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Ortiz-Vasco CC, Moreno S, Quintero-Navarro LA, Rojo-Rodríguez JB, Espín G. The stringent response regulates the poly-β-hydroxybutyrate (PHB) synthesis in Azotobacter vinelandii. PLoS One 2024; 19:e0299640. [PMID: 38574051 PMCID: PMC10994330 DOI: 10.1371/journal.pone.0299640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/13/2024] [Indexed: 04/06/2024] Open
Abstract
The stringent response exerted by (p)ppGpp and RNA-polymerase binding protein DksA regulates gene expression in diverse bacterial species. To control gene expression (p)ppGpp, synthesized by enzymes RelA and SpoT, interacts with two sites within the RNA polymerase; site 1, located in the interphase between subunits β' and ω (rpoZ), and site 2 located in the secondary channel that is dependent on DksA protein. In Escherichia coli, inactivation of dksA results in a reduced sigma factor RpoS expression. In Azotobacter vinelandii the synthesis of polyhydroxybutyrate (PHB) is under RpoS regulation. In this study, we found that the inactivation of relA or dksA, but not rpoZ, resulted in a negative effect on PHB synthesis. We also found that the dksA, but not the relA mutation reduced both rpoS transcription and RpoS protein levels, implying that (p)ppGpp and DksA control PHB synthesis through different mechanisms. Interestingly, despite expressing rpoS from a constitutive promoter in the dksA mutant, PHB synthesis was not restored to wild type levels. A transcriptomic analysis in the dksA mutant, revealed downregulation of genes encoding enzymes needed for the synthesis of acetyl-CoA, the precursor substrate for PHB synthesis. Together, these data indicate that DksA is required for optimal expression of RpoS which in turn activates transcription of genes for PHB synthesis. Additionally, DksA is required for optimal transcription of genes responsible for the synthesis of precursors for PHB synthesis.
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Affiliation(s)
- Cristian Camilo Ortiz-Vasco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | | | - Juliana Berenice Rojo-Rodríguez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
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2
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Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. PNAS NEXUS 2024; 3:pgae154. [PMID: 38650860 PMCID: PMC11034885 DOI: 10.1093/pnasnexus/pgae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
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Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Snoeck S, Guidi C, De Mey M. "Metabolic burden" explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli. Microb Cell Fact 2024; 23:96. [PMID: 38555441 PMCID: PMC10981312 DOI: 10.1186/s12934-024-02370-9] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Engineering bacterial strains to redirect the metabolism towards the production of a specific product has enabled the development of industrial biotechnology. However, rewiring the metabolism can have severe implications for a microorganism, rendering cells with stress symptoms such as a decreased growth rate, impaired protein synthesis, genetic instability and an aberrant cell size. On an industrial scale, this is reflected in processes that are not economically viable. MAIN TEXT In literature, most stress symptoms are attributed to "metabolic burden", however the actual triggers and stress mechanisms involved are poorly understood. Therefore, in this literature review, we aimed to get a better insight in how metabolic engineering affects Escherichia coli and link the observed stress symptoms to its cause. Understanding the possible implications that chosen engineering strategies have, will help to guide the reader towards optimising the envisioned process more efficiently. CONCLUSION This review addresses the gap in literature and discusses the triggers and effects of stress mechanisms that can be activated when (over)expressing (heterologous) proteins in Escherichia coli. It uncovers that the activation of the different stress mechanisms is complex and that many are interconnected. The reader is shown that care has to be taken when (over)expressing (heterologous) proteins as the cell's metabolism is tightly regulated.
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Affiliation(s)
- Sofie Snoeck
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Chiara Guidi
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium.
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4
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Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol 2024; 9:647-656. [PMID: 38443580 DOI: 10.1038/s41564-024-01609-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024]
Abstract
(p)ppGpp is a nucleotide alarmone that controls bacterial response to nutrient deprivation. Since elevated (p)ppGpp levels confer mecillinam resistance and are essential for broad-spectrum β-lactam resistance as mediated by the β-lactam-insensitive transpeptidase YcbB (LdtD), we hypothesized that (p)ppGpp might affect cell wall peptidoglycan metabolism. Here we report that (p)ppGpp-dependent β-lactam resistance does not rely on any modification of peptidoglycan metabolism, as established by analysis of Escherichia coli peptidoglycan structure using high-resolution mass spectrometry. Amino acid substitutions in the β or β' RNA polymerase (RNAP) subunits, alone or in combination with the CRISPR interference-mediated downregulation of three of seven ribosomal RNA operons, were sufficient for resistance, although β-lactams have no known impact on the RNAP or ribosomes. This implies that modifications of RNAP and ribosome functions are critical to prevent downstream effects of the inactivation of peptidoglycan transpeptidases by β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Constantin Anoyatis-Pelé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Olivier Langella
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Filippo Rusconi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
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5
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Kago G, Turnbough CL, Salazar JC, Payne SM. (p)ppGpp is required for virulence of Shigella flexneri. Infect Immun 2024; 92:e0033423. [PMID: 38099658 PMCID: PMC10790822 DOI: 10.1128/iai.00334-23] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Infection by the enteric pathogen Shigella flexneri requires transit through the gastrointestinal tract and invasion of and replication within the cells of the host colonic epithelium. This process exposes the pathogen to a range of diverse microenvironments. Furthermore, the unique composition and physical environment of the eukaryotic cell cytosol represents a stressful environment for S. flexneri, and extensive physiological adaptations are needed for the bacterium to thrive. In this work, we show that disrupting synthesis of the stringent response alarmone (p)ppGpp in S. flexneri diminished expression of key virulence genes, including ipaA, ipaB, ipaC, and icsA, and it reduced bacterial invasion and intercellular spread. Deletion of the (p)ppGpp synthase gene relA alone had no effect on S. flexneri virulence, but disruption of both relA and the (p)ppGpp synthase/hydrolase gene spoT resulted in loss of (p)ppGpp synthesis and virulence. While the relA spoT deletion mutant was able to invade a cultured human epithelial cell monolayer, albeit at reduced levels, it was unable to maintain the infection and spread to adjacent cells, as indicated by loss of plaque formation. Complementation with spoT on a plasmid vector restored plaque formation. Thus, SpoT alone is sufficient to provide the necessary level of (p)ppGpp for virulence. These results indicate that (p)ppGpp is required for S. flexneri virulence and adaptation to the intracellular environment, adding to the repertoire of signaling pathways that affect Shigella pathogenesis.
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Affiliation(s)
- Grace Kago
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Charles L. Turnbough
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Carlos Salazar
- Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Shelley M. Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, USA
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6
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Anderson SE, Vadia SE, McKelvy J, Levin PA. The transcription factor DksA exerts opposing effects on cell division depending on the presence of ppGpp. mBio 2023; 14:e0242523. [PMID: 37882534 PMCID: PMC10746185 DOI: 10.1128/mbio.02425-23] [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: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Cell division is a key step in the bacterial lifecycle that must be appropriately regulated to ensure survival. This work identifies the alarmone (p)ppGpp (ppGpp) as a general regulator of cell division, extending our understanding of the role of ppGpp beyond a signal for starvation and other stress. Even in nutrient-replete conditions, basal levels of ppGpp are essential for division to occur appropriately and for cell size to be maintained. This study establishes ppGpp as a "switch" that controls whether the transcription factor DksA behaves as a division activator or inhibitor. This unexpected finding enhances our understanding of the complex regulatory mechanisms employed by bacteria to coordinate division with diverse aspects of cell growth and stress response. Because division is an essential process, a better understanding of the mechanisms governing the assembly and activation of the division machinery could contribute to the development of novel therapeutics to treat bacterial infections.
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Affiliation(s)
- Sarah E. Anderson
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Stephen E. Vadia
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Jane McKelvy
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, 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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Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. J Biol Chem 2023; 299:104724. [PMID: 37075846 PMCID: PMC10232725 DOI: 10.1016/j.jbc.2023.104724] [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: 01/23/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
Bacterial pathogens like Mycobacterium tuberculosis (Mtb) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb. Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase to stabilize the open complex intermediate (RPo) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo. However, it is unknown how CarD achieves promoter-specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RPo stability and test this model using in vitro transcription from a panel of promoters with varying levels of RPo stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnAP3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RPo stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RPo. DNA supercoiling also influenced RPo stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNA polymerase-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
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Affiliation(s)
- Dennis X Zhu
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA.
