1
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Kędzierska B, Stodolna A, Bryszkowska K, Dylewski M, Potrykus K. A simple and unified protocol to purify all seven Escherichia coli RNA polymerase sigma factors. J Appl Genet 2024:10.1007/s13353-024-00870-3. [PMID: 38709457 DOI: 10.1007/s13353-024-00870-3] [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: 01/20/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
RNA polymerase sigma factors are indispensable in the process of bacterial transcription. They are responsible for a given gene's promoter region recognition on template DNA and hence determine specificity of RNA polymerase and play a significant role in gene expression regulation. Here, we present a simple and unified protocol for purification of all seven Escherichia coli RNA polymerase sigma factors. In our approach, we took advantage of the His8-SUMO tag, known to increase protein solubilization. Sigma factors were first purified in N-terminal fusions with this tag, which was followed by tag removal with Ulp1 protease. This allowed to obtain proteins in their native form. In addition, the procedure is simple and requires only one resin type. With the general protocol we employed, we were able to successfully purify σD, σE, σS, and σN. Final step modification was required for σF, while for σH and σFecI, denaturing conditions had to be applied. All seven sigma factors were fully functional in forming an active holoenzyme with core RNA polymerase which we demonstrated with EMSA studies.
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Affiliation(s)
- Barbara Kędzierska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Stodolna
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Bryszkowska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Maciej Dylewski
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland.
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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:S0966-842X(23)00363-3. [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] [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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Bartoli J, Tempier AC, Guzzi NL, Piras CM, Cascales E, Viala JPM. Characterization of a (p)ppApp Synthetase Belonging to a New Family of Polymorphic Toxin Associated with Temperate Phages. J Mol Biol 2023; 435:168282. [PMID: 37730083 DOI: 10.1016/j.jmb.2023.168282] [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: 07/21/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Polymorphic toxins (PTs) are a broad family of toxins involved in interbacterial competition and pathogenesis. PTs are modular proteins that are comprised of a conserved N-terminal domain responsible for its transport, and a variable C-terminal domain bearing toxic activity. Although the mode of transport has yet to be elucidated, a new family of putative PTs containing an N-terminal MuF domain, resembling the Mu coliphage F protein, was identified in prophage genetic elements. The C-terminal toxin domains of these MuF PTs are predicted to bear nuclease, metallopeptidase, ADP-ribosyl transferase and RelA_SpoT activities. In this study, we characterized the MuF-RelA_SpoT toxin associated with the temperate phage of Streptococcus pneumoniae SPNA45. We show that the RelA_SpoT domain has (p)ppApp synthetase activity, which is bactericidal under our experimental conditions. We further determine that the two genes located downstream encode two immunity proteins, one binding to and inactivating the toxin and the other detoxifying the cell via a pppApp hydrolase activity. Finally, based on protein sequence alignments, we propose a signature for (p)ppApp synthetases that distinguishes them from (p)ppGpp synthetases.
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Affiliation(s)
- Julia Bartoli
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Audrey C Tempier
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Noa L Guzzi
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France. https://twitter.com/NoaGzzi
| | - Chloé M Piras
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France. https://twitter.com/CascalesLab
| | - Julie P M Viala
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR 7255), Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ., CNRS - 31 Chemin Joseph Aiguier CS70071, 13402 Marseille Cedex 20, France.
