, we go over the persister cell and biofilm in extensive detail. This includes the biofilm formation cycle, antibiotic resistance, and treatment with various nanoparticles. Furthermore, the gene-level mechanism of persister cell formation and its therapeutic interventions with nanoparticles were discussed.
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Affiliation(s)
- Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Monawra 41411, Saudi Arabia
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14
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Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Nat Commun 2022; 13:1069. [PMID: 35217658 PMCID: PMC8881573 DOI: 10.1038/s41467-022-28675-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/07/2022] [Indexed: 11/08/2022] Open
Abstract
The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli. Bacterial responses to nutrient limitation and other stress conditions are often modulated by the nucleotide-based second messenger (p)ppGpp. Here, the authors show that (p)ppGpp inhibits the SRP membrane-protein insertion and secretion pathway by binding to GTPases Ffh and FtsY.
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15
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Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y. Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus. Front Mol Biosci 2021; 8:738752. [PMID: 34869582 PMCID: PMC8637172 DOI: 10.3389/fmolb.2021.738752] [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: 07/09/2021] [Accepted: 10/07/2021] [Indexed: 11/21/2022] Open
Abstract
Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution structures using this approach, one needs to obtain homogeneous and stable samples, which requires optimization of ribosome purification in a species-dependent manner. This is especially critical for the bacterial small ribosomal subunit that tends to be unstable in the absence of ligands. Here, we report a protocol for purification of stable 30 S from the Gram-positive bacterium Staphylococcus aureus and its cryo-EM structures: in presence of spermidine at a resolution ranging between 3.4 and 3.6 Å and in its absence at 5.3 Å. Using biochemical characterization and cryo-EM, we demonstrate the importance of spermidine for stabilization of the 30 S via preserving favorable conformation of the helix 44.
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Affiliation(s)
- Margarita Belinite
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.,Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
| | - Iskander Khusainov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yaser Hashem
- Architecture et Réactivité de l'ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France.,Institut Européen de Chimie et Biologie (IECB), ARNA U1212, Université de Bordeaux, Pessac, France
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16
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The Stringent Response Inhibits 70S Ribosome Formation in Staphylococcus aureus by Impeding GTPase-Ribosome Interactions. mBio 2021; 12:e0267921. [PMID: 34749534 PMCID: PMC8579695 DOI: 10.1128/mbio.02679-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of a stress signaling network termed the stringent response. RsgA, RbgA, Era, and HflX are four ribosome-associated GTPases (RA-GTPases) that bind to (p)ppGpp in Staphylococcus aureus. These enzymes are cofactors in ribosome assembly, where they cycle between the ON (GTP-bound) and OFF (GDP-bound) ribosome-associated states. Entry into the OFF state occurs upon hydrolysis of GTP, with GTPase activity increasing substantially upon ribosome association. When bound to (p)ppGpp, GTPase activity is inhibited, reducing 70S ribosome assembly and growth. Here, we determine how (p)ppGpp impacts RA-GTPase-ribosome interactions. We show that RA-GTPases preferentially bind to 5′-diphosphate-containing nucleotides GDP and ppGpp over GTP, which is likely exploited as a regulatory mechanism within the cell to shut down ribosome biogenesis during stress. Stopped-flow fluorescence and association assays reveal that when bound to (p)ppGpp, the association of RA-GTPases to ribosomal subunits is destabilized, both in vitro and within bacterial cells. Consistently, structural analysis of the ppGpp-bound RA-GTPase RsgA reveals an OFF-state conformation similar to the GDP-bound state, with the G2/switch I loop adopting a conformation incompatible with ribosome association. Altogether, we highlight (p)ppGpp-mediated inhibition of RA-GTPases as a major mechanism of stringent response-mediated ribosome assembly and growth control.
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17
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YbeY, éminence grise of ribosome biogenesis. Biochem Soc Trans 2021; 49:727-745. [PMID: 33929506 DOI: 10.1042/bst20200669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/30/2022]
Abstract
YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.
