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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Kim JS, Born A, Till JKA, Liu L, Kant S, Henen MA, Vögeli B, Vázquez-Torres A. Promiscuity of response regulators for thioredoxin steers bacterial virulence. Nat Commun 2022; 13:6210. [PMID: 36266276 PMCID: PMC9584953 DOI: 10.1038/s41467-022-33983-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
The exquisite specificity between a sensor kinase and its cognate response regulator ensures faithful partner selectivity within two-component pairs concurrently firing in a single bacterium, minimizing crosstalk with other members of this conserved family of paralogous proteins. We show that conserved hydrophobic and charged residues on the surface of thioredoxin serve as a docking station for structurally diverse response regulators. Using the OmpR protein, we identify residues in the flexible linker and the C-terminal β-hairpin that enable associations of this archetypical response regulator with thioredoxin, but are dispensable for interactions of this transcription factor to its cognate sensor kinase EnvZ, DNA or RNA polymerase. Here we show that the promiscuous interactions of response regulators with thioredoxin foster the flow of information through otherwise highly dedicated two-component signaling systems, thereby enabling both the transcription of Salmonella pathogenicity island-2 genes as well as growth of this intracellular bacterium in macrophages and mice.
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Affiliation(s)
- Ju-Sim Kim
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Alexandra Born
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA
| | - James Karl A. Till
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Lin Liu
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Sashi Kant
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Morkos A. Henen
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA ,grid.10251.370000000103426662Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
| | - Beat Vögeli
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA
| | - Andrés Vázquez-Torres
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA. .,Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA.
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3
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Roth M, Goodall ECA, Pullela K, Jaquet V, François P, Henderson IR, Krause KH. Transposon-Directed Insertion-Site Sequencing Reveals Glycolysis Gene gpmA as Part of the H2O2 Defense Mechanisms in Escherichia coli. Antioxidants (Basel) 2022; 11:antiox11102053. [PMID: 36290776 PMCID: PMC9598634 DOI: 10.3390/antiox11102053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a common effector of defense mechanisms against pathogenic infections. However, bacterial factors involved in H2O2 tolerance remain unclear. Here we used transposon-directed insertion-site sequencing (TraDIS), a technique allowing the screening of the whole genome, to identify genes implicated in H2O2 tolerance in Escherichia coli. Our TraDIS analysis identified 10 mutants with fitness defect upon H2O2 exposure, among which previously H2O2-associated genes (oxyR, dps, dksA, rpoS, hfq and polA) and other genes with no known association with H2O2 tolerance in E. coli (corA, rbsR, nhaA and gpmA). This is the first description of the impact of gpmA, a gene involved in glycolysis, on the susceptibility of E. coli to H2O2. Indeed, confirmatory experiments showed that the deletion of gpmA led to a specific hypersensitivity to H2O2 comparable to the deletion of the major H2O2 scavenger gene katG. This hypersensitivity was not due to an alteration of catalase function and was independent of the carbon source or the presence of oxygen. Transcription of gpmA was upregulated under H2O2 exposure, highlighting its role under oxidative stress. In summary, our TraDIS approach identified gpmA as a member of the oxidative stress defense mechanism in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Correspondence:
| | - Emily C. A. Goodall
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Vincent Jaquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- READS Unit, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals of Geneva, University Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
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Banerjee G, Quan F, Mondal AK, Sur S, Banerjee P, Chattopadhyay P. Interrelation between Stress Management and Secretion Systems of Ralstonia solanacearum: An In Silico Assessment. Pathogens 2022; 11:730. [PMID: 35889976 PMCID: PMC9325324 DOI: 10.3390/pathogens11070730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Ralstonia solanacearum (Rs), the causative agent of devastating wilt disease in several major and minor economic crops, is considered one of the most destructive bacterial plant pathogens. However, the mechanism(s) by which Rs counteracts host-associated environmental stress is still not clearly elucidated. To investigate possible stress management mechanisms, orthologs of stress-responsive genes in the Rs genome were searched using a reference set of known genes. The genome BLAST approach was used to find the distributions of these orthologs within different Rs strains. BLAST results were first confirmed from the KEGG Genome database and then reconfirmed at the protein level from the UniProt database. The distribution pattern of these stress-responsive factors was explored through multivariate analysis and STRING analysis. STRING analysis of stress-responsive genes in connection with different secretion systems of Rs was also performed. Initially, a total of 28 stress-responsive genes of Rs were confirmed in this study. STRING analysis revealed an additional 7 stress-responsive factors of Rs, leading to the discovery of a total of 35 stress-responsive genes. The segregation pattern of these 35 genes across 110 Rs genomes was found to be almost homogeneous. Increasing interactions of Rs stress factors were observed in six distinct clusters, suggesting six different types of stress responses: membrane stress response (MSR), osmotic stress response (OSR), oxidative stress response (OxSR), nitrosative stress response (NxSR), and DNA damage stress response (DdSR). Moreover, a strong network of these stress responses was observed with type 3 secretion system (T3SS), general secretory proteins (GSPs), and different types of pili (T4P, Tad, and Tat). To the best of our knowledge, this is the first report on overall stress response management by Rs and the potential connection with secretion systems.
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Fortuna A, Collalto D, Schiaffi V, Pastore V, Visca P, Ascenzioni F, Rampioni G, Leoni L. The Pseudomonas aeruginosa DksA1 protein is involved in H 2O 2 tolerance and within-macrophages survival and can be replaced by DksA2. Sci Rep 2022; 12:10404. [PMID: 35729352 PMCID: PMC9213440 DOI: 10.1038/s41598-022-14635-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 12/02/2022] Open
Abstract
In Gram-negative pathogens, the stringent response regulator DksA controls the expression of hundreds of genes, including virulence-related genes. Interestingly, Pseudomonas aeruginosa has two functional DksA paralogs: DksA1 is constitutively expressed and has a zinc-finger motif, while DksA2 is expressed only under zinc starvation conditions and does not contain zinc. DksA1 stimulates the production of virulence factors in vitro and is required for full pathogenicity in vivo. DksA2 can replace these DksA1 functions. Here, the role of dksA paralogs in P. aeruginosa tolerance to H2O2-induced oxidative stress has been investigated. The P. aeruginosa dksA1 dksA2 mutant showed impaired H2O2 tolerance in planktonic and biofilm-growing cultures and increased susceptibility to macrophages-mediated killing compared to the wild type. Complementation with either dksA1 or dksA2 genes restored the wild type phenotypes. The DksA-dependent tolerance to oxidative stress involves, at least in part, the positive transcriptional control of both katA and katE catalase-encoding genes. These data support the hypothesis that DksA1 and DksA2 are eco-paralogs with indistinguishable function but optimal activity under different environmental conditions, and highlight their mutual contribution to P. aeruginosa virulence.
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Affiliation(s)
| | | | - Veronica Schiaffi
- Department of Molecular and Cellular Biology "Charles Darwin", University Roma Sapienza, Rome, Italy
| | - Valentina Pastore
- Department of Molecular and Cellular Biology "Charles Darwin", University Roma Sapienza, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Molecular and Cellular Biology "Charles Darwin", University Roma Sapienza, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy.
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Kim JS, Liu L, Davenport B, Kant S, Morrison TE, Vazquez-Torres A. Oxidative stress activates transcription of Salmonella pathogenicity island-2 genes in macrophages. J Biol Chem 2022; 298:102130. [PMID: 35714768 PMCID: PMC9270255 DOI: 10.1016/j.jbc.2022.102130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
The type III secretion system encoded in the Salmonella pathogenicity island-2 (SPI-2) gene cluster facilitates intracellular growth of nontyphoidal Salmonella by interfering with the maturation of Salmonella-containing vacuoles along the degradative pathway. SPI-2 gene products also protect Salmonella against the antimicrobial activity of reactive oxygen species (ROS) synthesized by the phagocyte NADPH oxidase 2 (NOX2). However, a potential relationship between inflammatory ROS and the activation of transcription of SPI-2 genes by intracellular Salmonella is unclear. Here, we show that ROS engendered in the innate host response stimulate SPI-2 gene transcription. We found that the expression of SPI-2 genes in Salmonella-sustaining oxidative stress conditions involves DksA, a protein otherwise known to regulate the stringent response of bacteria to nutritional stress. We also demonstrate that the J and zinc-2-oxidoreductase domains of DnaJ as well as the ATPase activity of the DnaK chaperone facilitate loading of DksA onto RNA polymerase complexed with SPI-2 promoters. Furthermore, the DksA-driven transcription of SPI-2 genes in Salmonella experiencing oxidative stress is contingent on upstream OmpR, PhoP, and SsrB signaling events that participate in the removal of nucleoid proteins while simultaneously recruiting RNA polymerase to SPI-2 promoter regions. Taken together, our results suggest the activation of SPI-2 gene transcription in Salmonella subjected to ROS produced by the respiratory burst of macrophages protects this intracellular pathogen against NOX2-mediated killing. We propose that Salmonella have co-opted inflammatory ROS to induce SPI-2-mediated protective responses against NOX2 host defenses.
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Affiliation(s)
- Ju-Sim Kim
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA
| | - Lin Liu
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA
| | - Bennett Davenport
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA
| | - Sashi Kant
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA
| | - Thomas E Morrison
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA
| | - Andres Vazquez-Torres
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA; Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever, is an enzootic, obligate, intracellular bacterial pathogen. Nitric oxide (NO) synthesized by the inducible NO synthase (iNOS) is a potent antimicrobial component of innate immunity and has been implicated in the control of virulent Rickettsia spp. in diverse cell types. In this study, we examined the antibacterial role of NO on R. rickettsii. Our results indicate that NO challenge dramatically reduces R. rickettsii adhesion through the disruption of bacterial energetics. Additionally, NO-treated R. rickettsii cells were unable to synthesize protein or replicate in permissive cells. Activated, NO-producing macrophages restricted R. rickettsii infections, but inhibition of iNOS ablated the inhibition of bacterial growth. These data indicate that NO is a potent antirickettsial effector of innate immunity that targets energy generation in these pathogenic bacteria to prevent growth and subversion of infected host cells.