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4
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Wang M, Tang NY, Xie S, Watt RM. Functional Characterization of Small Alarmone Synthetase and Small Alarmone Hydrolase Proteins from Treponema denticola. Microbiol Spectr 2023; 11:e0510022. [PMID: 37289081 PMCID: PMC10434055 DOI: 10.1128/spectrum.05100-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
The stringent response enables bacteria to survive nutrient starvation, antibiotic challenge, and other threats to cellular survival. Two alarmone (magic spot) second messengers, guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp), which are synthesized by RelA/SpoT homologue (RSH) proteins, play central roles in the stringent response. The pathogenic oral spirochete bacterium Treponema denticola lacks a long-RSH homologue but encodes putative small alarmone synthetase (Tde-SAS, TDE1711) and small alarmone hydrolase (Tde-SAH, TDE1690) proteins. Here, we characterize the respective in vitro and in vivo activities of Tde-SAS and Tde-SAH, which respectively belong to the previously uncharacterized RSH families DsRel and ActSpo2. The tetrameric 410-amino acid (aa) Tde-SAS protein preferentially synthesizes ppGpp over pppGpp and a third alarmone, pGpp. Unlike RelQ homologues, alarmones do not allosterically stimulate the synthetic activities of Tde-SAS. The ~180 aa C-terminal tetratricopeptide repeat (TPR) domain of Tde-SAS acts as a brake on the alarmone synthesis activities of the ~220-aa N-terminal catalytic domain. Tde-SAS also synthesizes "alarmone-like" nucleotides such as adenosine tetraphosphate (ppApp), albeit at considerably lower rates. The 210-aa Tde-SAH protein efficiently hydrolyzes all guanosine and adenosine-based alarmones in a Mn(II) ion-dependent manner. Using a growth assays with a ΔrelAΔspoT strain of Escherichia coli that is deficient in pppGpp/ppGpp synthesis, we demonstrate that Tde-SAS can synthesize alarmones in vivo to restore growth in minimal media. Taken together, our results add to our holistic understanding of alarmone metabolism across diverse bacterial species. IMPORTANCE The spirochete bacterium Treponema denticola is a common component of the oral microbiota. However, it may play important pathological roles in multispecies oral infectious diseases such as periodontitis: a severe and destructive form of gum disease, which is a major cause of tooth loss in adults. The operation of the stringent response, a highly conserved survival mechanism, is known to help many bacterial species cause persistent or virulent infections. By characterizing the biochemical functions of the proteins putatively responsible for the stringent response in T. denticola, we may gain molecular insight into how this bacterium can survive within harsh oral environments and promote infection. Our results also expand our general understanding of proteins that synthesize nucleotide-based intracellular signaling molecules in bacteria.
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Affiliation(s)
- Miao Wang
- Faculty of Dentistry, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Nga-Yeung Tang
- Department of Pathology and Laboratory Medicine, Beaumont Health, Royal Oak, Michigan, USA
- Department of Pathology and Laboratory Medicine, Oakland University William Beaumont School of Medicine, Auburn Hills, Michigan, USA
| | - Shujie Xie
- Faculty of Dentistry, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Rory M. Watt
- Faculty of Dentistry, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
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5
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Sound the (Smaller) Alarm: The Triphosphate Magic Spot Nucleotide pGpp. Infect Immun 2023; 91:e0043222. [PMID: 36920208 PMCID: PMC10112252 DOI: 10.1128/iai.00432-22] [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: 03/16/2023] Open
Abstract
It has recently become evident that the bacterial stringent response is regulated by a triphosphate alarmone (pGpp) as well as the canonical tetra- and pentaphosphate alarmones ppGpp and pppGpp [together, (p)ppGpp]. Often dismissed in the past as an artifact or degradation product, pGpp has been confirmed as a deliberate endpoint of multiple synthetic pathways utilizing GMP, (p)ppGpp, or GDP/GTP as precursors. Some early studies concluded that pGpp functionally mimics (p)ppGpp and that its biological role is to make alarmone metabolism less dependent on the guanine energy charge of the cell by allowing GMP-dependent synthesis to continue when GDP/GTP has been depleted. However, recent reports that pGpp binds unique potential protein receptors and is the only alarmone synthesized by the intestinal pathogen Clostridioides difficile indicate that pGpp is more than a stand-in for the longer alarmones and plays a distinct biological role beyond its functional overlap (p)ppGpp.
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6
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Haas TM, Laventie B, Lagies S, Harter C, Prucker I, Ritz D, Saleem‐Batcha R, Qiu D, Hüttel W, Andexer J, Kammerer B, Jenal U, Jessen HJ. Photoaffinity Capture Compounds to Profile the Magic Spot Nucleotide Interactomes**. Angew Chem Int Ed Engl 2022; 61:e202201731. [PMID: 35294098 PMCID: PMC9310846 DOI: 10.1002/anie.202201731] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Indexed: 11/12/2022]
Abstract
Magic Spot Nucleotides (MSN) regulate the stringent response, a highly conserved bacterial stress adaptation mechanism, enabling survival under adverse external challenges. In times of antibiotic crisis, a detailed understanding of stringent response is essential, as potentially new targets for pharmacological intervention could be identified. In this study, we delineate the MSN interactome in Escherichia coli and Salmonella typhimurium applying a family of trifunctional photoaffinity capture compounds. We introduce MSN probes covering a diverse phosphorylation pattern, such as pppGpp, ppGpp, and pGpp. Our chemical proteomics approach provides datasets of putative MSN receptors both from cytosolic and membrane fractions that unveil new MSN targets. We find that the activity of the non‐Nudix hydrolase ApaH is potently inhibited by pppGpp, which itself is converted to pGpp by ApaH. The capture compounds described herein will be useful to identify MSN interactomes across bacterial species.