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18
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YbeY controls the type III and type VI secretion systems and biofilm formation through RetS in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.02171-20. [PMID: 33310711 PMCID: PMC8090875 DOI: 10.1128/aem.02171-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YbeY is a highly conserved RNase in bacteria and plays essential roles in the maturation of 16S rRNA, regulation of small RNAs (sRNAs) and bacterial responses to environmental stresses. Previously, we verified the role of YbeY in rRNA processing and ribosome maturation in Pseudomonas aeruginosa and demonstrated YbeY-mediated regulation of rpoS through a sRNA ReaL. In this study, we demonstrate that mutation of the ybeY gene results in upregulation of the type III secretion system (T3SS) genes as well as downregulation of the type VI secretion system (T6SS) genes and reduction of biofilm formation. By examining the expression of the known sRNAs in P. aeruginosa, we found that mutation of the ybeY gene leads to downregulation of the small RNAs RsmY/Z that control the T3SS, the T6SS and biofilm formation. Further studies revealed that the reduced levels of RsmY/Z are due to upregulation of retS Taken together, our results reveal the pleiotropic functions of YbeY and provide detailed mechanisms of YbeY-mediated regulation in P. aeruginosa IMPORTANCE Pseudomonas aeruginosa causes a variety of acute and chronic infections in humans. The type III secretion system (T3SS) plays an important role in acute infection and the type VI secretion system (T6SS) and biofilm formation are associated with chronic infections. Understanding of the mechanisms that control the virulence determinants involved in acute and chronic infections will provide clues for the development of effective treatment strategies. Our results reveal a novel RNase mediated regulation on the T3SS, T6SS and biofilm formation in P. aeruginosa.
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Wood TK, Song S. Forming and waking dormant cells: The ppGpp ribosome dimerization persister model. Biofilm 2020; 2:100018. [PMID: 33447804 PMCID: PMC7798447 DOI: 10.1016/j.bioflm.2019.100018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Procaryotes starve and face myriad stresses. The bulk population actively resists the stress, but a small population weathers the stress by entering a resting stage known as persistence. No mutations occur, and so persisters behave like wild-type cells upon removal of the stress and regrowth; hence, persisters are phenotypic variants. In contrast, resistant bacteria have mutations that allow cells to grow in the presence of antibiotics, and tolerant cells survive antibiotics better than actively-growing cells due to their slow growth (such as that of the stationary phase). In this review, we focus on the latest developments in studies related to the formation and resuscitation of persister cells and propose the guanosine pentaphosphate/tetraphosphate (henceforth ppGpp) ribosome dimerization persister (PRDP) model for entering and exiting the persister state.
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Affiliation(s)
- Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
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20
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(p)ppGpp and Its Role in Bacterial Persistence: New Challenges. Antimicrob Agents Chemother 2020; 64:AAC.01283-20. [PMID: 32718971 DOI: 10.1128/aac.01283-20] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Antibiotic failure not only is due to the development of resistance by pathogens but can also often be explained by persistence and tolerance. Persistence and tolerance can be included in the "persistent phenotype," with high relevance for clinics. Two of the most important molecular mechanisms involved in tolerance and persistence are toxin-antitoxin (TA) modules and signaling via guanosine pentaphosphate/tetraphosphate [(p)ppGpp], also known as "magic spot." (p)ppGpp is a very important stress alarmone which orchestrates the stringent response in bacteria; hence, (p)ppGpp is produced during amino acid or fatty acid starvation by proteins belonging to the RelA/SpoT homolog family (RSH). However, (p)ppGpp levels can also accumulate in response to a wide range of signals, including oxygen variation, pH downshift, osmotic shock, temperature shift, or even exposure to darkness. Furthermore, the stringent response is not only involved in responses to environmental stresses (starvation for carbon sources, fatty acids, and phosphates or heat shock), but it is also used in bacterial pathogenesis, host invasion, and antibiotic tolerance and persistence. Given the exhaustive and contradictory literature surrounding the role of (p)ppGpp in bacterial persistence, and with the aim of summarizing what is known so far about the magic spot in this bacterial stage, this review provides new insights into the link between the stringent response and persistence. Moreover, we review some of the innovative treatments that have (p)ppGpp as a target, which are in the spotlight of the scientific community as candidates for effective antipersistence agents.
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21
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Song S, Wood TK. Combatting Persister Cells With Substituted Indoles. Front Microbiol 2020; 11:1565. [PMID: 32733426 PMCID: PMC7358577 DOI: 10.3389/fmicb.2020.01565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Given that a subpopulation of most bacterial cells becomes dormant due to stress, and that the resting cells of pathogens can revive and reconstitute infections, it is imperative to find methods to treat dormant cells to eradicate infections. The dormant bacteria that are not spores or cysts are known as persister cells. Remarkably, in contrast to the original report that incorrectly indicated indole increases persistence, a large number of indole-related compounds have been found in the last few years that kill persister cells. Hence, in this review, along with a summary of recent results related to persister cell formation and resuscitation, we focus on the ability of indole and substituted indoles to combat the persister cells of both pathogens and non-pathogens.