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9
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Anderson SE, Vadia SE, McKelvy J, Levin PA. The transcription factor DksA exerts opposing effects on cell division depending on the presence of ppGpp. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540843. [PMID: 37293059 PMCID: PMC10245573 DOI: 10.1101/2023.05.15.540843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial cell size is a multifactorial trait that is influenced by variables including nutritional availability and the timing of cell division. Prior work revealed a negative correlation between the alarmone (p)ppGpp (ppGpp) and cell length in Escherichia coli , suggesting that ppGpp may promote assembly of the division machinery (divisome) and cytokinesis in this organism. To clarify this counterintuitive connection between a starvation induced stress response effector and cell proliferation, we undertook a systematic analysis of growth and division in E. coli cells defective in ppGpp synthesis and/or engineered to overproduce the alarmone. Our data indicate that ppGpp acts indirectly on divisome assembly through its role as a global mediator of transcription. Loss of either ppGpp (ppGpp 0 ) or the ppGpp-associated transcription factor DksA led to increased average length, with ppGpp 0 mutants also exhibiting a high frequency of extremely long filamentous cells. Using heat-sensitive division mutants and fluorescently labeled division proteins, we confirmed that ppGpp and DksA are cell division activators. We found that ppGpp and DksA regulate division through their effects on transcription, although the lack of known division genes or regulators in available transcriptomics data strongly suggests that this regulation is indirect. Surprisingly, we also found that DksA inhibits division in ppGpp 0 cells, contrary to its role in a wild-type background. We propose that the ability of ppGpp to switch DksA from a division inhibitor to a division activator helps tune cell length across different concentrations of ppGpp. Importance Cell division is a key step in the bacterial lifecycle that must be appropriately regulated to ensure survival. This work identifies the alarmone ppGpp as a general regulator of cell division, extending our understanding of the role of ppGpp beyond a signal for starvation and other stress. Even in nutrient replete conditions, basal levels of ppGpp are essential for division to occur appropriately and for cell size to be maintained. This study establishes ppGpp as a "switch" that controls whether the transcription factor DksA behaves as a division activator or inhibitor. This unexpected finding enhances our understanding of the complex regulatory mechanisms employed by bacteria to coordinate division with diverse aspects of cell growth and stress response. Because division is an essential process, a better understanding the mechanisms governing assembly and activation of the division machinery could contribute to the development of novel therapeutics to treat bacterial infections.
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10
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Ray A, Spiro S. DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans. J Bacteriol 2023; 205:e0002723. [PMID: 36920204 PMCID: PMC10127633 DOI: 10.1128/jb.00027-23] [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: 01/19/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either dksA1 (one of two dksA homologs in the P. denitrificans genome) or relA/spoT (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in nap promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that nap promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The dksA1 and relA/spoT genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second dksA homolog (dksA2) and relA/spoT have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. IMPORTANCE Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.
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Affiliation(s)
- Ashvini Ray
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Stephen Spiro
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
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11
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Huang C, Li W, Chen J. Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica. Int J Mol Sci 2023; 24:ijms24087612. [PMID: 37108773 PMCID: PMC10142893 DOI: 10.3390/ijms24087612] [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: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The stringent response is a rapid response system that is ubiquitous in bacteria, allowing them to sense changes in the external environment and undergo extensive physiological transformations. However, the regulators (p)ppGpp and DksA have extensive and complex regulatory patterns. Our previous studies demonstrated that (p)ppGpp and DksA in Yersinia enterocolitica positively co-regulated motility, antibiotic resistance, and environmental tolerance but had opposite roles in biofilm formation. To reveal the cellular functions regulated by (p)ppGpp and DksA comprehensively, the gene expression profiles of wild-type, ΔrelA, ΔrelAΔspoT, and ΔdksAΔrelAΔspoT strains were compared using RNA-Seq. Results showed that (p)ppGpp and DksA repressed the expression of ribosomal synthesis genes and enhanced the expression of genes involved in intracellular energy and material metabolism, amino acid transport and synthesis, flagella formation, and the phosphate transfer system. Additionally, (p)ppGpp and DksA inhibited amino acid utilization (such as arginine and cystine) and chemotaxis in Y. enterocolitica. Overall, the results of this study unraveled the link between (p)ppGpp and DksA in the metabolic networks, amino acid utilization, and chemotaxis in Y. enterocolitica and enhanced the understanding of stringent responses in Enterobacteriaceae.
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Affiliation(s)
- Can Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, 17 Qinghua East Rd., Beijing 100083, China
| | - Wenqian Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, 17 Qinghua East Rd., Beijing 100083, China
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, 17 Qinghua East Rd., Beijing 100083, China
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12
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Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533025. [PMID: 36993566 PMCID: PMC10055060 DOI: 10.1101/2023.03.16.533025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Bacterial pathogens like Mycobacterium tuberculosis ( Mtb ) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb . Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase (RNAP) to stabilize the open complex intermediate (RP o ) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo . However, it is unknown how CarD achieves promoter specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RP o stability and test this model using in vitro transcription from a panel of promoters with varying levels of RP o stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnA P3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RP o stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RP o . DNA supercoiling also influenced RP o stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNAP-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
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Abstract
As rapidly growing bacteria begin to exhaust essential nutrients, they enter a state of reduced growth, ultimately leading to stasis or quiescence. Investigation of the response to nutrient limitation has focused largely on the consequences of amino acid starvation, known as the "stringent response." Here, an uncharged tRNA in the A-site of the ribosome stimulates the ribosome-associated protein RelA to synthesize the hyperphosphorylated guanosine nucleotides (p)ppGpp that mediate a global slowdown of growth and biosynthesis. Investigations of the stringent response typically employ experimental methodologies that rapidly stimulate (p)ppGpp synthesis by abruptly increasing the fraction of uncharged tRNAs, either by explicit amino starvation or by inhibition of tRNA charging. Consequently, these methodologies inhibit protein translation, thereby interfering with the cellular pathways that respond to nutrient limitation. Thus, complete and/or rapid starvation is a problematic experimental paradigm for investigating bacterial responses to physiologically relevant nutrient-limited states.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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14
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Huang C, Meng J, Li W, Chen J. Similar and Divergent Roles of Stringent Regulator (p)ppGpp and DksA on Pleiotropic Phenotype of Yersinia enterocolitica. Microbiol Spectr 2022; 10:e0205522. [PMID: 36409141 PMCID: PMC9769547 DOI: 10.1128/spectrum.02055-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022] Open
Abstract
Stringent response plays an important role in the response of Enterobacteriaceae pathogens to rapid environmental changes. It has been shown that synergistic and antagonistic actions exist between the signaling molecules (p)ppGpp and DksA in several foodborne pathogens; however, the biological function of these molecules and their interactions in Yersinia are still unclear. This study systematically investigated the role of stringent response in Yersinia enterocolitica, a typical foodborne Enterobacteriaceae pathogen, by deleting the (p)ppGpp and DksA biosynthesis genes. (p)ppGpp and DksA copositively regulated most phenotypes, such as motility, antibiotic resistance, and tolerance to oxidative stress, whereas they exhibited independent and/or divergent roles in the growth and biofilm synthesis of Y. enterocolitica. Gene expression analysis revealed that (p)ppGpp- and DksA-deficiency reduced the transcription of flagellar synthesis genes (fliC and flgD) and biofilm synthesis genes (bssS and hmsHFRS), which could potentially contribute to changes in motility and biofilm formation. These results indicate that stringent response regulators (p)ppGpp and DksA have a synergistic role and independent or even completely opposite biological functions in regulating genes and phenotypes of Y. enterocolitica. Our findings revealed the biofunctional relationships between (p)ppGpp and DksA and the underlying molecular mechanisms in the regulation of the pathogenic phenotype of Y. enterocolitica. IMPORTANCE The synergetic actions between the stringent response signaling molecules, (p)ppGpp and DksA, have been widely reported. However, recent transcriptomic and phenotypic studies have suggested that independent or even opposite actions exist between them. In this study, we demonstrated that the knockout of (p)ppGpp and DksA affects the polymorphic phenotype of Yersinia enterocolitica. Although most of the tested phenotypes, such as motility, antibiotic resistance, and tolerance to oxidative stress, were copositively regulated by (p)ppGpp and DksA, it also showed inconsistencies in biofilm formation ability as well as some independent phenotypes. This study deepens our understanding of the strategies of foodborne pathogens to survive in complex environments, so as to provide theoretical basis for the control and treatment of these microorganisms.