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Affiliation(s)
- Thomas M. Haas
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Benoît‐Joseph Laventie
- Infection Biology Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Simon Lagies
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Caroline Harter
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Isabel Prucker
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Danilo Ritz
- Proteomics Core Facility Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Raspudin Saleem‐Batcha
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg im Breisgau Germany
| | - Danye Qiu
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Wolfgang Hüttel
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Jennifer Andexer
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg im Breisgau Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Urs Jenal
- Infection Biology Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Henning J. Jessen
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
- CIBSS—The Center for Biological Signaling Studies Albert-Ludwigs-Universität Freiburg 79104 Freiburg im Breisgau Germany
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7
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Haas TM, Laventie B, Lagies S, Harter C, Prucker I, Ritz D, Saleem‐Batcha R, Qiu D, Hüttel W, Andexer J, Kammerer B, Jenal U, Jessen HJ. Photoaffinity Capture Compounds to Profile the Magic Spot Nucleotide Interactomes**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Thomas M. Haas
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Benoît‐Joseph Laventie
- Infection Biology Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Simon Lagies
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Caroline Harter
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Isabel Prucker
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Danilo Ritz
- Proteomics Core Facility Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Raspudin Saleem‐Batcha
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg im Breisgau Germany
| | - Danye Qiu
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Wolfgang Hüttel
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Jennifer Andexer
- Institute of Pharmaceutical Sciences Albert-Ludwigs-Universität Freiburg Albertstraße 25 79104 Freiburg im Breisgau Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
| | - Urs Jenal
- Infection Biology Biozentrum University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Henning J. Jessen
- Institute of Organic Chemistry Albert-Ludwigs-Universität Freiburg Albertstraße 21 79104 Freiburg im Breisgau Germany
- CIBSS—The Center for Biological Signaling Studies Albert-Ludwigs-Universität Freiburg 79104 Freiburg im Breisgau Germany
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8
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Abstract
The "magic spot" alarmones (pp)pGpp, previously implicated in Clostridioides difficile antibiotic survival, are synthesized by the RelA-SpoT homolog (RSH) of C. difficile (RSHCd) and RelQCd. These enzymes are transcriptionally activated by diverse environmental stresses. RSHCd has previously been reported to synthesize ppGpp, but in this study, we found that both clostridial enzymes exclusively synthesize pGpp. While direct synthesis of pGpp from a GMP substrate, and (p)ppGpp hydrolysis into pGpp by NUDIX hydrolases, have previously been reported, there is no precedent for a bacterium synthesizing pGpp exclusively. Hydrolysis of the 5' phosphate or pyrophosphate from GDP or GTP substrates is necessary for activity by the clostridial enzymes, neither of which can utilize GMP as a substrate. Both enzymes are remarkably insensitive to the size of their metal ion cofactor, tolerating a broad array of metals that do not allow activity in (pp)pGpp synthetases from other organisms. It is clear that while C. difficile utilizes alarmone signaling, its mechanisms of alarmone synthesis are not directly homologous to those in more completely characterized organisms. IMPORTANCE Despite the role of the stringent response in antibiotic survival and recurrent infections, it has been a challenging target for antibacterial therapies because it is so ubiquitous. This is an especially relevant consideration for the treatment of Clostridioides difficile infection (CDI), as exposure to broad-spectrum antibiotics that harm commensal microbes is a major risk factor for CDI. Here, we report that both of the alarmone synthetase enzymes that mediate the stringent response in this organism employ a unique mechanism that requires the hydrolysis of two phosphate bonds and synthesize the triphosphate alarmone pGpp exclusively. Inhibitors targeted against these noncanonical synthetases have the potential to be highly specific and minimize detrimental effects to stringent response pathways in commensal microbes.
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9
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Purcell EB. Second messenger signaling in Clostridioides difficile. Curr Opin Microbiol 2021; 65:138-144. [PMID: 34864551 DOI: 10.1016/j.mib.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/18/2022]
Abstract
Small, diffusible second messenger molecules transmit information about extracellular conditions to intracellular machinery in order to influence transcription, translation, and metabolism. The enteropathogenic bacterium Clostridioides difficile coordinates its response to a dynamic and hostile environment via nucleotide second messengers. While riboswitch-mediated cyclic diguanylate regulation has been extensively characterized in C. difficile, signaling by cyclic diadenylate and by guanosine alarmones has only recently been confirmed in this organism. This review summarizes the current knowledge of how nucleotide second messenger signaling regulates physiological processes in C. difficile.
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Affiliation(s)
- Erin B Purcell
- Old Dominion University, Department of Chemistry and Biochemistry, 4501 Elkhorn Ave, Norfolk, VA 23529, United States.