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Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju, South Korea
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
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22
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Abstract
The increasing bacterial antibiotic resistance imposes a severe threat to human health. For the development of effective treatment and prevention strategies, it is critical to understand the mechanisms employed by bacteria to grow in the human body. Posttranscriptional regulation plays an important role in bacterial adaptation to environmental changes. RNases and small RNAs are key players in this regulation. In this study, we demonstrate critical roles of the RNase YbeY in the virulence of the pathogenic bacterium Pseudomonas aeruginosa. We further identify the small RNA ReaL as the direct target of YbeY and elucidate the YbeY-regulated pathway on the expression of bacterial virulence factors. Our results shed light on the complex regulatory network of P. aeruginosa and indicate that inference with the YbeY-mediated regulatory pathway might be a valid strategy for the development of a novel treatment strategy. Posttranscriptional regulation plays an essential role in the quick adaptation of pathogenic bacteria to host environments, and RNases play key roles in this process by modifying small RNAs and mRNAs. We find that the Pseudomonas aeruginosa endonuclease YbeY is required for rRNA processing and the bacterial virulence in a murine acute pneumonia model. Transcriptomic analyses reveal that knocking out the ybeY gene results in downregulation of oxidative stress response genes, including the catalase genes katA and katB. Consistently, the ybeY mutant is more susceptible to H2O2 and neutrophil-mediated killing. Overexpression of katA restores the bacterial tolerance to H2O2 and neutrophil killing as well as virulence. We further find that the downregulation of the oxidative stress response genes is due to defective expression of the stationary-phase sigma factor RpoS. We demonstrate an autoregulatory mechanism of RpoS and find that ybeY mutation increases the level of a small RNA, ReaL, which directly represses the translation of rpoS through the 5′ UTR of its mRNA and subsequently reduces the expression of the oxidative stress response genes. In vitro assays demonstrate direct degradation of ReaL by YbeY. Deletion of reaL or overexpression of rpoS in the ybeY mutant restores the bacterial tolerance to oxidative stress and the virulence. We also demonstrate that YbeZ binds to YbeY and is involved in the 16S rRNA processing and regulation of reaL and rpoS as well as the bacterial virulence. Overall, our results reveal pleiotropic roles of YbeY and the YbeY-mediated regulation of rpoS through ReaL.
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23
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Thompson CM, Malone JG. Nucleotide second messengers in bacterial decision making. Curr Opin Microbiol 2020; 55:34-39. [PMID: 32172083 PMCID: PMC7322531 DOI: 10.1016/j.mib.2020.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Structural analysis of NSM regulators reveals new mechanisms of NSM signalling. NSM proteins binding multiple ligands support crosstalk between signalling networks. NSM networks control structure and heterogeneity in complex microbial communities. The diversity of bacterial NSM regulators is far higher than previously thought. The (p)ppApp toxin suggests non-signalling roles exist for bacterial NSMs.
Since the initial discovery of bacterial nucleotide second messengers (NSMs), we have made huge progress towards understanding these complex signalling networks. Many NSM networks contain dozens of metabolic enzymes and binding targets, whose activity is tightly controlled at every regulatory level. They function as global regulators and in specific signalling circuits, controlling multiple aspects of bacterial behaviour and development. Despite these advances there is much still to discover, with current research focussing on the molecular mechanisms of signalling circuits, the role of the environment in controlling NSM pathways and attempts to understand signalling at the whole cell/community level. Here we examine recent developments in the NSM signalling field and discuss their implications for understanding this important driver of microbial behaviour.
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Affiliation(s)
- Catriona Ma Thompson
- Molecular Microbiology Department, John Innes Centre, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jacob G Malone
- Molecular Microbiology Department, John Innes Centre, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK.