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Fortuna A, Bähre H, Visca P, Rampioni G, Leoni L. The two Pseudomonas aeruginosa DksA stringent response proteins are largely interchangeable at the whole transcriptome level and in the control of virulence-related traits. Environ Microbiol 2021; 23:5487-5504. [PMID: 34327807 DOI: 10.1111/1462-2920.15693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022]
Abstract
The stringent response regulator DksA plays a key role in Gram negative bacteria adaptation to challenging environments. Intriguingly, the plant and human pathogen Pseudomonas aeruginosa is unique as it expresses two functional DksA paralogs: DksA1 and DksA2. However, the role of DksA2 in P. aeruginosa adaptive strategies has been poorly investigated so far. Here, RNA-Seq analysis and phenotypic assays showed that P. aeruginosa DksA1 and DksA2 proteins are largely interchangeable. Relative to wild type P. aeruginosa, transcription of 1779 genes was altered in a dksA1 dksA2 double mutant, and the wild type expression level of ≥90% of these genes was restored by in trans complementation with either dksA1 or dksA2. Interestingly, the expression of a small sub-set of genes seems to be preferentially or exclusively complemented by either dksA1 or dksA2. In addition, evidence has been provided that the DksA-dependent regulation of virulence genes expression is independent and hierarchically dominant over two major P. aeruginosa regulatory circuits, i.e., quorum sensing and cyclic-di-GMP signalling systems. Our findings support the prominent role of both DksA paralogs in P. aeruginosa environmental adaptation.
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Affiliation(s)
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
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Kim JS, Liu L, Vázquez-Torres A. The DnaK/DnaJ Chaperone System Enables RNA Polymerase-DksA Complex Formation in Salmonella Experiencing Oxidative Stress. mBio 2021; 12:e03443-20. [PMID: 33975942 DOI: 10.1128/mBio.03443-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous biochemical approaches showed that the oxidoreductase activity of the DnaJ protein facilitates the interaction of oxidized DksA with RNA polymerase. Investigations herein demonstrate that under biologically relevant conditions the DnaJ- and DksA-codependent activation of the stringent response in Salmonella undergoing oxidative stress involves the DnaK chaperone. Oxidation of DksA cysteine residues stimulates redox-based and holdase interactions with zinc-binding and C-terminal domains of DnaJ. Genetic and biochemical evidence indicates that His33 in the HPD motif in the J domain of DnaJ facilitates interactions of unfolded DksA with DnaK. A mutation in His33 in the J domain prevents the presentation of unfolded DksA to DnaK without limiting the oxidoreductase activity mapped to DnaJ's zinc-2 site. Thr199 in the ATPase catalytic site of DnaK is required for the formation of the DksA/RNA polymerase complex. The DnaK/DnaJ/DksA complex enables the formation of an enzymatically active RNA polymerase holoenzyme that stimulates transcription of branched-chain amino acid and histidine metabolic genes in Salmonella exposed to reactive oxygen species. The DnaK/DnaJ chaperone protects Salmonella against the cytotoxicity associated with reactive oxygen species generated by the phagocyte NADPH oxidase in the innate host response. The antioxidant defenses associated with DnaK/DnaJ can in part be ascribed to the elicitation of the DksA-dependent stringent response and the protection this chaperone system provides against protein carbonylation in Salmonella undergoing oxidative stress.IMPORTANCE DksA was discovered 30 years ago in a screen for suppressors that reversed the thermosensitivity of Escherichia coli mutant strains deficient in DnaK/DnaJ, raising the possibility that this chaperone system may control DksA function. Since its serendipitous discovery, DksA has emerged as a key activator of the transcriptional program called the stringent response in Gram-negative bacteria experiencing diverse adverse conditions, including nutritional starvation or oxidative stress. DksA activates the stringent response through the allosteric control this regulatory protein exerts on the kinetics of RNA polymerase promoter open complexes. Recent investigations have shown that DksA overexpression protects dnaKJ mutant bacteria against heat shock indirectly via the ancestral chaperone polyphosphate, casting doubt on a possible complexation of DnaK, DnaJ, and DksA. Nonetheless, research presented herein demonstrates that the cochaperones DnaK and DnaJ enable DksA/RNA polymerase complex formation in response to oxidative stress.
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Guillén S, Nadal L, Álvarez I, Mañas P, Cebrián G. Impact of the Resistance Responses to Stress Conditions Encountered in Food and Food Processing Environments on the Virulence and Growth Fitness of Non-Typhoidal Salmonellae. Foods 2021; 10:617. [PMID: 33799446 DOI: 10.3390/foods10030617] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 01/22/2023] Open
Abstract
The success of Salmonella as a foodborne pathogen can probably be attributed to two major features: its remarkable genetic diversity and its extraordinary ability to adapt. Salmonella cells can survive in harsh environments, successfully compete for nutrients, and cause disease once inside the host. Furthermore, they are capable of rapidly reprogramming their metabolism, evolving in a short time from a stress-resistance mode to a growth or virulent mode, or even to express stress resistance and virulence factors at the same time if needed, thanks to a complex and fine-tuned regulatory network. It is nevertheless generally acknowledged that the development of stress resistance usually has a fitness cost for bacterial cells and that induction of stress resistance responses to certain agents can trigger changes in Salmonella virulence. In this review, we summarize and discuss current knowledge concerning the effects that the development of resistance responses to stress conditions encountered in food and food processing environments (including acid, osmotic and oxidative stress, starvation, modified atmospheres, detergents and disinfectants, chilling, heat, and non-thermal technologies) exerts on different aspects of the physiology of non-typhoidal Salmonellae, with special emphasis on virulence and growth fitness.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Zhang W, Watanabe R, Konishi HA, Fujiwara T, Yoshimura SH, Kumeta M. Redox-Sensitive Cysteines Confer Proximal Control of the Molecular Crowding Barrier in the Nuclear Pore. Cell Rep 2020; 33:108484. [PMID: 33326779 DOI: 10.1016/j.celrep.2020.108484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 09/01/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022] Open
Abstract
The nuclear pore complex forms a highly crowded selective barrier with intrinsically disordered regions at the nuclear membrane to coordinate nucleocytoplasmic molecular communications. Although oxidative stress is known to alter the barrier function, the molecular mechanism underlying this adaptive control of the nuclear pore complex remains unknown. Here we uncover a systematic control of the crowding barrier within the nuclear pore in response to various redox environments. Direct measurements of the crowding states using a crowding-sensitive FRET (Förster resonance energy transfer) probe reveal specific roles of the nuclear pore subunits that adjust the degree of crowding in response to different redox conditions, by adaptively forming or disrupting redox-sensitive disulfide bonds. Relationships between crowding control and the barrier function of the nuclear pore are investigated by single-molecular fluorescence measurements of nuclear transport. Based on these findings, we propose a proximal control model of molecular crowding in vivo that is dynamically regulated at the molecular level.
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Affiliation(s)
- Wanzhen Zhang
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ryuji Watanabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hide A Konishi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Masahiro Kumeta
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
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14
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von Pein JB, Stocks CJ, Schembri MA, Kapetanovic R, Sweet MJ. An alloy of zinc and innate immunity: Galvanising host defence against infection. Cell Microbiol 2020; 23:e13268. [PMID: 32975847 DOI: 10.1111/cmi.13268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Innate immune cells such as macrophages and neutrophils initiate protective inflammatory responses and engage antimicrobial responses to provide frontline defence against invading pathogens. These cells can both restrict the availability of certain transition metals that are essential for microbial growth and direct toxic concentrations of metals towards pathogens as antimicrobial responses. Zinc is important for the structure and function of many proteins, however excess zinc can be cytotoxic. In recent years, several studies have revealed that innate immune cells can deliver toxic concentrations of zinc to intracellular pathogens. In this review, we discuss the importance of zinc status during infectious disease and the evidence for zinc intoxication as an innate immune antimicrobial response. Evidence for pathogen subversion of this response is also examined. The likely mechanisms, including the involvement of specific zinc transporters that facilitate delivery of zinc by innate immune cells for metal ion poisoning of pathogens are also considered. Precise mechanisms by which excess levels of zinc can be toxic to microorganisms are then discussed, particularly in the context of synergy with other antimicrobial responses. Finally, we highlight key unanswered questions in this emerging field, which may offer new opportunities for exploiting innate immune responses for anti-infective development.
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Affiliation(s)
- Jessica B von Pein
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Claudia J Stocks
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
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15
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Fernández-Coll L, Potrykus K, Cashel M, Balsalobre C. Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed. Sci Rep 2020; 10:16074. [PMID: 32999370 DOI: 10.1038/s41598-020-73069-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022] Open
Abstract
There is a growing appreciation for the diverse regulatory consequences of the family of proteins that bind to the secondary channel of E. coli RNA polymerase (RNAP), such as GreA, GreB or DksA. Similar binding sites could suggest a competition between them. GreA is characterised to rescue stalled RNAP complexes due to its antipause activity, but also it is involved in transcription fidelity and proofreading. Here, overexpression of GreA is noted to be lethal independent of its antipause activity. A library of random GreA variants has been used to isolate lethality suppressors to assess important residues for GreA functionality and its interaction with the RNA polymerase. Some mutant defects are inferred to be associated with altered binding competition with DksA, while other variants seem to have antipause activity defects that cannot reverse a GreA-sensitive pause site in a fliC::lacZ reporter system. Surprisingly, apparent binding and cleavage defects are found scattered throughout both the coiled-coil and globular domains. Thus, the coiled-coil of GreA is not just a measuring stick ensuring placement of acidic residues precisely at the catalytic centre but also seems to have binding functions. These lethality suppressor mutants may provide valuable tools for future structural and functional studies.