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Affiliation(s)
- Can Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, People’s Republic of China
| | - Wenqian Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
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15
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Mandel C, Yang H, Buchko GW, Abendroth J, Grieshaber N, Chiarelli T, Grieshaber S, Omsland A. Expression and structure of the Chlamydia trachomatis DksA ortholog. Pathog Dis 2022; 80:6564600. [PMID: 35388904 PMCID: PMC9126822 DOI: 10.1093/femspd/ftac007] [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: 11/16/2021] [Revised: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksACt) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksACt in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksACt is similar to the DksA ortholog of Escherichia coli (DksAEc), DksACt did not functionally complement DksAEc. Transcription of dksACt is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksACt and the correlation between dksACt and nrdR expression is consistent with a role for DksACt in the C. trachomatis developmental cycle.
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Affiliation(s)
- Cameron Mandel
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Hong Yang
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Garry W Buchko
- School of Molecular Biosciences, Washington State University, Pullman WA 99164, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Seattle Structural Genomics Center for Infectious Disease, WA, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, WA, USA.,UCB, Bainbridge Island, WA 98110, USA
| | - Nicole Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Travis Chiarelli
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Scott Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Anders Omsland
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
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16
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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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17
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Cohen H, Adani B, Cohen E, Piscon B, Azriel S, Desai P, Bähre H, McClelland M, Rahav G, Gal-Mor O. The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways. Gut Microbes 2022; 14:1997294. [PMID: 34923900 PMCID: PMC8726615 DOI: 10.1080/19490976.2021.1997294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DksA is a conserved RNA polymerase-binding protein known to play a key role in the stringent response of proteobacteria species, including many gastrointestinal pathogens. Here, we used RNA-sequencing of Escherichia coli, Salmonella bongori and Salmonella enterica serovar Typhimurium, together with phenotypic comparison to study changes in the DksA regulon, during Salmonella evolution. Comparative RNA-sequencing showed that under non-starved conditions, DksA controls the expression of 25%, 15%, and 20% of the E. coli, S. bongori, and S. enterica genes, respectively, indicating that DksA is a pleiotropic regulator, expanding its role beyond the canonical stringent response. We demonstrate that DksA is required for the growth of these three enteric bacteria species in minimal medium and controls the expression of the TCA cycle, glycolysis, pyrimidine biosynthesis, and quorum sensing. Interestingly, at multiple steps during Salmonella evolution, the type I fimbriae and various virulence genes encoded within SPIs 1, 2, 4, 5, and 11 have been transcriptionally integrated under the ancestral DksA regulon. Consequently, we show that DksA is necessary for host cells invasion by S. Typhimurium and S. bongori and for intracellular survival of S. Typhimurium in bone marrow-derived macrophages (BMDM). Moreover, we demonstrate regulatory inversion of the conserved motility-chemotaxis regulon by DksA, which acts as a negative regulator in E. coli, but activates this pathway in S. bongori and S. enterica. Overall, this study demonstrates the regulatory assimilation of multiple horizontally acquired virulence genes under the DksA regulon and provides new insights into the evolution of virulence genes regulation in Salmonella spp.
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Affiliation(s)
- Helit Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Boaz Adani
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Emiliano Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Bar Piscon
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Shalhevet Azriel
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Prerak Desai
- Janssen Research & Development, LLC, Raritan, New Jersey, USA,Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Heike Bähre
- Hannover Medical School, Research Core Unit Metabolomics, Hannover, Germany
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Galia Rahav
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel,Contact Ohad Gal-Mor The Infectious Diseases Research Laboratory Sheba Medical Cente, Tel-Hashomer, Israel
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18
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [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: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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19
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Büke F, Grilli J, Cosentino Lagomarsino M, Bokinsky G, Tans SJ. ppGpp is a bacterial cell size regulator. Curr Biol 2021; 32:870-877.e5. [PMID: 34990598 DOI: 10.1016/j.cub.2021.12.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/27/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
Growth and division are central to cell size. Bacteria achieve size homeostasis by dividing when growth has added a constant size since birth, termed the adder principle, by unknown mechanisms.1,2 Growth is well known to be regulated by guanosine tetraphosphate (ppGpp), which controls diverse processes from ribosome production to metabolic enzyme activity and replication initiation and whose absence or excess can induce stress, filamentation, and small growth-arrested cells.3-6 These observations raise unresolved questions about the relation between ppGpp and size homeostasis mechanisms during normal exponential growth. Here, to untangle effects of ppGpp and nutrients, we gained control of cellular ppGpp by inducing the synthesis and hydrolysis enzymes RelA and Mesh1. We found that ppGpp not only exerts control over the growth rate but also over cell division and thus the steady state cell size. In response to changes in ppGpp level, the added size already establishes its new constant value while the growth rate still adjusts, aided by accelerated or delayed divisions. Moreover, the magnitude of the added size and resulting steady-state birth size correlate consistently with the ppGpp level, rather than with the growth rate, which results in cells of different size that grow equally fast. Our findings suggest that ppGpp serves as a key regulator that coordinates cell size and growth control.
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Affiliation(s)
- Ferhat Büke
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands; AMOLF, Amsterdam, the Netherlands
| | - Jacopo Grilli
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34014 Trieste, Italy
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20143, Milan, Italy; Physics Department, University of Milan, and I.N.F.N., Via Celoria 16, 20133, Milan, Italy
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Sander J Tans
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands; AMOLF, Amsterdam, the Netherlands.
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20
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Kim N, Son JH, Kim K, Kim HJ, Shin M, Lee JC. DksA Modulates Antimicrobial Susceptibility of Acinetobacter baumannii. Antibiotics (Basel) 2021; 10:antibiotics10121472. [PMID: 34943684 PMCID: PMC8698368 DOI: 10.3390/antibiotics10121472] [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: 10/28/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 11/05/2022] Open
Abstract
The stringent response regulators, (p)ppGpp and DksA, modulate various genes involved in physiological processes, virulence, and antimicrobial resistance in pathogenic bacteria. This study investigated the role of DksA in the antimicrobial susceptibility of Acinetobacter baumannii. The ∆dksA mutant (KM0248D) of A. baumannii ATCC 17978 and its complemented strain (KM0248C) were used, in addition to the ∆dksA mutant strain (NY0298D) of clinical 1656-2 strain. The microdilution assay was used to determine the minimum inhibitory concentrations (MICs) of antimicrobial agents. Quantitative real-time PCR was performed to analyze the expression of genes associated with efflux pumps. The KM0248D strain exhibited an increase of MICs to quinolones and tetracyclines, whereas KM0248D and NY0298D strains exhibited a decrease of MICs to aminoglycosides. The expression of genes associated with efflux pumps, including adeB, adeI/J, abeM, and/or tetA, was upregulated in both ∆dksA mutant strains. The deletion of dksA altered bacterial morphology in the clinical 1656-2 strain. In conclusion, DksA modulates the antimicrobial susceptibility of A. baumannii. The ∆dksA mutant strains of A. baumannii upregulate efflux pump gene expression, whereas (p)ppGpp-deficient mutants downregulate efflux pump gene expression. (p)ppGpp and DksA conduct opposite roles in the antimicrobial susceptibility of A. baumannii via efflux pump gene regulation.