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10
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Anderson BW, Fung DK, Wang JD. Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. Annu Rev Genet 2021; 55:115-133. [PMID: 34416118 DOI: 10.1146/annurev-genet-021821-025827] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism by regulating enzymatic activities, especially those involved in purine nucleotide synthesis. Failure of metabolic regulation by (p)ppGpp results in the loss of coordination between metabolic and macromolecular processes, leading to cellular toxicity. In this review, we document how (p)ppGpp and newly characterized nucleotides pGpp and (p)ppApp directly regulate these enzymatic targets for metabolic remodeling. We examine targets' common determinants for alarmone interaction as well as their evolutionary diversification. We highlight classical and emerging themes in nucleotide signaling, including oligomerization and allostery along with metabolic interconversion and crosstalk, illustrating how they allow optimized bacterial adaptation to their environmental niches.
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Affiliation(s)
- Brent W Anderson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
| | - Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
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11
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Chau NYE, Ahmad S, Whitney JC, Coombes BK. Emerging and divergent roles of pyrophosphorylated nucleotides in bacterial physiology and pathogenesis. PLoS Pathog 2021; 17:e1009532. [PMID: 33984072 PMCID: PMC8118318 DOI: 10.1371/journal.ppat.1009532] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacteria inhabit diverse environmental niches and consequently must modulate their metabolism to adapt to stress. The nucleotide second messengers guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) (collectively referred to as (p)ppGpp) are essential for survival during nutrient starvation. (p)ppGpp is synthesized by the RelA-SpoT homologue (RSH) protein family and coordinates the control of cellular metabolism through its combined effect on over 50 proteins. While the role of (p)ppGpp has largely been associated with nutrient limitation, recent studies have shown that (p)ppGpp and related nucleotides have a previously underappreciated effect on different aspects of bacterial physiology, such as maintaining cellular homeostasis and regulating bacterial interactions with a host, other bacteria, or phages. (p)ppGpp produced by pathogenic bacteria facilitates the evasion of host defenses such as reactive nitrogen intermediates, acidic pH, and the complement system. Additionally, (p)ppGpp and pyrophosphorylated derivatives of canonical adenosine nucleotides called (p)ppApp are emerging as effectors of bacterial toxin proteins. Here, we review the RSH protein family with a focus on its unconventional roles during host infection and bacterial competition.
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Affiliation(s)
- N. Y Elizabeth Chau
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shehryar Ahmad
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - John C. Whitney
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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12
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Potrykus K, Cashel M, Bange G. Editorial: (p)ppGpp and Its Homologs: Enzymatic and Mechanistic Diversity Among the Microbes. Front Microbiol 2021; 12:658282. [PMID: 33841386 PMCID: PMC8026867 DOI: 10.3389/fmicb.2021.658282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Gert Bange
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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13
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Topka-Bielecka G, Dydecka A, Necel A, Bloch S, Nejman-Faleńczyk B, Węgrzyn G, Węgrzyn A. Bacteriophage-Derived Depolymerases against Bacterial Biofilm. Antibiotics (Basel) 2021; 10:175. [PMID: 33578658 PMCID: PMC7916357 DOI: 10.3390/antibiotics10020175] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 12/11/2022] Open
Abstract
In addition to specific antibiotic resistance, the formation of bacterial biofilm causes another level of complications in attempts to eradicate pathogenic or harmful bacteria, including difficult penetration of drugs through biofilm structures to bacterial cells, impairment of immunological response of the host, and accumulation of various bioactive compounds (enzymes and others) affecting host physiology and changing local pH values, which further influence various biological functions. In this review article, we provide an overview on the formation of bacterial biofilm and its properties, and then we focus on the possible use of phage-derived depolymerases to combat bacterial cells included in this complex structure. On the basis of the literature review, we conclude that, although these bacteriophage-encoded enzymes may be effective in destroying specific compounds involved in the formation of biofilm, they are rarely sufficient to eradicate all bacterial cells. Nevertheless, a combined therapy, employing depolymerases together with antibiotics and/or other antibacterial agents or factors, may provide an effective approach to treat infections caused by bacteria able to form biofilms.