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16
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Gray MJ. Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. J Bacteriol 2020; 202:e00133-20. [PMID: 32341074 DOI: 10.1128/JB.00133-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/21/2020] [Indexed: 01/24/2023] Open
Abstract
Bacteria synthesize inorganic polyphosphate (polyP) in response to a variety of different stress conditions. polyP protects bacteria by acting as a protein-stabilizing chaperone, metal chelator, or regulator of protein function, among other mechanisms. However, little is known about how stress signals are transmitted in the cell to lead to increased polyP accumulation. Previous work in the model enterobacterium Escherichia coli has indicated that the RNA polymerase-binding regulatory protein DksA is required for polyP synthesis in response to nutrient limitation stress. In this work, I set out to characterize the role of DksA in polyP regulation in more detail. I found that overexpression of DksA increases cellular polyP content (explaining the long-mysterious phenotype of dksA overexpression rescuing growth of a dnaK mutant at high temperatures) and characterized the roles of known functional residues of DksA in this process, finding that binding to RNA polymerase is required but that none of the other functions of DksA appear to be necessary. Transcriptomics revealed genome-wide transcriptional changes upon nutrient limitation, many of which were affected by DksA, and follow-up experiments identified complex interactions between DksA and the stress-sensing alternative sigma factors FliA, RpoN, and RpoE that impact polyP production, indicating that regulation of polyP synthesis is deeply entwined in the multifactorial stress response network of E. coli IMPORTANCE Inorganic polyphosphate (polyP) is an evolutionarily ancient, widely conserved biopolymer required for stress resistance and pathogenesis in diverse bacteria, but we do not understand how its synthesis is regulated. In this work, I gained new insights into this process by characterizing the role of the transcriptional regulator DksA in polyP regulation in Escherichia coli and identifying previously unknown links between polyP synthesis and the stress-responsive alternative sigma factors FliA, RpoN, and RpoE.
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17
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Stocks CJ, von Pein JB, Curson JEB, Rae J, Phan MD, Foo D, Bokil NJ, Kambe T, Peters KM, Parton RG, Schembri MA, Kapetanovic R, Sweet MJ. Frontline Science: LPS-inducible SLC30A1 drives human macrophage-mediated zinc toxicity against intracellular Escherichia coli. J Leukoc Biol 2020; 109:287-297. [PMID: 32441444 PMCID: PMC7891337 DOI: 10.1002/jlb.2hi0420-160r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
TLR-inducible zinc toxicity is an antimicrobial mechanism utilized by macrophages, however knowledge of molecular mechanisms mediating this response is limited. Here, we show that E. coli exposed to zinc stress within primary human macrophages reside in membrane-bound vesicular compartments. Since SLC30A zinc exporters can deliver zinc into the lumen of vesicles, we examined LPS-regulated mRNA expression of Slc30a/SLC30A family members in primary mouse and human macrophages. A number of these transporters were dynamically regulated in both cell populations. In human monocyte-derived macrophages, LPS strongly up-regulated SLC30A1 mRNA and protein expression. In contrast, SLC30A1 was not LPS-inducible in macrophage-like PMA-differentiated THP-1 cells. We therefore ectopically expressed SLC30A1 in these cells, finding that this was sufficient to promote zinc-containing vesicle formation. The response was similar to that observed following LPS stimulation. Ectopically expressed SLC30A1 localized to both the plasma membrane and intracellular zinc-containing vesicles within LPS-stimulated THP-1 cells. Inducible overexpression of SLC30A1 in THP-1 cells infected with the Escherichia coli K-12 strain MG1655 augmented the zinc stress response of intracellular bacteria and promoted clearance. Furthermore, in THP-1 cells infected with an MG1655 zinc stress reporter strain, all bacteria contained within SLC30A1-positive compartments were subjected to zinc stress. Thus, SLC30A1 marks zinc-containing compartments associated with TLR-inducible zinc toxicity in human macrophages, and its ectopic over-expression is sufficient to initiate this antimicrobial pathway in these cells. Finally, SLC30A1 silencing did not compromise E. coli clearance by primary human macrophages, suggesting that other zinc exporters may also contribute to the zinc toxicity response.
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Affiliation(s)
- Claudia J Stocks
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jessica B von Pein
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - James E B Curson
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - James Rae
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia
| | - Minh-Duy Phan
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Darren Foo
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Nilesh J Bokil
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kate M Peters
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, St. Lucia, Queensland, Australia.,IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
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18
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Fitzsimmons LF, Liu L, Kant S, Kim JS, Till JK, Jones-Carson J, Porwollik S, McClelland M, Vazquez-Torres A. SpoT Induces Intracellular Salmonella Virulence Programs in the Phagosome. mBio 2020; 11:e03397-19. [PMID: 32098823 DOI: 10.1128/mBio.03397-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Pathogenic bacteria experience nutritional challenges during colonization and infection of mammalian hosts. Binding of the alarmone nucleotide guanosine tetraphosphate (ppGpp) to RNA polymerase coordinates metabolic adaptations and virulence gene transcription, increasing the fitness of diverse Gram-positive and Gram-negative bacteria as well as that of actinomycetes. Gammaproteobacteria such as Salmonella synthesize ppGpp by the combined activities of the closely related RelA and SpoT synthetases. Due to its profound inhibitory effects on growth, ppGpp must be removed; in Salmonella, this process is catalyzed by the vital hydrolytic activity of the bifunctional SpoT protein. Because SpoT hydrolase activity is essential in cells expressing a functional RelA, we have a very limited understanding of unique roles these two synthetases may assume during interactions of bacterial pathogens with their hosts. We describe here a SpoT truncation mutant that lacks ppGpp synthetase activity and all C-terminal regulatory domains but retains excellent hydrolase activity. Our studies of this mutant reveal that SpoT uniquely senses the acidification of phagosomes, inducing virulence programs that increase Salmonella fitness in an acute model of infection. Our investigations indicate that the coexistence of RelA/SpoT homologues in a bacterial cell is driven by the need to mount a stringent response to a myriad of physiological and host-specific signatures. Guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), together named (p)ppGpp, regulate diverse aspects of Salmonella pathogenesis, including synthesis of nutrients, resistance to inflammatory mediators, and expression of secretion systems. In Salmonella, these nucleotide alarmones are generated by the synthetase activities of RelA and SpoT proteins. In addition, the (p)ppGpp hydrolase activity of the bifunctional SpoT protein is essential to preserve cell viability. The contribution of SpoT to physiology and pathogenesis has proven elusive in organisms such as Salmonella, because the hydrolytic activity of this RelA and SpoT homologue (RSH) is vital to prevent inhibitory effects of (p)ppGpp produced by a functional RelA. Here, we describe the biochemical and functional characterization of a spoT-Δctd mutant Salmonella strain encoding a SpoT protein that lacks the C-terminal regulatory elements collectively referred to as “ctd.” Salmonella expressing the spoT-Δctd variant hydrolyzes (p)ppGpp with similar kinetics to those of wild-type bacteria, but it is defective at synthesizing (p)ppGpp in response to acidic pH. Salmonella spoT-Δctd mutants have virtually normal adaptations to nutritional, nitrosative, and oxidative stresses, but poorly induce metal cation uptake systems and Salmonella pathogenicity island 2 (SPI-2) genes in response to the acidic pH of the phagosome. Importantly, spoT-Δctd mutant Salmonella replicates poorly intracellularly and is attenuated in a murine model of acute salmonellosis. Collectively, these investigations indicate that (p)ppGpp synthesized by SpoT serves a unique function in the adaptation of Salmonella to the intracellular environment of host phagocytes that cannot be compensated by the presence of a functional RelA.
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19
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Min KB, Yoon SS. Transcriptome analysis reveals that the RNA polymerase-binding protein DksA1 has pleiotropic functions in Pseudomonas aeruginosa. J Biol Chem 2020; 295:3851-3864. [PMID: 32047111 DOI: 10.1074/jbc.ra119.011692] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/09/2020] [Indexed: 12/20/2022] Open
Abstract
The stringent response (SR) is a highly conserved stress response in bacteria. It is composed of two factors, (i) a nucleotide alarmone, guanosine tetra- and pentaphosphate ((p)ppGpp), and (ii) an RNA polymerase-binding protein, DksA, that regulates various phenotypes, including bacterial virulence. The clinically significant opportunistic bacterial pathogen Pseudomonas aeruginosa possesses two genes, dksA1 and dksA2, that encode DksA proteins. It remains elusive, however, which of these two genes plays a more important role in SR regulation. In this work, we compared genome-wide, RNA-Seq-based transcriptome profiles of ΔdksA1, ΔdksA2, and ΔdksA1ΔdksA2 mutants to globally assess the effects of these gene deletions on transcript levels coupled with phenotypic analyses. The ΔdksA1 mutant exhibited substantial defects in a wide range of phenotypes, including quorum sensing (QS), anaerobiosis, and motility, whereas the ΔdksA2 mutant exhibited no significant phenotypic changes, suggesting that the dksA2 gene may not have an essential function in P. aeruginosa under the conditions used here. Of note, the ΔdksA1 mutants displayed substantially increased transcription of genes involved in polyamine biosynthesis, and we also detected increased polyamine levels in these mutants. Because SAM is a shared precursor for the production of both QS autoinducers and polyamines, these findings suggest that DksA1 deficiency skews the flow of SAM toward polyamine production rather than to QS signaling. Together, our results indicate that DksA1, but not DksA2, controls many important phenotypes in P. aeruginosa We conclude that DksA1 may represent a potential target whose inhibition may help manage recalcitrant P. aeruginosa infections.