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21
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Pulschen AA, Fernandes AZN, Cunha AF, Sastre DE, Matsuguma BE, Gueiros-Filho FJ. Many birds with one stone: targeting the (p)ppGpp signaling pathway of bacteria to improve antimicrobial therapy. Biophys Rev 2021; 13:1039-1051. [DOI: 10.1007/s12551-021-00895-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
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22
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Kim N, Son JH, Kim K, Kim HJ, Kim YJ, Shin M, Lee JC. Global regulator DksA modulates virulence of Acinetobacter baumannii. Virulence 2021; 12:2750-2763. [PMID: 34696704 PMCID: PMC8583241 DOI: 10.1080/21505594.2021.1995253] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
DksA with (p)ppGpp regulates a wide range of gene transcriptions during the stringent response. The aim of this study was to identify a DksA ortholog in Acinetobacter baumannii and clarify the roles of DksA in bacterial physiology and virulence. The ∆dksA mutant and its complemented strains were constructed using A. baumannii ATCC 17978. The AlS_0248 in A. baumannii ATCC 17978 was identified to dksA using sequence homology, protein structure prediction, and gene expression patterns under different culture conditions. The ∆dksA mutant strain showed a filamentous morphology compared with the wild-type (WT) strain. Bacterial growth was decreased in the ∆dksA mutant strain under static conditions. Surface motility was decreased in the ∆dksA mutant strain compared with the WT strain. In contrast, biofilm formation was increased and biofilm-associated genes, such as bfmR/S and csuC/D/E, were upregulated in the ∆dksA mutant strain. The ∆dksA mutant strain produced less autoinducers than the WT strain. The expression of abaI and abaR was significantly decreased in the ∆dksA mutant strain. Furthermore, the ∆dksA mutant strain showed less bacterial burden and milder histopathological changes in the lungs of mice than the WT strain. Mice survival was also significantly different between the ∆dksA mutant and WT strains. Conclusively, DksA is directly or indirectly involved in regulating a wide range of genes associated with bacterial physiology and virulence, which contributes to the pathogenesis of A. baumannii. Thus, DksA is a potential anti-virulence target for A. baumannii infection.
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Affiliation(s)
- Nayeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Joo Hee Son
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyeongmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo Jeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yoo Jeong Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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23
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Bayon-Vicente G, Marchand E, Ducrotois J, Dufrasne FE, Hallez R, Wattiez R, Leroy B. Analysis of the Involvement of the Isoleucine Biosynthesis Pathway in Photoheterotrophic Metabolism of Rhodospirillum rubrum. Front Microbiol 2021; 12:731976. [PMID: 34621257 PMCID: PMC8490811 DOI: 10.3389/fmicb.2021.731976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/26/2021] [Indexed: 12/05/2022] Open
Abstract
Purple non-sulfur bacteria (PNSB) are recognized as a highly versatile group of bacteria that assimilate a broad range of carbon sources. Growing heterotrophically, PNSB such as Rhodospirillum rubrum (Rs. rubrum) generate reduced equivalents that are used for biomass production. However, under photoheterotrophic conditions, more reduced electron carriers than required to produce biomass are generated. The excess of reduced equivalents still needs to be oxidized for the metabolism to optimally operate. These metabolic reactions are known as electron sinks. Most PNSB rely on the CO2-fixing Calvin cycle and H2 production to oxidize these reduced equivalents. In addition to these well-described electron sinks, the involvement of some pathways, such as polyhydroxyalkanoate (PHA) biosynthesis, in redox poise is still controversial and requires further studies. Among them, isoleucine biosynthesis has been recently highlighted as one of these potential pathways. Here, we explore the role of isoleucine biosynthesis in Rs. rubrum. Our results demonstrate that the isoleucine content is higher under illuminated conditions and that submitting Rs. rubrum to light stress further increases this phenomenon. Moreover, we explore the production of (p)ppGpp in Rs. rubrum and its potential link with light stress. We further demonstrate that a fully functional isoleucine biosynthesis pathway could be an important feature for the onset of Rs. rubrum growth under photoheterotrophic conditions even in the presence of an exogenous isoleucine source. Altogether, our data suggest that isoleucine biosynthesis could play a key role in redox homeostasis.
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Affiliation(s)
- Guillaume Bayon-Vicente
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Elie Marchand
- Bacterial Cell Cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Jeson Ducrotois
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - François E. Dufrasne
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Regis Hallez
- Bacterial Cell Cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
- Namur Research College (NARC), University of Namur, Namur, Belgium
- WELBIO, University of Namur, Namur, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
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A Proteomics Approach to Identify Possible Biomarkers of Early and Late Stages of E. coli-induced Urinary Tract Infections. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As one of the most common bacterial infections globally, urinary tract infections (UTI)s affect the bladder and kidneys of many the bladders and kidneys of many. Along with gram-negative bacteria, Escherichia coli (E. coli) causes nearly 40% of nosocomial UTIs, 25% of recurrent infections, and between 80 to 90% of community-acquired infections. Proteomics, commonly used to study changes in protein expression of organisms, can be used to explore candidate biomarkers useful for the diagnosis of pathological conditions. Here, protein profiles of samples from patients diagnosed with E. coli-induced UTI were compared to identify distinctive proteins. Extracted proteins from bacteria from patients’ urine samples were separated into excisable spots using 2D-gel electrophoresis. The gels were then analyzed using Progenesis SameSpot software to select uniquely expressed protein spots, excised, and analyzed by LC/MS. The results were then compared against a database of known proteins. We identified two proteins, outer membrane protein A (OmpA) and RNA polymerase-binding transcription factor (DksA), involved in the survival of E. coli in the harsh environment of the host. We suggest their use as a part of a battery of possible biomarkers proteins for E. coli-induced UTI, and suggest that their overexpression is possibly associated with the stage of infection, early or late.
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25
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Abstract
Bioinformatic analysis showed previously that a majority of promoters in the photoheterotrophic alphaproteobacterium Rhodobacter sphaeroides lack the thymine at the last position of the -10 element (-7T), a base that is very highly conserved in promoters in bacteria other than alphaproteobacteria. The absence of -7T was correlated with low promoter activity using purified R. sphaeroides RNA polymerase (RNAP), but the transcription factor CarD compensated by activating almost all promoters lacking -7T tested in vitro, including rRNA promoters. Here, we show that a previously uncharacterized R. sphaeroides promoter, the promoter for carD itself, has high basal activity relative to other tested R. sphaeroides promoters despite lacking -7T, and its activity is inhibited rather than activated by CarD. This high basal activity is dependent on a consensus-extended -10 element (TGn) and specific features in the spacer immediately upstream of the extended -10 element. CarD negatively autoregulates its own promoter by producing abortive transcripts, limiting promoter escape, and reducing full-length mRNA synthesis. This mechanism of negative regulation differs from that employed by classical repressors, in which the transcription factor competes with RNA polymerase for binding to the promoter, and with the mechanism of negative regulation used by transcription factors like DksA/ppGpp and TraR that allosterically inhibit the rate of open complex formation. IMPORTANCE R. sphaeroides CarD activates many promoters by binding directly to RNAP and DNA just upstream of the -10 element. In contrast, we show here that CarD inhibits its own promoter using the same interactions with RNAP and DNA used for activation. Inhibition results from increasing abortive transcript formation, thereby decreasing promoter escape and full-length RNA synthesis. We propose that the combined interactions of RNAP with CarD, with the extended -10 element and with features in the adjacent -10/-35 spacer DNA, stabilize the promoter complex, reducing promoter clearance. These findings support previous predictions that the effects of CarD on transcription can be either positive or negative, depending on the kinetic properties of the specific promoter.