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Affiliation(s)
- Gracja Topka-Bielecka
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.T.-B.); (A.D.); (A.N.); (B.N.-F.); (G.W.)
| | - Aleksandra Dydecka
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.T.-B.); (A.D.); (A.N.); (B.N.-F.); (G.W.)
| | - Agnieszka Necel
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.T.-B.); (A.D.); (A.N.); (B.N.-F.); (G.W.)
| | - Sylwia Bloch
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.T.-B.); (A.D.); (A.N.); (B.N.-F.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.T.-B.); (A.D.); (A.N.); (B.N.-F.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
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14
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Steinchen W, Ahmad S, Valentini M, Eilers K, Majkini M, Altegoer F, Lechner M, Filloux A, Whitney JC, Bange G. Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism. Mol Microbiol 2021; 115:1339-1356. [PMID: 33448498 DOI: 10.1111/mmi.14684] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The guanosine nucleotide-based second messengers ppGpp and pppGpp (collectively: (p)ppGpp) enable adaptation of microorganisms to environmental changes and stress conditions. In contrast, the closely related adenosine nucleotides (p)ppApp are involved in type VI secretion system (T6SS)-mediated killing during bacterial competition. Long RelA-SpoT Homolog (RSH) enzymes regulate synthesis and degradation of (p)ppGpp (and potentially also (p)ppApp) through their synthetase and hydrolase domains, respectively. Small alarmone hydrolases (SAH) that consist of only a hydrolase domain are found in a variety of bacterial species, including the opportunistic human pathogen Pseudomonas aeruginosa. Here, we present the structure and mechanism of P. aeruginosa SAH showing that the enzyme promiscuously hydrolyses (p)ppGpp and (p)ppApp in a strictly manganese-dependent manner. While being dispensable for P. aeruginosa growth or swimming, swarming, and twitching motilities, its enzymatic activity is required for biofilm formation. Moreover, (p)ppApp-degradation by SAH provides protection against the T6SS (p)ppApp synthetase effector Tas1, suggesting that SAH enzymes can also serve as defense proteins during interbacterial competition.
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Affiliation(s)
- Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Mohamad Majkini
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
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15
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Potrykus K, Thomas NE, Bruhn-Olszewska B, Sobala M, Dylewski M, James T, Cashel M. Estimates of Rel Seq, Mesh1, and SAH Mex Hydrolysis of (p)ppGpp and (p)ppApp by Thin Layer Chromatography and NADP/NADH Coupled Assays. Front Microbiol 2020; 11:581271. [PMID: 33193211 PMCID: PMC7644958 DOI: 10.3389/fmicb.2020.581271] [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: 07/08/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The Mesh1 class of hydrolases found in bacteria, metazoans and humans was discovered as able to cleave an intact pyrophosphate residue esterified on the 3'hydroxyl of (p)ppGpp in a Mn2+ dependent reaction. Here, thin layer chromatography (TLC) qualitative evidence is presented indicating the substrate specificity of Mesh1 from Drosophila melanogaster and human MESH1 also extends to the (p)ppApp purine analogs. More importantly, we developed real time enzymatic assays, coupling ppNpp hydrolysis to NADH oxidation and pppNpp hydrolysis to NADP+ reduction, which facilitate estimation of kinetic constants. Furthermore, by using this assay technique we confirmed TLC observations and also revealed that purified small alarmone hydrolase (SAHMex) from Methylobacterium extorquens displays a strong hydrolase activity toward (p)ppApp but only negligible activity toward (p)ppGpp. In contrast, the substrate specificity of the hydrolase present in catalytically active N-terminal domain of the RSH protein from Streptococcus equisimilis (RelSeq) includes (p)ppGpp but not (p)ppApp. It is noteworthy that the RSH protein from M. extorquens (RSHMex) has been recently shown to synthesize both (p)ppApp and (p)ppGpp.
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Affiliation(s)
- Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Nathan E Thomas
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Bożena Bruhn-Olszewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Michał Sobala
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Maciej Dylewski
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Tamara James
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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16
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Fernández-Coll L, Cashel M. Possible Roles for Basal Levels of (p)ppGpp: Growth Efficiency Vs. Surviving Stress. Front Microbiol 2020; 11:592718. [PMID: 33162969 PMCID: PMC7581894 DOI: 10.3389/fmicb.2020.592718] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 11/18/2022] Open
Abstract
Two (p)ppGpp nucleotide analogs, sometimes abbreviated simply as ppGpp, are widespread in bacteria and plants. Their name alarmone reflects a view of their function as intracellular hormone-like protective alarms that can increase a 100-fold when sensing any of an array of physical or nutritional dangers, such as abrupt starvation, that trigger lifesaving adjustments of global gene expression and physiology. The diversity of mechanisms for stress-specific adjustments of this sort is large and further compounded by almost infinite microbial diversity. The central question raised by this review is whether the small basal levels of (p)ppGpp functioning during balanced growth serve very different roles than alarmone-like functions. Recent discoveries that abrupt amino acid starvation of Escherichia coli, accompanied by very high levels of ppGpp, occasion surprising instabilities of transfer RNA (tRNA), ribosomal RNA (rRNA), and ribosomes raises new questions. Is this destabilization, a mode of regulation linearly related to (p)ppGpp over the entire continuum of (p)ppGpp levels, including balanced growth? Are regulatory mechanisms exerted by basal (p)ppGpp levels fundamentally different than for high levels? There is evidence from studies of other organisms suggesting special regulatory features of basal levels compared to burst of (p)ppGpp. Those differences seem to be important even during bacterial infection, suggesting that unbalancing the basal levels of (p)ppGpp may become a future antibacterial treatment. A simile for this possible functional duality is that (p)ppGpp acts like a car’s brake, able to stop to avoid crashes as well as to slow down to drive safely.