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Affiliation(s)
- Kyung Bae Min
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea .,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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20
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Adolfsen KJ, Chou WK, Brynildsen MP. Transcriptional Regulation Contributes to Prioritized Detoxification of Hydrogen Peroxide over Nitric Oxide. J Bacteriol 2019; 201:e00081-19. [PMID: 31061166 PMCID: PMC6597392 DOI: 10.1128/jb.00081-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/26/2019] [Indexed: 11/20/2022] Open
Abstract
Hydrogen peroxide (H2O2) and nitric oxide (NO·) are toxic metabolites that immune cells use to attack pathogens. These antimicrobials can be present at the same time in phagosomes, and it remains unclear how bacteria deal with these insults when simultaneously present. Here, using Escherichia coli, we observed that simultaneous exposure to H2O2 and NO· leads to prioritized detoxification, where enzymatic removal of NO· is impeded until H2O2 has been eliminated. This phenomenon is reminiscent of carbon catabolite repression (CCR), where preferred carbon sources are catabolized prior to less desirable substrates; however, H2O2 and NO· are toxic, growth-inhibitory compounds rather than growth-promoting nutrients. To understand how NO· detoxification is delayed by H2O2 whereas H2O2 detoxification proceeds unimpeded, we confirmed that the effect depended on Hmp, which is the main NO· detoxification enzyme, and used an approach that integrated computational modeling and experimentation to delineate and test potential mechanisms. Plausible interactions included H2O2-dependent inhibition of hmp transcription and translation, direct inhibition of Hmp catalysis, and competition for reducing equivalents between Hmp and H2O2-degrading enzymes. Experiments illustrated that Hmp catalysis and NAD(P)H supply were not impaired by H2O2, whereas hmp transcription and translation were diminished. A dependence of this phenomenon on transcriptional regulation parallels CCR, and we found it to involve the transcriptional repressor NsrR. Collectively, these data suggest that bacterial regulation of growth inhibitor detoxification has similarities to the regulation of growth substrate consumption, which could have ramifications for infectious disease, bioremediation, and biocatalysis from inhibitor-containing feedstocks.IMPORTANCE Bacteria can be exposed to H2O2 and NO· concurrently within phagosomes. In such multistress situations, bacteria could have evolved to simultaneously degrade both toxic metabolites or preferentially detoxify one over the other. Here, we found that simultaneous exposure to H2O2 and NO· leads to prioritized detoxification, where detoxification of NO· is hampered until H2O2 has been eliminated. This phenomenon resembles CCR, where bacteria consume one substrate over others in carbon source mixtures. Further experimentation revealed a central role for transcriptional regulation in the prioritization of H2O2 over NO·, which is also important to CCR. This study suggests that regulatory scenarios observed in bacterial consumption of growth-promoting compound mixtures can be conserved in bacterial detoxification of toxic metabolite mixtures.
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Affiliation(s)
- Kristin J Adolfsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Wen Kang Chou
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
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21
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Chandrangsu P, Huang X, Gaballa A, Helmann JD. Bacillus subtilis FolE is sustained by the ZagA zinc metallochaperone and the alarmone ZTP under conditions of zinc deficiency. Mol Microbiol 2019; 112:751-765. [PMID: 31132310 DOI: 10.1111/mmi.14314] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 12/23/2022]
Abstract
Bacteria tightly regulate intracellular zinc levels to ensure sufficient zinc to support essential functions, while preventing toxicity. The bacterial response to zinc limitation includes the expression of putative zinc metallochaperones belonging to subfamily 1 of the COG0523 family of G3E GTPases. However, the client proteins and the metabolic processes served by these chaperones are unclear. Here, we demonstrate that the Bacillus subtilis YciC zinc metallochaperone (here renamed ZagA for ZTP activated GTPase A) supports de novo folate biosynthesis under conditions of zinc limitation, and interacts directly with the zinc-dependent GTP cyclohydrolase IA, FolE (GCYH-IA). Furthermore, we identify a role for the alarmone ZTP, a modified purine biosynthesis intermediate, in the response to zinc limitation. ZTP, a signal of 10-formyl-tetrahydrofolate (10f-THF) deficiency in bacteria, transiently accumulates as FolE begins to fail, stimulates the interaction between ZagA and FolE, and thereby helps to sustain folate synthesis despite declining zinc availability.
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Affiliation(s)
- Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.,W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps College, Claremont, CA, 91711, USA
| | - Xiaojuan Huang
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
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22
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Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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23
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Gray MJ. Inorganic Polyphosphate Accumulation in Escherichia coli Is Regulated by DksA but Not by (p)ppGpp. J Bacteriol 2019; 201:e00664-18. [PMID: 30745375 DOI: 10.1128/JB.00664-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/07/2019] [Indexed: 12/25/2022] Open
Abstract
Production of inorganic polyphosphate (polyP) by bacteria is triggered by a variety of different stress conditions. polyP is required for stress survival and virulence in diverse pathogenic microbes. Previous studies have hypothesized a model for regulation of polyP synthesis in which production of the stringent-response second messenger (p)ppGpp directly stimulates polyP accumulation. In this work, I have now shown that this model is incorrect, and (p)ppGpp is not required for polyP synthesis in Escherichia coli However, stringent mutations of RNA polymerase that frequently arise spontaneously in strains defective in (p)ppGpp synthesis and null mutations of the stringent-response-associated transcription factor DksA both strongly inhibit polyP accumulation. The loss of polyP synthesis in a mutant lacking DksA was reversed by deletion of the transcription elongation factor GreA, suggesting that competition between these proteins for binding to the secondary channel of RNA polymerase plays an important role in controlling polyP activation. These results provide new insights into the poorly understood regulation of polyP synthesis in bacteria and indicate that the relationship between polyP and the stringent response is more complex than previously suspected.IMPORTANCE Production of polyP in bacteria is required for virulence and stress response, but little is known about how bacteria regulate polyP levels in response to changes in their environments. Understanding this regulation is important for understanding how pathogenic microbes resist killing by disinfectants, antibiotics, and the immune system. In this work, I have clarified the connections between polyP regulation and the stringent response to starvation stress in Escherichia coli and demonstrated an important and previously unknown role for the transcription factor DksA in controlling polyP levels.
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24
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Schäfer H, Turgay K. Spx, a versatile regulator of the Bacillus subtilis stress response. Curr Genet 2019; 65:871-876. [DOI: 10.1007/s00294-019-00950-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 01/16/2023]
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25
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Boyle WK, Groshong AM, Drecktrah D, Boylan JA, Gherardini FC, Blevins JS, Samuels DS, Bourret TJ. DksA Controls the Response of the Lyme Disease Spirochete Borrelia burgdorferi to Starvation. J Bacteriol 2019; 201. [PMID: 30478087 DOI: 10.1128/JB.00582-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 12/17/2022] Open
Abstract
The pathogenic spirochete Borrelia burgdorferi senses and responds to changes in the environment, including changes in nutrient availability, throughout its enzootic cycle in Ixodes ticks and vertebrate hosts. This study examined the role of DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA mutant B. burgdorferi strains were subjected to starvation by shifting cultures grown in rich complete medium, Barbour-Stoenner-Kelly II (BSK II) medium, to a defined mammalian tissue culture medium, RPMI 1640, for 6 h under microaerobic conditions (5% CO2, 3% O2). Microarray analyses of wild-type B. burgdorferi revealed that genes encoding flagellar components, ribosomal proteins, and DNA replication machinery were downregulated in response to starvation. DksA mediated transcriptomic responses to starvation in B. burgdorferi, as the dksA-deficient strain differentially expressed only 47 genes in response to starvation compared to the 500 genes differentially expressed in wild-type strains. Consistent with a role for DksA in the starvation response of B. burgdorferi, fewer CFU of dksA mutants were observed after prolonged starvation in RPMI 1640 medium than CFU of wild-type B. burgdorferi spirochetes. Transcriptomic analyses revealed a partial overlap between the DksA regulon and the regulon of RelBbu, the guanosine tetraphosphate and guanosine pentaphosphate [(p)ppGpp] synthetase that controls the stringent response; the DksA regulon also included many plasmid-borne genes. Additionally, the dksA mutant exhibited constitutively elevated (p)ppGpp levels compared to those of the wild-type strain, implying a regulatory relationship between DksA and (p)ppGpp. Together, these data indicate that DksA, along with (p)ppGpp, directs the stringent response to effect B. burgdorferi adaptation to its environment.IMPORTANCE The Lyme disease bacterium Borrelia burgdorferi survives diverse environmental challenges as it cycles between its tick vectors and various vertebrate hosts. B. burgdorferi must withstand prolonged periods of starvation while it resides in unfed Ixodes ticks. In this study, the regulatory protein DksA is shown to play a pivotal role controlling the transcriptional responses of B. burgdorferi to starvation. The results suggest that DksA gene regulatory activity impacts B. burgdorferi metabolism, virulence gene expression, and the ability of this bacterium to complete its natural life cycle.