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26
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Mutational Activation of Antibiotic-Resistant Mechanisms in the Absence of Major Drug Efflux Systems of Escherichia coli. J Bacteriol 2021; 203:e0010921. [PMID: 33972351 DOI: 10.1128/jb.00109-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations are one of the common means by which bacteria acquire resistance to antibiotics. In an Escherichia coli mutant lacking major antibiotic efflux pumps AcrAB and AcrEF, mutations can activate alternative pathways that lead to increased antibiotic resistance. In this work, we isolated and characterized compensatory mutations of this nature mapping in four different regulatory genes, baeS, crp, hns, and rpoB. The gain-of-function mutations in baeS constitutively activated the BaeSR two-component regulatory system to increase the expression of the MdtABC efflux pump. Missense or insertion mutations in crp and hns caused derepression of an operon coding for the MdtEF efflux pump. Interestingly, despite the dependence of rpoB missense mutations on MdtABC for their antibiotic resistance phenotype, neither the expression of the mdtABCD-baeSR operon nor that of other known antibiotic efflux pumps went up. Instead, the transcriptome sequencing (RNA-seq) data revealed a gene expression profile resembling that of a "stringent" RNA polymerase where protein and DNA biosynthesis pathways were downregulated but pathways to combat various stresses were upregulated. Some of these activated stress pathways are also controlled by the general stress sigma factor RpoS. The data presented here also show that compensatory mutations can act synergistically to further increase antibiotic resistance to a level similar to the efflux pump-proficient parental strain. Together, the findings highlight a remarkable genetic ability of bacteria to circumvent antibiotic assault, even in the absence of a major intrinsic antibiotic resistance mechanism. IMPORTANCE Antibiotic resistance among bacterial pathogens is a chronic health concern. Bacteria possess or acquire various mechanisms of antibiotic resistance, and chief among them is the ability to accumulate beneficial mutations that often alter antibiotic targets. Here, we explored E. coli's ability to amass mutations in a background devoid of a major constitutively expressed efflux pump and identified mutations in several regulatory genes that confer resistance by activating specific or pleiotropic mechanisms.
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Virus-Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1 vir Infection. Int J Mol Sci 2021; 22:ijms22116159. [PMID: 34200430 PMCID: PMC8201110 DOI: 10.3390/ijms22116159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
The virus–host interaction requires a complex interplay between the phage strategy of reprogramming the host machinery to produce and release progeny virions, and the host defense against infection. Using RNA sequencing, we investigated the phage–host interaction to resolve the phenomenon of improved lytic development of P1vir phage in a DksA-deficient E. coli host. Expression of the ant1 and kilA P1vir genes in the wild-type host was the highest among all and most probably leads to phage virulence. Interestingly, in a DksA-deficient host, P1vir genes encoding lysozyme and holin are downregulated, while antiholins are upregulated. Gene expression of RepA, a protein necessary for replication initiating at the phage oriR region, is increased in the dksA mutant; this is also true for phage genes responsible for viral morphogenesis and architecture. Still, it seems that P1vir is taking control of the bacterial protein, sugar, and lipid metabolism in both, the wild type and dksA− hosts. Generally, bacterial hosts are reacting by activating their SOS response or upregulating the heat shock proteins. However, only DksA-deficient cells upregulate their sulfur metabolism and downregulate proteolysis upon P1vir infection. We conclude that P1vir development is enhanced in the dksA mutant due to several improvements, including replication and virion assembly, as well as a less efficient lysis.
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Cech GM, Kloska A, Krause K, Potrykus K, Cashel M, Szalewska-Pałasz A. Virus-Host Interaction Gets Curiouser and Curiouser. PART I: Phage P1 vir Enhanced Development in an E. coli DksA-Deficient Cell. Int J Mol Sci 2021; 22:ijms22115890. [PMID: 34072628 PMCID: PMC8198154 DOI: 10.3390/ijms22115890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteriophage P1 is among the best described bacterial viruses used in molecular biology. Here, we report that deficiency in the host cell DksA protein, an E. coli global transcription regulator, improves P1 lytic development. Using genetic and microbiological approaches, we investigated several aspects of P1vir biology in an attempt to understand the basis of this phenomenon. We found several minor improvements in phage development in the dksA mutant host, including more efficient adsorption to bacterial cell and phage DNA replication. In addition, gene expression of the main repressor of lysogeny C1, the late promoter activator Lpa, and lysozyme are downregulated in the dksA mutant. We also found nucleotide substitutions located in the phage immunity region immI, which may be responsible for permanent virulence of phage P1vir. We suggest that downregulation of C1 may lead to a less effective repression of lysogeny maintaining genes and that P1vir may be balancing between lysis and lysogeny, although finally it is able to enter the lytic pathway only. The mentioned improvements, such as more efficient replication and more “gentle” cell lysis, while considered minor individually, together may account for the phenomenon of a more efficient P1 phage development in a DksA-deficient host.
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Affiliation(s)
- Grzegorz M. Cech
- Department of Bacterial Molecular Genetics, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (K.K.); (K.P.); (A.S.-P.)
- Correspondence: ; Tel.: +48-58-523-60-25
| | - Anna Kloska
- Department of Medical Biology and Genetics, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Klaudyna Krause
- Department of Bacterial Molecular Genetics, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (K.K.); (K.P.); (A.S.-P.)
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (K.K.); (K.P.); (A.S.-P.)
| | - Michael Cashel
- Intramural Program, Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (K.K.); (K.P.); (A.S.-P.)
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Porrini C, Ramarao N, Tran SL. Dr. NO and Mr. Toxic - the versatile role of nitric oxide. Biol Chem 2021; 401:547-572. [PMID: 31811798 DOI: 10.1515/hsz-2019-0368] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/04/2019] [Indexed: 12/25/2022]
Abstract
Nitric oxide (NO) is present in various organisms from humans, to plants, fungus and bacteria. NO is a fundamental signaling molecule implicated in major cellular functions. The role of NO ranges from an essential molecule to a potent mediator of cellular damages. The ability of NO to react with a broad range of biomolecules allows on one hand its regulation and a gradient concentration and on the other hand to exert physiological as well as pathological functions. In humans, NO is implicated in cardiovascular homeostasis, neurotransmission and immunity. However, NO can also contribute to cardiovascular diseases (CVDs) or septic shock. For certain denitrifying bacteria, NO is part of their metabolism as a required intermediate of the nitrogen cycle. However, for other bacteria, NO is toxic and harmful. To survive, those bacteria have developed processes to resist this toxic effect and persist inside their host. NO also contributes to maintain the host/microbiota homeostasis. But little is known about the impact of NO produced during prolonged inflammation on microbiota integrity, and some pathogenic bacteria take advantage of the NO response to colonize the gut over the microbiota. Taken together, depending on the environmental context (prolonged production, gradient concentration, presence of partners for interaction, presence of oxygen, etc.), NO will exert its beneficial or detrimental function. In this review, we highlight the dual role of NO for humans, pathogenic bacteria and microbiota, and the mechanisms used by each organism to produce, use or resist NO.
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Affiliation(s)
- Constance Porrini
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Nalini Ramarao
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Seav-Ly Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021; 203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
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31
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Oguienko A, Petushkov I, Pupov D, Esyunina D, Kulbachinskiy A. Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase. RNA Biol 2021; 18:2028-2037. [PMID: 33573428 DOI: 10.1080/15476286.2021.1889254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The bacterial σ factor plays the central role in promoter recognition by RNA polymerase (RNAP). The primary σ factor, involved in transcription of housekeeping genes, was also shown to participate in the initiation of RNA synthesis and promoter escape by RNAP. In the open promoter complex, the σ finger formed by σ region 3.2 directly interacts with the template DNA strand upstream of the transcription start site. Here, we analysed the role of the σ finger in transcription initiation by four alternative σ factors in Escherichia coli, σ38, σ32, σ28 and σ24. We found that deletions of the σ finger to various extent compromise the activity of RNAP holoenzymes containing alternative σ factors, especially at low NTP concentrations. All four σs are able to utilize NADH as a noncanonical priming substrate but it has only mild effects on the efficiency of transcription initiation. The mediators of the stringent response, transcription factor DksA and the alarmone ppGpp decrease RNAP activity and promoter complex stability for all four σ factors on tested promoters. For all σs except σ38, deletions of the σ finger conversely increase the stability of promoter complexes and decrease their sensitivity to DksA and ppGpp. The result suggests that the σ finger plays a universal role in transcription initiation by alternative σ factors and sensitizes promoter complexes to the action of global transcription regulators DksA and ppGpp by modulating promoter complex stability.