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24
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Takada H, Roghanian M, Murina V, Dzhygyr I, Murayama R, Akanuma G, Atkinson GC, Garcia-Pino A, Hauryliuk V. The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation of 'Long' RelA-SpoT Homolog Enzymes by Ribosomal Complexes. Front Microbiol 2020; 11:277. [PMID: 32184768 PMCID: PMC7058999 DOI: 10.3389/fmicb.2020.00277] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
The (p)ppGpp-mediated stringent response is a bacterial stress response implicated in virulence and antibiotic tolerance. Both synthesis and degradation of the (p)ppGpp alarmone nucleotide are mediated by RelA-SpoT Homolog (RSH) enzymes which can be broadly divided in two classes: single-domain 'short' and multi-domain 'long' RSH. The regulatory ACT (Aspartokinase, Chorismate mutase and TyrA)/RRM (RNA Recognition Motif) domain is a near-universal C-terminal domain of long RSHs. Deletion of RRM in both monofunctional (synthesis-only) RelA as well as bifunctional (i.e., capable of both degrading and synthesizing the alarmone) Rel renders the long RSH cytotoxic due to overproduction of (p)ppGpp. To probe the molecular mechanism underlying this effect we characterized Escherichia coli RelA and Bacillus subtilis Rel RSHs lacking RRM. We demonstrate that, first, the cytotoxicity caused by the removal of RRM is counteracted by secondary mutations that disrupt the interaction of the RSH with the starved ribosomal complex - the ultimate inducer of (p)ppGpp production by RelA and Rel - and, second, that the hydrolytic activity of Rel is not abrogated in the truncated mutant. Therefore, we conclude that the overproduction of (p)ppGpp by RSHs lacking the RRM domain is not explained by a lack of auto-inhibition in the absence of RRM or/and a defect in (p)ppGpp hydrolysis. Instead, we argue that it is driven by misregulation of the RSH activation by the ribosome.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Ievgen Dzhygyr
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO, Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
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25
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Bennison DJ, Irving SE, Corrigan RM. The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly. Cells 2019; 8:cells8111313. [PMID: 31653044 PMCID: PMC6912228 DOI: 10.3390/cells8111313] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
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Affiliation(s)
- Daniel J Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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26
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The Ps and Qs of alarmone synthesis in Staphylococcus aureus. PLoS One 2019; 14:e0213630. [PMID: 31613897 PMCID: PMC6793942 DOI: 10.1371/journal.pone.0213630] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
During the stringent response, bacteria synthesize guanosine-3’,5’-bis(diphosphate) (ppGpp) and guanosine-5’-triphosphate 3’-diphosphate (pppGpp), which act as secondary messengers to promote cellular survival and adaptation. (p)ppGpp ‘alarmones’ are synthesized and/or hydrolyzed by proteins belonging to the RelA/SpoT Homologue (RSH) family. Many bacteria also encode ‘small alarmone synthetase’ (SAS) proteins (e.g. RelP, RelQ) which may also be capable of synthesizing a third alarmone: guanosine-5’-phosphate 3’-diphosphate (pGpp). Here, we report the biochemical properties of the Rel (RSH), RelP and RelQ proteins from Staphylococcus aureus (Sa-Rel, Sa-RelP, Sa-RelQ, respectively). Sa-Rel synthesized pppGpp more efficiently than ppGpp, but lacked the ability to produce pGpp. Sa-Rel efficiently hydrolyzed all three alarmones in a Mn(II) ion-dependent manner. The removal of the C-terminal regulatory domain of Sa-Rel increased its rate of (p)ppGpp synthesis ca. 10-fold, but had negligible effects on its rate of (pp)pGpp hydrolysis. Sa-RelP and Sa-RelQ efficiently synthesized pGpp in addition to pppGpp and ppGpp. The alarmone-synthesizing abilities of Sa-RelQ, but not Sa-RelP, were allosterically-stimulated by the addition of pppGpp, ppGpp or pGpp. The respective (pp)pGpp-synthesizing activities of Sa-RelP/Sa-RelQ were compared and contrasted with SAS homologues from Enterococcus faecalis (Ef-RelQ) and Streptococcus mutans (Sm-RelQ, Sm-RelP). Results indicated that EF-RelQ, Sm-RelQ and Sa-RelQ were functionally equivalent; but exhibited considerable variations in their respective biochemical properties, and the degrees to which alarmones and single-stranded RNA molecules allosterically modulated their respective alarmone-synthesizing activities. The respective (pp)pGpp-synthesizing capabilities of Sa-RelP and Sm-RelP proteins were inhibited by pGpp, ppGpp and pppGpp. Our results support the premise that RelP and RelQ proteins may synthesize pGpp in addition to (p)ppGpp within S. aureus and other Gram-positive bacterial species.
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