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26
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Chou WK, Brynildsen MP. Loss of DksA leads to multi-faceted impairment of nitric oxide detoxification by Escherichia coli. Free Radic Biol Med 2019; 130:288-296. [PMID: 30366060 DOI: 10.1016/j.freeradbiomed.2018.10.435] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 10/17/2018] [Accepted: 10/20/2018] [Indexed: 02/07/2023]
Abstract
Human immune cells use a battery of toxic chemicals to eliminate invading bacteria. One of those compounds is nitric oxide (NO) and pathogens have evolved various strategies to defend themselves against this immune effector. Enzymatic detoxification is a common approach used by many bacteria, and Escherichia coli employs several enzymes to deal with NO, such as Hmp a flavohemoprotein. In addition to nitrosative stress, nutrient deprivation has been found to play an important role in phagosomal antimicrobial activity. Interestingly, recent work in Salmonella has suggested that DksA, a transcription regulator associated with the stringent response, is a molecular node for integration of nutritional and nitrosative stress signals. Here, we found that, in E. coli, loss of DksA profoundly impairs aerobic NO detoxification, approaching the detoxification capacity of Δhmp, which exhibits little-to-no NO detoxification within aerobic conditions. Investigation of this phenotype revealed that under NO stress ΔdksA suffered from low hmp transcript levels, considerably impaired protein output from the hmp promoter, and reduced catalysis by Hmp when present. These data demonstrate that DksA is critical for NO detoxification by E. coli and that loss of this regulator leads to NO defense deficiencies that span multiple levels.
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Affiliation(s)
- Wen Kang Chou
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544 United States
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544 United States.
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27
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Kim JS, Liu L, Fitzsimmons LF, Wang Y, Crawford MA, Mastrogiovanni M, Trujillo M, Till JKA, Radi R, Dai S, Vázquez-Torres A. DksA-DnaJ redox interactions provide a signal for the activation of bacterial RNA polymerase. Proc Natl Acad Sci U S A 2018; 115:E11780-E11789. [PMID: 30429329 PMCID: PMC6294903 DOI: 10.1073/pnas.1813572115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
RNA polymerase is the only known protein partner of the transcriptional regulator DksA. Herein, we demonstrate that the chaperone DnaJ establishes direct, redox-based interactions with oxidized DksA. Cysteine residues in the zinc finger of DksA become oxidized in Salmonella exposed to low concentrations of hydrogen peroxide (H2O2). The resulting disulfide bonds unfold the globular domain of DksA, signaling high-affinity interaction of the C-terminal α-helix to DnaJ. Oxidoreductase and chaperone activities of DnaJ reduce the disulfide bonds of its client and promote productive interactions between DksA and RNA polymerase. Simultaneously, guanosine tetraphosphate (ppGpp), which is synthesized by RelA in response to low concentrations of H2O2, binds at site 2 formed at the interface of DksA and RNA polymerase and synergizes with the DksA/DnaJ redox couple, thus activating the transcription of genes involved in amino acid biosynthesis and transport. However, the high concentrations of ppGpp produced by Salmonella experiencing oxidative stress oppose DksA/DnaJ-dependent transcription. Cumulatively, the interplay of DksA, DnaJ, and ppGpp on RNA polymerase protects Salmonella from the antimicrobial activity of the NADPH phagocyte oxidase. Our research has identified redox-based signaling that activates the transcriptional activity of the RNA polymerase regulator DksA.
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Affiliation(s)
- Ju-Sim Kim
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Lin Liu
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Liam F Fitzsimmons
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Yang Wang
- Department of Pharmaceutical Sciences, University of Colorado Skaags School of Pharmacy and Pharmaceutical Sciences, Aurora, CO 80045
| | - Matthew A Crawford
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - James Karl A Till
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay;
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, 11800 Montevideo, Uruguay
| | - Shaodong Dai
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
- Department of Pharmaceutical Sciences, University of Colorado Skaags School of Pharmacy and Pharmaceutical Sciences, Aurora, CO 80045
| | - Andrés Vázquez-Torres
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO 80045;
- Research Service, Veterans Affairs Eastern Colorado Health Care System, Denver, CO 80220
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28
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Fernández-Coll L, Potrykus K, Cashel M. Puzzling conformational changes affecting proteins binding to the RNA polymerase. Proc Natl Acad Sci U S A 2018; 115:12550-2. [PMID: 30498028 DOI: 10.1073/pnas.1818361115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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29
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Basu P, Bhadra RK. Post-transcriptional regulation of cholera toxin production in Vibrio cholerae by the stringent response regulator DksA. Microbiology (Reading) 2018; 165:102-112. [PMID: 30444469 DOI: 10.1099/mic.0.000743] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Expression of cholera toxin (CT), the principal virulence factor of the cholera pathogen Vibrio cholerae, is positively modulated by the RNA polymerase binding unusual transcription factor DksA (DksAVc) of the stringent response pathway. Here we report that even though CT (encoded by the genes ctxAB) production is downregulated in the V. cholerae ΔdksA (ΔdksAVc) mutant, the expression of the ctxA gene as well as the genes encoding different virulence regulators, namely, AphA, TcpP and ToxT, were also upregulated. Since DksAVc positively regulates HapR, a known negative regulator of CT production, the increased expression of different virulence genes in ΔdksAVc was due most probably to downregulation of HapR. There was no secretion/transport-related defect in ΔdksAVc cells because whole cell lysates of the mutant showed a negligible amount of CT accumulation similar to WT cells. To understand further, the hapR gene was deleted in ΔdksAVc background, however, the double mutant failed to rescue the CT production defect suggesting strongly towards post-transcriptional/translational regulation by DksAVc. This hypothesis was further confirmed when the site-directed mutagenesis of each or both of the conserved aspartic acid residues at positions 68 and 71 of DksAVc, which are essential for transcription initiation during the stringent response, had no effect in the regulation of CT expression. Interestingly, progressive deletion analysis indicated that the C4-type Zn finger motif present in the C-terminus of DksAVc is essential for optimal CT production. Since this motif plays important roles in DNA/RNA binding, the present study indicates a novel complex post-transcriptional regulation of CT expression by DksAVc.
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Affiliation(s)
- Pallabi Basu
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata-700 032, India
| | - Rupak K Bhadra
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata-700 032, India
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30
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Fitzsimmons L, Liu L, Porwollik S, Chakraborty S, Desai P, Tapscott T, Henard C, McClelland M, Vazquez-Torres A. Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response. PLoS Pathog 2018; 14:e1007388. [PMID: 30365536 DOI: 10.1371/journal.ppat.1007388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/07/2018] [Accepted: 10/07/2018] [Indexed: 12/13/2022] Open
Abstract
The metabolic processes that enable the replication of intracellular Salmonella under nitrosative stress conditions engendered in the innate response of macrophages are poorly understood. A screen of Salmonella transposon mutants identified the ABC-type high-affinity zinc uptake system ZnuABC as a critical determinant of the adaptation of Salmonella to the nitrosative stress generated by the enzymatic activity of inducible nitric oxide (NO) synthase of mononuclear phagocytic cells. NO limits the virulence of a znuB mutant in an acute murine model of salmonellosis. The ZnuABC transporter is crucial for the glycolytic function of fructose bisphosphate aldolase, thereby fueling growth of Salmonella during nitrosative stress produced in the innate response of macrophages. Our investigations demonstrate that glycolysis mediates resistance of Salmonella to the antimicrobial activity of NO produced in an acute model of infection. The ATP synthesized by substrate-level phosphorylation at the payoff phase of glycolysis and acetate fermentation powers the replication of Salmonella experiencing high levels of nitrosative stress. In contrast, despite its high potential for ATP synthesis, oxidative phosphorylation is a major target of inhibition by NO and contributes little to the antinitrosative defenses of intracellular Salmonella. Our investigations have uncovered a previously unsuspected conjunction between zinc homeostasis, glucose metabolism and cellular energetics in the adaptation of intracellular Salmonella to the reactive nitrogen species synthesized in the innate host response. Microbial pathogens are exposed to multiple antimicrobial defenses during their associations with host cells. Nitric oxide generated in the innate response exerts widespread antimicrobial activity against a variety of pathogenic microorganisms. Nitric oxide has high affinity for metal groups of terminal cytochromes of the respiratory chain, and thus nitrosative stress exerts extreme deleterious actions against the cellular energetics that rely on oxidative phosphorylation. Intracellular Salmonella have resolved this dilemma by satisfying a significant portion of their energetic demands via substrate level phosphorylation in the payoff phase of glycolysis and acetate fermentation. A high affinity zinc uptake system promotes antinitrosative defense of intracellular Salmonella by in great part supporting the enzymatic activity of an essential enzyme in the preparatory phase of glycolysis. Our research provides novel insights into the metabolic and energetic adaptations that allow a bacterial pathogen to thrive in the midst of the innate host response of vertebrate cells.
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31
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Smirnova J, Kabin E, Tõugu V, Palumaa P. Redox properties of Cys 2His 2 and Cys 4 zinc fingers determined by electrospray ionization mass spectrometry. FEBS Open Bio 2018; 8:923-931. [PMID: 29928572 PMCID: PMC5985984 DOI: 10.1002/2211-5463.12422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/12/2018] [Accepted: 03/23/2018] [Indexed: 01/05/2023] Open
Abstract
Zinc finger (ZF) protein motifs, stabilized by binding of Zn(II), typically function as interaction modules that bind nucleic acids, proteins and other molecules. The elucidation of the redox states of ZF proteins in cellular conditions, which depend on their midpoint redox potentials, is important for understanding of ZF functioning. In the present study we determined the midpoint redox potentials for representatives of Cys2His2 and Cys4 types of ZF proteins in apo and Zn(II)-bound forms using electrospray ionization mass spectrometry. The midpoint redox potentials of the apo forms of Cys2His2 and Cys4 ZF proteins were -326 and -365 mV (pH 7.5), respectively. These values are close to the cytosolic redox potential of approx. -350 mV (pH 7.5) and thus we can conclude that the apo form of Cys2His2-type ZF proteins is predominantly reduced but apo forms of Cys4-type ZF proteins should be substantially oxidized in the cytoplasm. As expected, Zn(II) binding stabilized the reduced forms of both ZF proteins: the corresponding redox potential values were -284 and -301 mV, respectively. Consequently, binding of Zn(II) ions to ZF motifs can act as a sensitive switch that activates the functioning of the ZF motifs within the cell, and also protects them from oxidation and can function as part of a redox-sensitive regulation mechanism of cellular functions.