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Affiliation(s)
- Llorenç Fernández-Coll
- Intramural Research Program, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD, United States
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD, United States
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17
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The (p)ppGpp Synthetase RSH Mediates Stationary-Phase Onset and Antibiotic Stress Survival in Clostridioides difficile. J Bacteriol 2020; 202:JB.00377-20. [PMID: 32661079 DOI: 10.1128/jb.00377-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022] Open
Abstract
The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventative and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stress, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile Here, we report that the C. difficile (p)ppGpp synthetase RSH is incapable of utilizing GTP or GMP as a substrate but readily synthesizes ppGpp from GDP. The enzyme also utilizes many structurally diverse metal cofactors for reaction catalysis and remains functionally stable at a wide range of environmental pHs. Transcription of rsh is stimulated by stationary-phase onset and by exposure to the antibiotics clindamycin and metronidazole. Chemical inhibition of RSH by the ppGpp analog relacin increases antibiotic susceptibility in epidemic C. difficile R20291, indicating that RSH inhibitors may be a viable strategy for drug development against C. difficile infection. Finally, transcriptional suppression of rsh also increases bacterial antibiotic susceptibility, suggesting that RSH contributes to C. difficile antibiotic tolerance and survival.IMPORTANCE Clostridioides difficile infection (CDI) is an urgent public health threat with a high recurrence rate, in part because the causative bacterium has a high rate of antibiotic survival. The (p)ppGpp-mediated bacterial stringent response plays a role in antibiotic tolerance in diverse pathogens and is a potential target for development of new antimicrobials because the enzymes that metabolize (p)ppGpp have no mammalian homologs. We report that stationary-phase onset and antibiotics induce expression of the clostridial ppGpp synthetase RSH and that both chemical inhibition and translational suppression of RSH increase C. difficile antibiotic susceptibility. This demonstrates that development of RSH inhibitors to serve as adjuvants to antibiotic therapy is a potential approach for the development of new strategies to combat CDI.
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18
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Steinchen W, Zegarra V, Bange G. (p)ppGpp: Magic Modulators of Bacterial Physiology and Metabolism. Front Microbiol 2020; 11:2072. [PMID: 33013756 PMCID: PMC7504894 DOI: 10.3389/fmicb.2020.02072] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/06/2020] [Indexed: 01/21/2023] Open
Abstract
When bacteria experience growth-limiting environmental conditions, the synthesis of the hyperphosphorylated guanosine derivatives (p)ppGpp is induced by enzymes of the RelA/SpoT homology (RSH)-type protein family. High levels of (p)ppGpp induce a process called "stringent response", a major cellular reprogramming during which ribosomal RNA (rRNA) and transfer RNA (tRNA) synthesis is downregulated, stress-related genes upregulated, messenger RNA (mRNA) stability and translation altered, and allocation of scarce resources optimized. The (p)ppGpp-mediated stringent response is thus often regarded as an all-or-nothing paradigm induced by stress. Over the past decades, several binding partners of (p)ppGpp have been uncovered displaying dissociation constants from below one micromolar to more than one millimolar and thus coincide with the accepted intracellular concentrations of (p)ppGpp under non-stringent (basal levels) and stringent conditions. This suggests that the ability of (p)ppGpp to modulate target proteins or processes would be better characterized as an unceasing continuum over a concentration range instead of being an abrupt switch of biochemical processes under specific conditions. We analyzed the reported binding affinities of (p)ppGpp targets and depicted a scheme for prioritization of modulation by (p)ppGpp. In this ranking, many enzymes of e.g., nucleotide metabolism are among the first targets to be affected by rising (p)ppGpp while more fundamental processes such as DNA replication are among the last. This preference should be part of (p)ppGpp's "magic" in the adaptation of microorganisms while still maintaining their potential for outgrowth once a stressful condition is overcome.