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Affiliation(s)
| | - Ivan Petushkov
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, Russia
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Boyle WK, Richards CL, Dulebohn DP, Zalud AK, Shaw JA, Lovas S, Gherardini FC, Bourret TJ. DksA-dependent regulation of RpoS contributes to Borrelia burgdorferi tick-borne transmission and mammalian infectivity. PLoS Pathog 2021; 17:e1009072. [PMID: 33600418 PMCID: PMC7924775 DOI: 10.1371/journal.ppat.1009072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/02/2021] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Throughout its enzootic cycle, the Lyme disease spirochete Borreliella (Borrelia) burgdorferi, senses and responds to changes in its environment using a small repertoire of transcription factors that coordinate the expression of genes required for infection of Ixodes ticks and various mammalian hosts. Among these transcription factors, the DnaK suppressor protein (DksA) plays a pivotal role in regulating gene expression in B. burgdorferi during periods of nutrient limitation and is required for mammalian infectivity. In many pathogenic bacteria, the gene regulatory activity of DksA, along with the alarmone guanosine penta- and tetra-phosphate ((p)ppGpp), coordinate the stringent response to various environmental stresses, including nutrient limitation. In this study, we sought to characterize the role of DksA in regulating the transcriptional activity of RNA polymerase and its role in the regulation of RpoS-dependent gene expression required for B. burgdorferi infectivity. Using in vitro transcription assays, we observed recombinant DksA inhibits RpoD-dependent transcription by B. burgdorferi RNA polymerase independent of ppGpp. Additionally, we determined the pH-inducible expression of RpoS-dependent genes relies on DksA, but this relationship is independent of (p)ppGpp produced by Relbbu. Subsequent transcriptomic and western blot assays indicate DksA regulates the expression of BBD18, a protein previously implicated in the post-transcriptional regulation of RpoS. Moreover, we observed DksA was required for infection of mice following intraperitoneal inoculation or for transmission of B. burgdorferi by Ixodes scapularis nymphs. Together, these data suggest DksA plays a central role in coordinating transcriptional responses in B. burgdorferi required for infectivity through DksA’s interactions with RNA polymerase and post-transcriptional control of RpoS. Lyme disease, caused by the spirochete bacteria Borreliella (Borrelia) burgdorferi, is the most common vector-borne illness in North America. The ability of B. burgdorferi to establish infection is predicated by its ability to coordinate the expression of virulence factors in response to diverse environmental stimuli encountered within Ixodes ticks and mammalian hosts. Previous studies have shown an essential role for the alternative sigma factor RpoS in regulating the expression of genes required for the successful transmission of B. burgdorferi by Ixodes ticks and infection of mammalian hosts. The DnaK suppressor protein (DksA) is a global gene regulator in B. burgdorferi that contributes to the expression of RpoS-dependent genes. In this study, using in vitro transcription assays, we determined DksA exerts its gene regulatory function through direct interactions with the B. burgdorferi RNA polymerase and controls the expression of RpoS-dependent genes required for mammalian infection by post-transcriptionally regulating cellular levels of RpoS. Our results demonstrate the utility of in vitro transcription assays to determine how gene regulatory proteins like DksA control gene expression in B. burgdorferi and reveal a novel role for DksA in the infectious cycle of B. burgdorferi.
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Affiliation(s)
- William K. Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Crystal L. Richards
- Laboratory of Bacteriology, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Daniel P. Dulebohn
- Laboratory of Bacteriology, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Amanda K. Zalud
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Jeff A. Shaw
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, United States of America
| | - Frank C. Gherardini
- Laboratory of Bacteriology, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Travis J. Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
- * E-mail:
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Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. Structural basis of ribosomal RNA transcription regulation. Nat Commun 2021; 12:528. [PMID: 33483500 PMCID: PMC7822876 DOI: 10.1038/s41467-020-20776-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
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Affiliation(s)
- Yeonoh Shin
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - M. Zuhaib Qayyum
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Danil Pupov
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Daria Esyunina
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Andrey Kulbachinskiy
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Katsuhiko S. Murakami
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
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(p)ppGpp-Dependent Regulation of the Nucleotide Hydrolase PpnN Confers Complement Resistance in Salmonella enterica Serovar Typhimurium. Infect Immun 2021; 89:IAI.00639-20. [PMID: 33139383 DOI: 10.1128/iai.00639-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
The stringent response is an essential mechanism of metabolic reprogramming during environmental stress that is mediated by the nucleotide alarmones guanosine tetraphosphate and pentaphosphate [(p)ppGpp]. In addition to physiological adaptations, (p)ppGpp also regulates virulence programs in pathogenic bacteria, including Salmonella enterica serovar Typhimurium. S Typhimurium is a common cause of acute gastroenteritis, but it may also spread to systemic tissues, resulting in severe clinical outcomes. During infection, S Typhimurium encounters a broad repertoire of immune defenses that it must evade for successful host infection. Here, we examined the role of the stringent response in S Typhimurium resistance to complement-mediated killing and found that the (p)ppGpp synthetase-hydrolase, SpoT, is required for bacterial survival in human serum. We identified the nucleotide hydrolase, PpnN, as a target of the stringent response that is required to promote bacterial fitness in serum. Using chromatography and mass spectrometry, we show that PpnN hydrolyzes purine and pyrimidine monophosphates to generate free nucleobases and ribose 5'-phosphate, and that this metabolic activity is required for conferring resistance to complement killing. In addition to PpnN, we show that (p)ppGpp is required for the biosynthesis of the very long and long O-antigen in the outer membrane, known to be important for complement resistance. Our results provide new insights into the role of the stringent response in mediating evasion of the innate immune system by pathogenic bacteria.
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Cheng-Guang H, Gualerzi CO. The Ribosome as a Switchboard for Bacterial Stress Response. Front Microbiol 2021; 11:619038. [PMID: 33584583 PMCID: PMC7873864 DOI: 10.3389/fmicb.2020.619038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 12/29/2022] Open
Abstract
As free-living organisms, bacteria are subject to continuous, numerous and occasionally drastic environmental changes to which they respond with various mechanisms which enable them to adapt to the new conditions so as to survive. Here we describe three situations in which the ribosome and its functions represent the sensor or the target of the stress and play a key role in the subsequent cellular response. The three stress conditions which are described are those ensuing upon: a) zinc starvation; b) nutritional deprivation, and c) temperature downshift.
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Bubnov DM, Yuzbashev TV, Fedorov AS, Bondarenko FV, Savchenko AS, Vybornaya TV, Filippova SS, Sineoky SP. Glutamyl- and Glutaminyl-tRNA Synthetases Are a Promising Target for the Design of an L-Threonine–Producing Strain. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820080037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Myers AR, Thistle DP, Ross W, Gourse RL. Guanosine Tetraphosphate Has a Similar Affinity for Each of Its Two Binding Sites on Escherichia coli RNA Polymerase. Front Microbiol 2020; 11:587098. [PMID: 33250875 PMCID: PMC7676912 DOI: 10.3389/fmicb.2020.587098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
During nutrient deprivation, the bacterial cell undergoes a stress response known as the stringent response. This response is characterized by induction of the nucleotide derivative guanosine tetraphosphate (ppGpp) that dramatically modulates the cell's transcriptome. In Escherichia coli, ppGpp regulates transcription of as many as 750 genes within 5 min of induction by binding directly to RNA polymerase (RNAP) at two sites ~60 Å apart. One proposal for the presence of two sites is that they have different affinities for ppGpp, expanding the dynamic range over which ppGpp acts. We show here, primarily using the Differential Radial Capillary Action of Ligand Assay (DRaCALA), that ppGpp has a similar affinity for each site, contradicting the proposal. Because the ppGpp binding sites are formed by interactions of the β' subunit of RNAP with two small protein factors, the ω subunit of RNAP which contributes to Site 1 and the transcription factor DksA which contributes to Site 2, variation in the concentrations of ω or DksA potentially could differentially regulate ppGpp occupancy of the two sites. It was shown previously that DksA varies little at different growth rates or growth phases, but little is known about variation of the ω concentration. Therefore, we raised an anti-ω antibody and performed Western blots at different times in growth and during a stringent response. We show here that ω, like DksA, changes little with growth conditions. Together, our data suggest that the two ppGpp binding sites fill in parallel, and occupancy with changing nutritional conditions is determined by variation in the ppGpp concentration, not by variation in ω or DksA.