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Affiliation(s)
- Julia Smirnova
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Ekaterina Kabin
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Vello Tõugu
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
| | - Peep Palumaa
- Department of Chemistry and Biotechnology Tallinn University of Technology Estonia
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32
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Tapscott T, Kim JS, Crawford MA, Fitzsimmons L, Liu L, Jones-Carson J, Vázquez-Torres A. Guanosine tetraphosphate relieves the negative regulation of Salmonella pathogenicity island-2 gene transcription exerted by the AT-rich ssrA discriminator region. Sci Rep 2018; 8:9465. [PMID: 29930310 PMCID: PMC6013443 DOI: 10.1038/s41598-018-27780-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/01/2018] [Indexed: 01/09/2023] Open
Abstract
The repressive activity of ancestral histone-like proteins helps integrate transcription of foreign genes with discrepant AT content into existing regulatory networks. Our investigations indicate that the AT-rich discriminator region located between the −10 promoter element and the transcription start site of the regulatory gene ssrA plays a distinct role in the balanced expression of the Salmonella pathogenicity island-2 (SPI2) type III secretion system. The RNA polymerase-binding protein DksA activates the ssrAB regulon post-transcriptionally, whereas the alarmone guanosine tetraphosphate (ppGpp) relieves the negative regulation imposed by the AT-rich ssrA discriminator region. An increase in the GC-content of the ssrA discriminator region enhances ssrAB transcription and SsrB translation, thus activating the expression of downstream SPI2 genes. A Salmonella strain expressing a GC-rich ssrA discriminator region is attenuated in mice and grows poorly intracellularly. The combined actions of ppGpp and DksA on SPI2 expression enable Salmonella to grow intracellularly, and cause disease in a murine model of infection. Collectively, these findings indicate that (p)ppGpp relieves the negative regulation associated with the AT-rich discriminator region in the promoter of the horizontally-acquired ssrA gene, whereas DksA activates ssrB gene expression post-transcriptionally. The combined effects of (p)ppGpp and DksA on the ssrAB locus facilitate a balanced SPI2 virulence gene transcription that is essential for Salmonella pathogenesis.
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Affiliation(s)
- Timothy Tapscott
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ju-Sim Kim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Matthew A Crawford
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Liam Fitzsimmons
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jessica Jones-Carson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.,Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, USA
| | - Andrés Vázquez-Torres
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO, USA. .,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA. .,Veterans Affairs Eastern Colorado Health Care System, Denver, CO, USA.
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33
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Patterson-West J, James TD, Fernández-Coll L, Iben JR, Moon K, Knipling L, Cashel M, Hinton DM. The E. coli Global Regulator DksA Reduces Transcription during T4 Infection. Viruses 2018; 10:E308. [PMID: 29882792 DOI: 10.3390/v10060308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/16/2023] Open
Abstract
Bacteriophage T4 relies on host RNA polymerase to transcribe three promoter classes: early (Pe, requires no viral factors), middle (Pm, requires early proteins MotA and AsiA), and late (Pl, requires middle proteins gp55, gp33, and gp45). Using primer extension, RNA-seq, RT-qPCR, single bursts, and a semi-automated method to document plaque size, we investigated how deletion of DksA or ppGpp, two E. coli global transcription regulators, affects T4 infection. Both ppGpp⁰ and ΔdksA increase T4 wild type (wt) plaque size. However, ppGpp⁰ does not significantly alter burst size or latent period, and only modestly affects T4 transcript abundance, while ΔdksA increases burst size (2-fold) without affecting latent period and increases the levels of several Pe transcripts at 5 min post-infection. In a T4motAam infection, ΔdksA increases plaque size and shortens latent period, and the levels of specific middle RNAs increase due to more transcription from Pe’s that extend into these middle genes. We conclude that DksA lowers T4 early gene expression. Consequently, ΔdksA results in a more productive wt infection and ameliorates the poor expression of middle genes in a T4motAam infection. As DksA does not inhibit Pe transcription in vitro, regulation may be indirect or perhaps requires additional factors.
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Fitzsimmons LF, Liu L, Kim JS, Jones-Carson J, Vázquez-Torres A. Salmonella Reprograms Nucleotide Metabolism in Its Adaptation to Nitrosative Stress. mBio 2018; 9:e00211-18. [PMID: 29487237 DOI: 10.1128/mBio.00211-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The adaptations that protect pathogenic microorganisms against the cytotoxicity of nitric oxide (NO) engendered in the immune response are incompletely understood. We show here that salmonellae experiencing nitrosative stress suffer dramatic losses of the nucleoside triphosphates ATP, GTP, CTP, and UTP while simultaneously generating a massive burst of the alarmone nucleotide guanosine tetraphosphate. RelA proteins associated with ribosomes overwhelmingly synthesize guanosine tetraphosphate in response to NO as a feedback mechanism to transient branched-chain amino acid auxotrophies. Guanosine tetraphosphate activates the transcription of valine biosynthetic genes, thereby reestablishing branched-chain amino acid biosynthesis that enables the translation of the NO-consuming flavohemoglobin Hmp. Guanosine tetraphosphate synthesized by RelA protects salmonellae from the metabolic stress inflicted by reactive nitrogen species generated in the mammalian host response. This research illustrates the importance of nucleotide metabolism in the adaptation of salmonellae to the nutritional stress imposed by NO released in the innate host response. Nitric oxide triggers dramatic drops in nucleoside triphosphates, the building blocks that power DNA replication; RNA transcription; translation; cell division; and the biosynthesis of fatty acids, lipopolysaccharide, and peptidoglycan. Concomitantly, this diatomic gas stimulates a burst of guanosine tetraphosphate. Global changes in nucleotide metabolism may contribute to the potent bacteriostatic activity of nitric oxide. In addition to inhibiting numerous growth-dependent processes, guanosine tetraphosphate positively regulates the transcription of branched-chain amino acid biosynthesis genes, thereby facilitating the translation of antinitrosative defenses that mediate recovery from nitrosative stress.
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Cooper KG, Chong A, Starr T, Finn CE, Steele-Mortimer O. Predictable, Tunable Protein Production in Salmonella for Studying Host-Pathogen Interactions. Front Cell Infect Microbiol 2017; 7:475. [PMID: 29201859 PMCID: PMC5696353 DOI: 10.3389/fcimb.2017.00475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/31/2017] [Indexed: 12/30/2022] Open
Abstract
Here we describe the use of synthetic genetic elements to improve the predictability and tunability of episomal protein production in Salmonella. We used a multi-pronged approach, in which a series of variable-strength synthetic promoters were combined with a synthetic transcriptional terminator, and plasmid copy number variation. This yielded a series of plasmids that drive uniform production of fluorescent and endogenous proteins, over a wide dynamic range. We describe several examples where this system is used to fine-tune constitutive expression in Salmonella, providing an efficient means to titrate out toxic effects of protein production.
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Affiliation(s)
- Kendal G Cooper
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Audrey Chong
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Tregei Starr
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Ciaran E Finn
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Olivia Steele-Mortimer
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
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Shakir S, Vinh J, Chiappetta G. Quantitative analysis of the cysteine redoxome by iodoacetyl tandem mass tags. Anal Bioanal Chem 2017; 409:3821-3830. [PMID: 28389918 PMCID: PMC5427158 DOI: 10.1007/s00216-017-0326-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/04/2022]
Abstract
The redox conditions that reign inside a cell have a determining effect on a number of biological processes. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are key redox players and have been linked to a number of pathologies. They have also been shown to play an important regulating role in cell signaling events. On the proteome level, thiol groups of cysteinyl side chains constitute the major targets of ROS and RNS. A number of analytical techniques based on mass spectrometry have been developed to characterize the cysteine redoxome, often facing a number of technical challenges, mostly related to the lability, heterogeneity, and low abundance of the oxidized forms. Furthermore, any posttranslational modification (PTM) quantification method needs to take the parent protein’s expression level into account. While taking all these limitations into consideration, we have developed a quantitative analytical strategy named OxiTMT, based on chemical labeling with iodoacetyl isobaric tandem mass tags (iodoTMT). OxiTMT allowed the generation of quantitative redox data that could be normalized by the protein’s expression profile in up to three different conditions. The method was tested on Escherichia coli with or without an oxidative treatment. Results showed the method to be adequate for the analysis of cysteine PTMs with a good coverage of the cysteine redoxome, especially for the low abundant oxidized species. Some of the challenges that face reporter ion quantification of PTMs by mass spectrometry were also assessed. This study serves as a proof of concept of the established protocol and consequent data treatment step. The use of tandem mass tags opens the ways towards the application of the method to the study of tissues and sera. OxiTMT workflow ![]()
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Affiliation(s)
- Shakir Shakir
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France
| | - Joelle Vinh
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France
| | - Giovanni Chiappetta
- ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMPB), CNRS USR 3149, 10 rue Vauquelin, 75231, Paris cedex 05, France.