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Affiliation(s)
- Wieland Steinchen
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | | | - Gert Bange
- Department of Chemistry, Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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19
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Fung DK, Yang J, Stevenson DM, Amador-Noguez D, Wang JD. Small Alarmone Synthetase SasA Expression Leads to Concomitant Accumulation of pGpp, ppApp, and AppppA in Bacillus subtilis. Front Microbiol 2020; 11:2083. [PMID: 32983059 PMCID: PMC7492591 DOI: 10.3389/fmicb.2020.02083] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
(p)ppGpp is a highly conserved bacterial alarmone which regulates many aspects of cellular physiology and metabolism. In Gram-positive bacteria such as B. subtilis, cellular (p)ppGpp level is determined by the bifunctional (p)ppGpp synthetase/hydrolase RelA and two small alarmone synthetases (SASs) YjbM (SasB) and YwaC (SasA). However, it is less clear whether these enzymes are also involved in regulation of alarmones outside of (p)ppGpp. Here we developed an improved LC-MS-based method to detect a broad spectrum of metabolites and alarmones from bacterial cultures with high efficiency. By characterizing the metabolomic signatures of SasA expressing B. subtilis, we identified strong accumulation of the (p)ppGpp analog pGpp, as well as accumulation of ppApp and AppppA. The induced accumulation of these alarmones is abolished in the catalytically dead sasA mutant, suggesting that it is a consequence of SasA synthetase activity. In addition, we also identified depletion of specific purine nucleotides and their precursors including IMP precursors FGAR, SAICAR and AICAR (ZMP), as well as GTP and GDP. Furthermore, we also revealed depletion of multiple pyrimidine precursors such as orotate and orotidine 5′-phosphate. Taken together, our work shows that induction of a single (p)ppGpp synthetase can cause concomitant accumulation and potential regulatory interplay of multiple alarmones.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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20
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Haas TM, Qiu D, Häner M, Angebauer L, Ripp A, Singh J, Koch HG, Jessen-Trefzer C, Jessen HJ. Four Phosphates at One Blow: Access to Pentaphosphorylated Magic Spot Nucleotides and Their Analysis by Capillary Electrophoresis. J Org Chem 2020; 85:14496-14506. [PMID: 32502348 PMCID: PMC7684580 DOI: 10.1021/acs.joc.0c00841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
complex phosphorylation pattern of natural and modified pentaphosphorylated
magic spot nucleotides is generated in a highly efficient way. A cyclic
pyrophosphoryl phosphoramidite (cPyPA) reagent is used to introduce
four phosphates on nucleosides regioselectively in a one-flask key
transformation. The obtained magic spot nucleotides are used to develop
a capillary electrophoresis UV detection method, enabling nucleotide
assignment in complex bacterial extracts.
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Affiliation(s)
- Thomas M Haas
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany.,CIBSS, Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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21
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Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp. J Mol Biol 2020; 432:4108-4126. [PMID: 32446804 DOI: 10.1016/j.jmb.2020.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 10/24/2022]
Abstract
The alarmones pppGpp and ppGpp mediate starvation response and maintain purine homeostasis to protect bacteria. In the bacterial phyla Firmicutes and Bacteroidetes, xanthine phosphoribosyltransferase (XPRT) is a purine salvage enzyme that produces the nucleotide XMP from PRPP and xanthine. Combining structural, biochemical, and genetic analyses, we show that pppGpp and ppGpp, as well as a third newly identified alarmone pGpp, all directly interact with XPRT from the Gram-positive bacterium Bacillus subtilis and inhibit XPRT activity by competing with its substrate PRPP. Structural analysis reveals that ppGpp binds the PRPP binding motif within the XPRT active site. This motif is present in another (p)ppGpp target, the purine salvage enzyme HPRT, suggesting evolutionary conservation in different enzymes. However, XPRT oligomeric interaction is distinct from HPRT in that XPRT forms a symmetric dimer with two (p)ppGpp binding sites at the dimer interface. (p)ppGpp's interaction with an XPRT bridging loop across the interface results in XPRT cooperatively binding (p)ppGpp. Also, XPRT displays differential regulation by the alarmones as it is potently inhibited by both ppGpp and pGpp, but only modestly by pppGpp. Lastly, we demonstrate that the alarmones are necessary for protecting GTP homeostasis against excess environmental xanthine in B. subtilis, suggesting that regulation of XPRT is key for regulating the purine salvage pathway.