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Affiliation(s)
| | | | | | - Richard L. Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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Pletnev P, Pupov D, Pshanichnaya L, Esyunina D, Petushkov I, Nesterchuk M, Osterman I, Rubtsova M, Mardanov A, Ravin N, Sergiev P, Kulbachinskiy A, Dontsova O. Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor. Nucleic Acids Res 2020; 48:10802-10819. [PMID: 32997144 PMCID: PMC7641759 DOI: 10.1093/nar/gkaa798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 09/09/2020] [Accepted: 09/12/2020] [Indexed: 01/24/2023] Open
Abstract
In bacteria, rapid adaptation to changing environmental conditions depends on the interplay between housekeeping and alternative σ factors, responsible for transcription of specific regulons by RNA polymerase (RNAP). In comparison with alternative σ factors, primary σs contain poorly conserved region 1.1, whose functions in transcription are only partially understood. We found that a single mutation in region 1.1 in Escherichia coli σ70 rewires transcription regulation during cell growth resulting in profound phenotypic changes. Despite its destabilizing effect on promoter complexes, this mutation increases the activity of rRNA promoters and also decreases RNAP sensitivity to the major regulator of stringent response DksA. Using total RNA sequencing combined with single-cell analysis of gene expression we showed that changes in region 1.1 disrupt the balance between the "greed" and "fear" strategies thus making the cells more susceptible to environmental threats and antibiotics. Our results reveal an unexpected role of σ region 1.1 in growth-dependent transcription regulation and suggest that changes in this region may facilitate rapid switching of RNAP properties in evolving bacterial populations.
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Affiliation(s)
- Philipp Pletnev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Mikhail Nesterchuk
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Ilya Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Petr Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Olga Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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Irving SE, Choudhury NR, Corrigan RM. The stringent response and physiological roles of (pp)pGpp in bacteria. Nat Rev Microbiol 2020; 19:256-271. [PMID: 33149273 DOI: 10.1038/s41579-020-00470-y] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 01/10/2023]
Abstract
The stringent response is a stress signalling system mediated by the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) in response to nutrient deprivation. Recent research highlights the complexity and broad range of functions that these alarmones control. This Review provides an update on our current understanding of the enzymes involved in ppGpp, pppGpp and guanosine 5'-monophosphate 3'-diphosphate (pGpp) (collectively (pp)pGpp) turnover, including those shown to produce pGpp and its analogue (pp)pApp. We describe the well-known interactions with RNA polymerase as well as a broader range of cellular target pathways controlled by (pp)pGpp, including DNA replication, transcription, nucleotide synthesis, ribosome biogenesis and function, as well as lipid metabolism. Finally, we review the role of ppGpp and pppGpp in bacterial pathogenesis, providing examples of how these nucleotides are involved in regulating many aspects of virulence and chronic infection.
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Affiliation(s)
- Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Naznin R Choudhury
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
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Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors. Microorganisms 2020; 8:microorganisms8101622. [PMID: 33096715 PMCID: PMC7588896 DOI: 10.3390/microorganisms8101622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential role in the bacterial cell. For instance, some regulators specifically modify the transcription of virulence genes, thereby being indispensable to pathogenic bacteria. Here, we provide a comprehensive overview of important transcription factors and DNA-binding proteins described for the virulent bacterium Francisella tularensis, the causative agent of tularemia. This is an unexplored research area, and the poorly described networks of transcription factors merit additional experimental studies to help elucidate the molecular mechanisms of pathogenesis in this bacterium, and how they contribute to disease.
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41
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Characterization of RelA in Acinetobacter baumannii. J Bacteriol 2020; 202:JB.00045-20. [PMID: 32229531 DOI: 10.1128/jb.00045-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/26/2020] [Indexed: 12/21/2022] Open
Abstract
In response to nutrient depletion, the RelA and SpoT proteins generate the signaling molecule (p)ppGpp, which then controls a number of downstream effectors to modulate cell physiology. In Acinetobacter baumannii strain AB5075, a relA ortholog (ABUW_3302) was identified by a transposon insertion that conferred an unusual colony phenotype. An in-frame deletion in relA (ΔrelA) failed to produce detectable levels of ppGpp when amino acid starvation was induced with serine hydroxamate. The ΔrelA mutant was blocked from switching from the virulent opaque colony variant (VIR-O) to the avirulent translucent colony variant (AV-T), but the rate of AV-T to VIR-O switching was unchanged. In addition, the ΔrelA mutation resulted in a pronounced hypermotile phenotype on 0.35% agar plates. This hypermotility was dependent on the activation of a LysR regulator ABUW_1132, which was required for expression of AbaR, a LuxR family quorum-sensing regulator. In the ΔrelA mutant, ABUW_1132 was also required for the increased expression of an operon composed of the ABUW_3766-ABUW_3773 genes required for production of the surfactant-like lipopeptide acinetin 505. Additional phenotypes identified in the ΔrelA mutant included (i) cell elongation at high density, (ii) reduced formation of persister cells tolerant to colistin and rifampin, and (iii) decreased virulence in a Galleria mellonella model.IMPORTANCE Acinetobacter baumannii is a pathogen of worldwide importance. Due to the increasing prevalence of antibiotic resistance, these infections are becoming increasingly difficult to treat. New therapies are required to combat multidrug-resistant isolates. The role of RelA in A. baumannii is largely unknown. This study demonstrates that like in other bacteria, RelA controls a variety of functions, including virulence. Strategies to inhibit the activity of RelA and the resulting production of ppGpp could inhibit virulence and may represent a new therapeutic approach.
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Kumar J, Chauhan AS, Shah RL, Gupta JA, Rathore AS. Amino acid supplementation for enhancing recombinant protein production in
E. coli. Biotechnol Bioeng 2020; 117:2420-2433. [DOI: 10.1002/bit.27371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/03/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Jashwant Kumar
- Department of Chemical EngineeringIndian Institute of TechnologyNew Delhi India
| | - Ashish S. Chauhan
- Department of Chemical EngineeringIndian Institute of TechnologyNew Delhi India
| | - Rohan L. Shah
- Department of Chemical EngineeringIndian Institute of TechnologyNew Delhi India
| | - Jaya A. Gupta
- Department of Chemical EngineeringIndian Institute of TechnologyNew Delhi India
| | - Anurag S. Rathore
- Department of Chemical EngineeringIndian Institute of TechnologyNew Delhi India
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43
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Establishment of an in vitro RNA polymerase transcription system: a new tool to study transcriptional activation in Borrelia burgdorferi. Sci Rep 2020; 10:8246. [PMID: 32427963 PMCID: PMC7237435 DOI: 10.1038/s41598-020-65104-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/27/2020] [Indexed: 12/04/2022] Open
Abstract
The Lyme disease spirochete Borrelia burgdorferi exhibits dramatic changes in gene expression as it transits between its tick vector and vertebrate host. A major hurdle to understanding the mechanisms underlying gene regulation in B. burgdorferi has been the lack of a functional assay to test how gene regulatory proteins and sigma factors interact with RNA polymerase to direct transcription. To gain mechanistic insight into transcriptional control in B. burgdorferi, and address sigma factor function and specificity, we developed an in vitro transcription assay using the B. burgdorferi RNA polymerase holoenzyme. We established reaction conditions for maximal RNA polymerase activity by optimizing pH, temperature, and the requirement for divalent metals. Using this assay system, we analyzed the promoter specificity of the housekeeping sigma factor RpoD to promoters encoding previously identified RpoD consensus sequences in B. burgdorferi. Collectively, this study established an in vitro transcription assay that revealed RpoD-dependent promoter selectivity by RNA polymerase and the requirement of specific metal cofactors for maximal RNA polymerase activity. The establishment of this functional assay will facilitate molecular and biochemical studies on how gene regulatory proteins and sigma factors exert control of gene expression in B. burgdorferi required for the completion of its enzootic cycle.