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Henard CA, Guarnieri MT, Knoshaug EP. The Chlorella vulgaris S-Nitrosoproteome under Nitrogen-Replete and -Deplete Conditions. Front Bioeng Biotechnol 2017; 4:100. [PMID: 28144611 PMCID: PMC5239800 DOI: 10.3389/fbioe.2016.00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/27/2016] [Indexed: 01/12/2023] Open
Affiliation(s)
- Calvin A Henard
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
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Jones-Carson J, Husain M, Liu L, Orlicky DJ, Vázquez-Torres A. Cytochrome bd-Dependent Bioenergetics and Antinitrosative Defenses in Salmonella Pathogenesis. mBio 2016; 7:e02052-16. [PMID: 27999164 DOI: 10.1128/mBio.02052-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the course of an infection, Salmonella enterica occupies diverse anatomical sites with various concentrations of oxygen (O2) and nitric oxide (NO). These diatomic gases compete for binding to catalytic metal groups of quinol oxidases. Enterobacteriaceae express two evolutionarily distinct classes of quinol oxidases that differ in affinity for O2 and NO as well as stoichiometry of H+ translocated across the cytoplasmic membrane. The investigations presented here show that the dual function of bacterial cytochrome bd in bioenergetics and antinitrosative defense enhances Salmonella virulence. The high affinity of cytochrome bd for O2 optimizes respiratory rates in hypoxic cultures, and thus, this quinol oxidase maximizes bacterial growth under O2-limiting conditions. Our investigations also indicate that cytochrome bd, rather than cytochrome bo, is an intrinsic component of the adaptive antinitrosative toolbox of Salmonella Accordingly, induction of cytochrome bd helps Salmonella grow and respire in the presence of inhibitory NO. The combined antinitrosative defenses of cytochrome bd and the flavohemoglobin Hmp account for a great part of the adaptations that help Salmonella recover from the antimicrobial activity of NO. Moreover, the antinitrosative defenses of cytochrome bd and flavohemoglobin Hmp synergize to promote Salmonella growth in systemic tissues. Collectively, our investigations indicate that cytochrome bd is a critical means by which Salmonella resists the nitrosative stress that is engendered in the innate response of mammalian hosts while it concomitantly allows for proper O2 utilization in tissue hypoxia. IMPORTANCE It is becoming quite apparent that metabolism is critically important to the virulence potential of pathogenic microorganisms. Bacterial cells use a variety of terminal electron acceptors to power electron transport chains and metabolic processes. Of all the electron acceptors available to bacteria, utilization of O2 yields the most energy while diversifying the type of substrates that a pathogen can use. Recent investigations have demonstrated important roles for bd-type quinol oxidases with high affinity for O2 in bacterial pathogenesis. The investigations presented here have revealed that cytochrome bd potentiates virulence of a clinically relevant bacterial pathogen by fueling bioenergetics of prokaryotic cells while protecting the respiratory chain against NO toxicity. The adaptive antinitrosative defenses afforded by cytochrome bd synergize with other NO-detoxifying systems to preserve cellular bioenergetics, thereby promoting bacterial virulence in tissue hypoxia.
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Fang FC, Frawley ER, Tapscott T, Vázquez-Torres A. Discrimination and Integration of Stress Signals by Pathogenic Bacteria. Cell Host Microbe 2016; 20:144-153. [PMID: 27512902 PMCID: PMC5111874 DOI: 10.1016/j.chom.2016.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/23/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
Abstract
For pathogenic bacteria, the ability to sense and respond to environmental stresses encountered within the host is critically important, allowing them to adapt to changing conditions and express virulence genes appropriately. This review considers the diverse molecular mechanisms by which stress conditions are sensed by bacteria, how related signals are discriminated, and how stress responses are integrated, highlighting recent studies in selected bacterial pathogens of clinical relevance.
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Affiliation(s)
- Ferric C Fang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Department Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Elaine R Frawley
- Department Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Timothy Tapscott
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Veterans Affairs Eastern Colorado Health Care System, 1055 Clermont Street, Denver, CO 80220, USA
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Abstract
Pathogenic bacteria must withstand diverse host environments during infection. Environmental signals, such as pH, temperature, nutrient limitation, etc., not only trigger adaptive responses within bacteria to these specific stress conditions but also direct the expression of virulence genes at an appropriate time and place. An appreciation of stress responses and their regulation is therefore essential for an understanding of bacterial pathogenesis. This review considers specific stresses in the host environment and their relevance to pathogenesis, with a particular focus on the enteric pathogen Salmonella.
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Affiliation(s)
- Ferric C Fang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-7735, USA; Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-7735, USA.
| | - Elaine R Frawley
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-7735, USA
| | - Timothy Tapscott
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Crawford MA, Tapscott T, Fitzsimmons LF, Liu L, Reyes AM, Libby SJ, Trujillo M, Fang FC, Radi R, Vázquez-Torres A. Redox-Active Sensing by Bacterial DksA Transcription Factors Is Determined by Cysteine and Zinc Content. mBio 2016; 7:e02161-15. [PMID: 27094335 DOI: 10.1128/mBio.02161-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The four-cysteine zinc finger motif of the bacterial RNA polymerase regulator DksA is essential for protein structure, canonical control of the stringent response to nutritional limitation, and thiol-based sensing of oxidative and nitrosative stress. This interdependent relationship has limited our understanding of DksA-mediated functions in bacterial pathogenesis. Here, we have addressed this challenge by complementing ΔdksA Salmonella with Pseudomonas aeruginosa dksA paralogues that encode proteins differing in cysteine and zinc content. We find that four-cysteine, zinc-bound (C4) and two-cysteine, zinc-free (C2) DksA proteins are able to mediate appropriate stringent control in Salmonella and that thiol-based sensing of reactive species is conserved among C2 and C4 orthologues. However, variations in cysteine and zinc content determine the threshold at which individual DksA proteins sense and respond to reactive species. In particular, zinc acts as an antioxidant, dampening cysteine reactivity and raising the threshold of posttranslational thiol modification with reactive species. Consequently, C2 DksA triggers transcriptional responses in Salmonella at levels of oxidative or nitrosative stress normally tolerated by Salmonella expressing C4 orthologues. Inappropriate transcriptional regulation by C2 DksA increases the susceptibility of Salmonella to the antimicrobial effects of hydrogen peroxide and nitric oxide, and attenuates virulence in macrophages and mice. Our findings suggest that the redox-active sensory function of DksA proteins is finely tuned to optimize bacterial fitness according to the levels of oxidative and nitrosative stress encountered by bacterial species in their natural and host environments. In order to cause disease, pathogenic bacteria must rapidly sense and respond to antimicrobial pressures encountered within the host. Prominent among these stresses, and of particular relevance to intracellular pathogens such as Salmonella, are nutritional restriction and the enzymatic generation of reactive oxygen and nitrogen species. The conserved transcriptional regulator DksA controls adaptive responses to nutritional limitation, as well as to oxidative and nitrosative stress. Here, we demonstrate that each of these functions contributes to bacterial pathogenesis. Our observations highlight the importance of metabolic adaptation in bacterial pathogenesis and show the mechanism by which DksA orthologues are optimized to sense the levels of oxidative and nitrosative stress encountered in their natural habitats. An improved understanding of the conserved processes used by bacteria to sense, respond to, and limit host defense will inform the development of novel strategies to treat infections caused by pathogenic, potentially multidrug-resistant bacteria.
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Wippel K, Long SR. Contributions of Sinorhizobium meliloti Transcriptional Regulator DksA to Bacterial Growth and Efficient Symbiosis with Medicago sativa. J Bacteriol 2016; 198:1374-83. [PMID: 26883825 DOI: 10.1128/JB.00013-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/09/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The stringent response, mediated by the (p)ppGpp synthetase RelA and the RNA polymerase-binding protein DksA, is triggered by limiting nutrient conditions. For some bacteria, it is involved in regulation of virulence. We investigated the role of two DksA-like proteins from the Gram-negative nitrogen-fixing symbiont Sinorhizobium meliloti in free-living culture and in interaction with its host plant Medicago sativa The two paralogs, encoded by the genes SMc00469 and SMc00049, differ in the constitution of two major domains required for function in canonical DksA: the DXXDXA motif at the tip of a coiled-coil domain and a zinc finger domain. Using mutant analyses of single, double, and triple deletions for SMc00469(designated dksA),SMc00049, and relA, we found that the ΔdksA mutant but not the ΔSMc00049 mutant showed impaired growth on minimal medium, reduced nodulation on the host plant, and lower nitrogen fixation activity in early nodules, while its nod gene expression was normal. The ΔrelA mutant showed severe pleiotropic phenotypes under all conditions tested. Only S. meliloti dksA complemented the metabolic defects of an Escherichia coli dksA mutant. Modifications of the DXXDXA motif in SMc00049 failed to establish DksA function. Our results imply a role for transcriptional regulator DksA in the S. meliloti-M. sativa symbiosis. IMPORTANCE The stringent response is a bacterial transcription regulation process triggered upon nutritional stress.Sinorhizobium meliloti, a soil bacterium establishing agriculturally important root nodule symbioses with legume plants, undergoes constant molecular adjustment during host interaction. Analyzing the components of the stringent response in this alphaproteobacterium helps understand molecular control regarding the development of plant interaction. Using mutant analyses, we describe how the lack of DksA influences symbiosis with Medicago sativa and show that a second paralogous S. meliloti protein cannot substitute for this missing function. This work contributes to the field by showing the similarities and differences of S. meliloti DksA-like proteins to orthologs from other species, adding information to the diversity of the stringent response regulatory system.
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Orman MA, Brynildsen MP. Persister formation in Escherichia coli can be inhibited by treatment with nitric oxide. Free Radic Biol Med 2016; 93:145-54. [PMID: 26849946 PMCID: PMC4898466 DOI: 10.1016/j.freeradbiomed.2016.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/15/2016] [Accepted: 02/01/2016] [Indexed: 12/01/2022]
Abstract
Bacterial persisters are phenotypic variants that survive extraordinary concentrations of antibiotics, and are thought to underlie the propensity of biofilm infections to relapse. Unfortunately many aspects of persister physiology remain ill-defined, which prevents progress toward eradicating the phenotype. Recently, we identified respiration within non-growing Escherichia coli populations as a potential target for the elimination type I persisters, which are those that arise from passage through stationary phase. Here we discovered that nitric oxide (NO) treatment at the onset of stationary phase significantly reduced type I persister formation through its ability to inhibit respiration. NO decreased protein and RNA degradation in stationary phase cells, and produced populations that were more fit for protein synthesis and growth resumption upon introduction into fresh media than untreated controls. Overall, this data shows that NO, which is a therapeutically-relevant compound, has the potential to decrease the incidence of recurrent infections from persisters.