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22
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A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proc Natl Acad Sci U S A 2020; 117:10500-10510. [PMID: 32345719 PMCID: PMC7229694 DOI: 10.1073/pnas.1916617117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The alarmone (p)ppGpp is a central signaling nucleotide that is synthesized by RelA-SpoT Homologue (RSH) enzymes, and rewires bacterial physiology in response to stress. It is an unanswered question why bacteria often carry multiple (p)ppGpp-synthesising RSHs in the same genome. We have answered that question for five subfamilies of small alarmone synthetases (SASs) by discovering that they are toxins of a novel toxin−antitoxin system, and that they act by synthesizing ppGpp and its unusual analogue—ppApp. These distinct toxic SAS (toxSAS) subfamilies are neutralized by six neighboring antitoxin genes. The toxSAS system and its weaponizing of nucleotide second messengers gives a new angle to the hotly debated and controversial topic of cross-talk between TAs and the alarmone-mediated stringent response. Under stressful conditions, bacterial RelA-SpoT Homolog (RSH) enzymes synthesize the alarmone (p)ppGpp, a nucleotide second messenger. (p)ppGpp rewires bacterial transcription and metabolism to cope with stress, and, at high concentrations, inhibits the process of protein synthesis and bacterial growth to save and redirect resources until conditions improve. Single-domain small alarmone synthetases (SASs) are RSH family members that contain the (p)ppGpp synthesis (SYNTH) domain, but lack the hydrolysis (HD) domain and regulatory C-terminal domains of the long RSHs such as Rel, RelA, and SpoT. We asked whether analysis of the genomic context of SASs can indicate possible functional roles. Indeed, multiple SAS subfamilies are encoded in widespread conserved bicistronic operon architectures that are reminiscent of those typically seen in toxin−antitoxin (TA) operons. We have validated five of these SASs as being toxic (toxSASs), with neutralization by the protein products of six neighboring antitoxin genes. The toxicity of Cellulomonas marina toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate pools, and is counteracted by its HD domain-containing antitoxin. Thus, the ToxSAS–antiToxSAS system with its multiple different antitoxins exemplifies how ancient nucleotide-based signaling mechanisms can be repurposed as TA modules during evolution, potentially multiple times independently.
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23
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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24
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Toxin discovery reveals fresh ammunition for bacterial warfare. Nature 2020; 575:599-600. [PMID: 31768037 DOI: 10.1038/d41586-019-03217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Ruwe M, Persicke M, Busche T, Müller B, Kalinowski J. Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum. Front Microbiol 2019; 10:2769. [PMID: 31849906 PMCID: PMC6892785 DOI: 10.3389/fmicb.2019.02769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
The alarmone species ppGpp and pppGpp are elementary components of bacterial physiology as they both coordinate the bacterial stress response and serve as fine-tuners of general metabolism during conditions of balanced growth. Since the regulation of (p)ppGpp metabolism and the effects of (p)ppGpp on cellular processes are highly complex and show massive differences between bacterial species, the underlying molecular mechanisms have so far only been insufficiently investigated for numerous microorganisms. In this study, (p)ppGpp physiology in the actinobacterial model organism Corynebacterium glutamicum was analyzed by phenotypic characterization and RNAseq-based transcriptome analysis. Total nutrient starvation was identified as the most effective method to induce alarmone production, whereas traditional induction methods such as the addition of serine hydroxamate (SHX) or mupirocin did not show a strong accumulation of (p)ppGpp. The predominant alarmone in C. glutamicum represents guanosine tetraphosphate, whose stress-associated production depends on the presence of the bifunctional RSH enzyme Rel. Interestingly, in addition to ppGpp, another substance yet not identified accumulated strongly under inducing conditions. A C. glutamicum triple mutant (Δrel,ΔrelS,ΔrelH) unable to produce alarmones [(p)ppGpp0 strain] exhibited unstable growth characteristics and interesting features such as an influence of illumination on its physiology, production of amino acids as well as differences in vitamin and carotenoid production. Differential transcriptome analysis using RNAseq provided numerous indications for the molecular basis of the observed phenotype. An evaluation of the (p)ppGpp-dependent transcriptional regulation under total nutrient starvation revealed a complex interplay with the involvement of ribosome-mediated transcriptional attenuation, the stress-responsive sigma factors σB and σH and transcription factors such as McbR, the master regulator of sulfur metabolism. In addition to the differential regulation of genes connected with various cell functions, the transcriptome analysis revealed conserved motifs within the promoter regions of (p)ppGpp-dependently and independently regulated genes. In particular, the representatives of translation-associated genes are both (p)ppGpp-dependent transcriptionally downregulated and show a highly conserved and so far unknown TTTTG motif in the -35 region, which is also present in other actinobacterial genera.
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Affiliation(s)
- Matthias Ruwe
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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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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