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Yang HW, Yu M, Lee JH, Chatnaparat T, Zhao Y. The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora. BMC Genomics 2020; 21:261. [PMID: 32228459 PMCID: PMC7106674 DOI: 10.1186/s12864-020-6699-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/24/2020] [Indexed: 01/30/2023] Open
Abstract
Background The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an essential role in virulence in the fire blight pathogen Erwinia amylovora. Here, we present transcriptomic analyses to uncover the overall effect of (p) ppGpp-mediated stringent response in E. amylovora in the hrp-inducing minimal medium (HMM). Results In this study, we investigated the transcriptomic changes of the (p) ppGpp0 mutant under the type III secretion system (T3SS)-inducing condition using RNA-seq. A total of 1314 differentially expressed genes (DEGs) was uncovered, representing more than one third (36.8%) of all genes in the E. amylovora genome. Compared to the wild-type, the (p) ppGpp0 mutant showed down-regulation of genes involved in peptide ATP-binding cassette (ABC) transporters and virulence-related processes, including type III secretion system (T3SS), biofilm, and motility. Interestingly, in contrast to previous reports, the (p) ppGpp0 mutant showed up-regulation of amino acid biosynthesis genes, suggesting that it might be due to that these amino acid biosynthesis genes are indirectly regulated by (p) ppGpp in E. amylovora or represent specific culturing condition used. Furthermore, the (p) ppGpp0 mutant exhibited up-regulation of genes involved in translation, SOS response, DNA replication, chromosome segregation, as well as biosynthesis of nucleotide, fatty acid and lipid. Conclusion These findings suggested that in HMM environment, E. amylovora might use (p) ppGpp as a signal to activate virulence gene expression, and simultaneously mediate the balance between virulence and survival by negatively regulating DNA replication, translation, cell division, as well as biosynthesis of nucleotide, amino acid, fatty acid, and lipid. Therefore, (p) ppGpp could be a promising target for developing novel control measures to fight against this devastating disease of apples and pears.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA.
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Osaka N, Kanesaki Y, Watanabe M, Watanabe S, Chibazakura T, Takada H, Yoshikawa H, Asai K. Novel (p)ppGpp 0 suppressor mutations reveal an unexpected link between methionine catabolism and GTP synthesis in Bacillus subtilis. Mol Microbiol 2020; 113:1155-1169. [PMID: 32052499 DOI: 10.1111/mmi.14484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 11/29/2022]
Abstract
In bacteria, guanosine (penta)tetra-phosphate ([p]ppGpp) is essential for controlling intracellular metabolism that is needed to adapt to environmental changes, such as amino acid starvation. The (p)ppGpp0 strain of Bacillus subtilis, which lacks (p)ppGpp synthetase, is unable to form colonies on minimal medium. Here, we found suppressor mutations in the (p)ppGpp0 strain, in the purine nucleotide biosynthesis genes, prs, purF and rpoB/C, which encode RNA polymerase core enzymes. In comparing our work with prior studies of ppGpp0 suppressors, we discovered that methionine addition masks the suppression on minimal medium, especially of rpoB/C mutations. Furthermore, methionine addition increases intracellular GTP in rpoB suppressor and this effect is decreased by inhibiting GTP biosynthesis, indicating that methionine addition activated GTP biosynthesis and inhibited growth under amino acid starvation conditions in (p)ppGpp0 backgrounds. Furthermore, we propose that the increase in intracellular GTP levels induced by methionine is due to methionine derivatives that increase the activity of the de novo GTP biosynthesis enzyme, GuaB. Our study sheds light on the potential relationship between GTP homeostasis and methionine metabolism, which may be the key to adapting to environmental changes.
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Affiliation(s)
- Natsuki Osaka
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Megumi Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | | | - Kei Asai
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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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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Jensen D, Manzano AR, Rammohan J, Stallings CL, Galburt EA. CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase. Nucleic Acids Res 2020; 47:6685-6698. [PMID: 31127308 PMCID: PMC6648326 DOI: 10.1093/nar/gkz449] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/11/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
The pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, enacts unique transcriptional regulatory mechanisms when subjected to host-derived stresses. Initiation of transcription by the Mycobacterial RNA polymerase (RNAP) has previously been shown to exhibit different open complex kinetics and stabilities relative to Escherichia coli (Eco) RNAP. However, transcription initiation rates also depend on the kinetics following open complex formation such as initial nucleotide incorporation and subsequent promoter escape. Here, using a real-time fluorescence assay, we present the first in-depth kinetic analysis of initial transcription and promoter escape for the Mtb RNAP. We show that in relation to Eco RNAP, Mtb displays slower initial nucleotide incorporation but faster overall promoter escape kinetics on the Mtb rrnAP3 promoter. Furthermore, in the context of the essential transcription factors CarD and RbpA, Mtb promoter escape is slowed via differential effects on initially transcribing complexes. Finally, based on their ability to increase the rate of open complex formation and decrease the rate of promoter escape, we suggest that CarD and RbpA are capable of activation or repression depending on the rate-limiting step of a given promoter's basal initiation kinetics.
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Affiliation(s)
- Drake Jensen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jayan Rammohan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA. E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation. eLife 2019; 8:e49375. [PMID: 31841111 PMCID: PMC6970531 DOI: 10.7554/elife.49375] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022] Open
Abstract
TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.
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Affiliation(s)
- James Chen
- The Rockefeller UniversityNew YorkUnited States
| | | | | | - Albert Y Chen
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
| | | | - Richard L Gourse
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
| | - Wilma Ross
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
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Zhang Y, Teper D, Xu J, Wang N. Stringent response regulators (p)ppGpp and DksA positively regulate virulence and host adaptation of Xanthomonas citri. MOLECULAR PLANT PATHOLOGY 2019; 20:1550-1565. [PMID: 31621195 PMCID: PMC6804348 DOI: 10.1111/mpp.12865] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The bacterial stringent response is a response to nutrition deprivation and other stress conditions. In Gram-negative bacteria, this process is mediated by the small signal molecules guanosine pentaphosphate pppGpp and guanosine tetraphosphate ppGpp (collectively referred to as (p)ppGpp), and the RNA polymerase-binding transcription factor DksA. The (p)ppGpp synthetase RelA and the bifunctional (p)ppGpp synthase/hydrolase SpoT are responsible for cellular (p)ppGpp levels. Here, we investigated the roles of DksA and (p)ppGpp in the virulence traits of Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker. ΔdksA and (p)ppGpp-deficient ΔspoTΔrelA strains caused reduced virulence and compromised growth in host plants, indicating that DksA and (p)ppGpp are required for full virulence of Xcc. To characterize the effect of stringent response regulators on gene expression, RNA-seq was conducted using ΔdksA and ΔspoTΔrelA mutant strains grown in hrp-inducing XVM2 medium. Transcriptome analyses showed that DksA and (p)ppGpp repressed the expression of genes encoding tRNAs, ribosome proteins, iron acquisition and flagellum assembly, and enhanced the expression of genes for histidine metabolism, type 3 secretion system (T3SS), type 2 secretion system (T2SS) and TonB-dependent transporters. Phenotypically, the ΔdksA and ΔspoTΔrelA strains displayed altered motility, enhanced siderophore production and were unable to cause the hypersensitive response on non-host plants. In conclusion, stringent response regulators DksA and (p)ppGpp play an important role in virulence, nutrition uptake and host adaptation of Xcc.
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Affiliation(s)
- Yanan Zhang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences, University of FloridaLake Alfred33850 FLUnited States
| | - Doron Teper
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences, University of FloridaLake Alfred33850 FLUnited States
| | - Jin Xu
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences, University of FloridaLake Alfred33850 FLUnited States
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences, University of FloridaLake Alfred33850 FLUnited States
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