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Affiliation(s)
- Mehmet A Orman
- Department of Chemical and Biological Engineering, Princeton University, 205 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, 205 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544, USA.
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Crawford MA, Henard CA, Tapscott T, Porwollik S, McClelland M, Vázquez-Torres A. DksA-Dependent Transcriptional Regulation in Salmonella Experiencing Nitrosative Stress. Front Microbiol 2016; 7:444. [PMID: 27065993 PMCID: PMC4815678 DOI: 10.3389/fmicb.2016.00444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/18/2016] [Indexed: 01/12/2023] Open
Abstract
Redox-based signaling is fundamental to the capacity of bacteria to sense, and respond to, nitrosative and oxidative stress encountered in natural and host environments. The conserved RNA polymerase regulatory protein DksA is a thiol-based sensor of reactive nitrogen and oxygen species. DksA-dependent transcriptional control promotes antinitrosative and antioxidative defenses that contribute to Salmonella pathogenesis. The specific adaptive changes mediated by DksA in response to reactive species, however, have not been elucidated. Herein, we characterize DksA-dependent changes in gene expression in Salmonella enterica experiencing nitrosative stress. Genome-wide expression analysis of wild-type and ΔdksA Salmonella exposed to the nitric oxide (•NO) donor DETA NONOate demonstrated •NO- and DksA-dependent regulatory control of 427 target genes. Transcriptional changes centered primarily on genes encoding aspects of cellular metabolism. Several antioxidants and oxidoreductases important in redox buffering, •NO detoxification, and damage repair were also observed to be up-regulated in an •NO- and DksA-dependent manner. Compared to wild-type bacteria, •NO-treated ΔdksA Salmonella exhibited a de-repression of genes encoding components of iron homeostasis and failed to activate sulfur assimilation and cysteine biosynthetic operons. As cysteine is integral to efficient antinitrosative and antioxidative defense and repair programs, we further examined the redox-responsive transcriptional control of cysteine biosynthesis by DksA. These investigations revealed that the activation of genes comprising cysteine biosynthesis also occurs in response to hydrogen peroxide, is dependent upon the redox-sensing zinc finger motif of DksA, and requires the transcriptional regulator CysB. Our observations demonstrate that DksA mediates global adaptation to nitrosative stress in Salmonella and provide unique insight into a novel regulatory mechanism by which cysteine biosynthesis is controlled in response to reactive oxygen and nitrogen species.
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Affiliation(s)
- Matthew A Crawford
- Department of Immunology and Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Calvin A Henard
- Department of Immunology and Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Timothy Tapscott
- Molecular Biology Program, University of Colorado School of Medicine Aurora, CO, USA
| | - Steffen Porwollik
- Department of Pathology and Laboratory Medicine, University of California, Irvine Irvine, CA, USA
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, University of California, Irvine Irvine, CA, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of MedicineAurora, CO, USA; Veterans Affairs Eastern Colorado Health Care SystemDenver, CO, USA
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Song M, Kim JS, Liu L, Husain M, Vázquez-Torres A. Antioxidant Defense by Thioredoxin Can Occur Independently of Canonical Thiol-Disulfide Oxidoreductase Enzymatic Activity. Cell Rep 2016; 14:2901-11. [PMID: 26997275 DOI: 10.1016/j.celrep.2016.02.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/21/2016] [Accepted: 02/15/2016] [Indexed: 01/21/2023] Open
Abstract
The thiol-disulfide oxidoreductase CXXC catalytic domain of thioredoxin contributes to antioxidant defense in phylogenetically diverse organisms. We find that although the oxidoreductase activity of thioredoxin-1 protects Salmonella enterica serovar Typhimurium from hydrogen peroxide in vitro, it does not appear to contribute to Salmonella's antioxidant defenses in vivo. Nonetheless, thioredoxin-1 defends Salmonella from oxidative stress resulting from NADPH phagocyte oxidase macrophage expression during the innate immune response in mice. Thioredoxin-1 binds to the flexible linker, which connects the receiver and effector domains of SsrB, thereby keeping this response regulator in the soluble fraction. Thioredoxin-1, independently of thiol-disulfide exchange, activates intracellular SPI2 gene transcription required for Salmonella resistance to both reactive species generated by NADPH phagocyte oxidase and oxygen-independent lysosomal host defenses. These findings suggest that the horizontally acquired virulence determinant SsrB is regulated post-translationally by ancestrally present thioredoxin.
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Affiliation(s)
- Miryoung Song
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19(th) Avenue, Aurora, CO 80045, USA
| | - Ju-Sim Kim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19(th) Avenue, Aurora, CO 80045, USA
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19(th) Avenue, Aurora, CO 80045, USA
| | - Maroof Husain
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19(th) Avenue, Aurora, CO 80045, USA; Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama, Birmingham, 619 South 19(th) Street, Birmingham, AL 35249-6810, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19(th) Avenue, Aurora, CO 80045, USA; Veterans Affairs Eastern Colorado Health Care System, 1055 Clermont Street, Denver, CO 80220, USA.
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Astuti RI, Watanabe D, Takagi H. Nitric oxide signaling and its role in oxidative stress response in Schizosaccharomyces pombe. Nitric Oxide 2016; 52:29-40. [DOI: 10.1016/j.niox.2015.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/14/2015] [Accepted: 11/21/2015] [Indexed: 01/19/2023]
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Rice CJ, Ramachandran VK, Shearer N, Thompson A. Transcriptional and Post-Transcriptional Modulation of SPI1 and SPI2 Expression by ppGpp, RpoS and DksA in Salmonella enterica sv Typhimurium. PLoS One 2015; 10:e0127523. [PMID: 26039089 PMCID: PMC4454661 DOI: 10.1371/journal.pone.0127523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 12/02/2022] Open
Abstract
The expression of genes within Salmonella Pathogenicity Islands 1 and 2 (SPI1, SPI2) is required to facilitate invasion and intracellular replication respectively of S. Typhimurium in host cell lines. Control of their expression is complex and occurs via a variety of factors operating at transcriptional and post-transcriptional levels in response to the environmental stimuli found within the host. Several of the factors that modulate SPI1 and SPI2 expression are involved in the redistribution or modification of RNA polymerase (RNAP) specificity. These factors include the bacterial alarmone, ppGpp, the alternative sigma factor, RpoS, and the RNAP accessory protein, DksA. In this report we show not only how these three factors modulate SPI1 and SPI2 expression but also how they contribute to the 'phased' expression of SPI1 and SPI2 during progress through late-log and stationary phase in aerobic rich broth culture conditions. In addition, we demonstrate that the expression of at least one SPI1-encoded protein, SipC is subject to DksA-dependent post-transcriptional control.
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Affiliation(s)
| | | | - Neil Shearer
- Institute of Food Research, Norwich, NR4 7UA, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich, NR4 7UA, United Kingdom
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Oh YT, Lee KM, Bari W, Raskin DM, Yoon SS. (p)ppGpp, a Small Nucleotide Regulator, Directs the Metabolic Fate of Glucose in Vibrio cholerae. J Biol Chem 2015; 290:13178-90. [PMID: 25882848 DOI: 10.1074/jbc.m115.640466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 12/20/2022] Open
Abstract
When V. cholerae encounters nutritional stress, it activates (p)ppGpp-mediated stringent response. The genes relA and relV are involved in the production of (p)ppGpp, whereas the spoT gene encodes an enzyme that hydrolyzes it. Herein, we show that the bacterial capability to produce (p)ppGpp plays an essential role in glucose metabolism. The V. cholerae mutants defective in (p)ppGpp production (i.e. ΔrelAΔrelV and ΔrelAΔrelVΔspoT mutants) lost their viability because of uncontrolled production of organic acids, when grown with extra glucose. In contrast, the ΔrelAΔspoT mutant, a (p)ppGpp overproducer strain, exhibited better growth in the presence of the same glucose concentration. An RNA sequencing analysis demonstrated that transcriptions of genes consisting of an operon for acetoin biosynthesis were markedly elevated in N16961, a seventh pandemic O1 strain, but not in its (p)ppGpp(0) mutant during glucose-stimulated growth. Transposon insertion in acetoin biosynthesis gene cluster resulted in glucose-induced loss of viability of the ΔrelAΔspoT mutant, further suggesting the crucial role of acetoin production in balanced growth under glucose-rich environments. Additional deletion of the aphA gene, encoding a negative regulator for acetoin production, failed to rescue the (p)ppGpp(0) mutant from the defective glucose-mediated growth, suggesting that (p)ppGpp-mediated acetoin production occurs independent of the presence of AphA. Overall, our results reveal that (p)ppGpp, in addition to its well known role as a stringent response mediator, positively regulates acetoin production that contributes to the successful glucose metabolism and consequently the proliferation of V. cholerae cells under a glucose-rich environment, a condition that may mimic the human intestine.
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Affiliation(s)
- Young Taek Oh
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science and
| | - Kang-Mu Lee
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science and
| | - Wasimul Bari
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science and
| | - David M Raskin
- the Marian University College of Osteopathic Medicine, Indianapolis, Indiana 46222
| | - Sang Sun Yoon
- From the Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Science and the Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 120-752, Korea and
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Abstract
DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensitivity in vitro. Together, these data suggest that DksA responds to changes in pH by shifting between alternate conformations, in which competing interactions between the N- and C-terminal regions modify the protein activity.
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Affiliation(s)
- Ran Furman
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Eric M. Danhart
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Monali NandyMazumdar
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Mark P. Foster
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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