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Nutrient Sensing and Biofilm Modulation: The Example of L-arginine in Pseudomonas. Int J Mol Sci 2022; 23:ijms23084386. [PMID: 35457206 PMCID: PMC9028604 DOI: 10.3390/ijms23084386] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Bacterial biofilm represents a multicellular community embedded within an extracellular matrix attached to a surface. This lifestyle confers to bacterial cells protection against hostile environments, such as antibiotic treatment and host immune response in case of infections. The Pseudomonas genus is characterised by species producing strong biofilms difficult to be eradicated and by an extraordinary metabolic versatility which may support energy and carbon/nitrogen assimilation under multiple environmental conditions. Nutrient availability can be perceived by a Pseudomonas biofilm which, in turn, readapts its metabolism to finally tune its own formation and dispersion. A growing number of papers is now focusing on the mechanism of nutrient perception as a possible strategy to weaken the biofilm barrier by environmental cues. One of the most important nutrients is amino acid L-arginine, a crucial metabolite sustaining bacterial growth both as a carbon and a nitrogen source. Under low-oxygen conditions, L-arginine may also serve for ATP production, thus allowing bacteria to survive in anaerobic environments. L-arginine has been associated with biofilms, virulence, and antibiotic resistance. L-arginine is also a key precursor of regulatory molecules such as polyamines, whose involvement in biofilm homeostasis is reported. Given the biomedical and biotechnological relevance of biofilm control, the state of the art on the effects mediated by the L-arginine nutrient on biofilm modulation is presented, with a special focus on the Pseudomonas biofilm. Possible biotechnological and biomedical applications are also discussed.
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Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. mSystems 2021; 6:e0090621. [PMID: 34636676 PMCID: PMC8510549 DOI: 10.1128/msystems.00906-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae, nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae, and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria, Flavobacteriales, and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog in a Brocadia MAG was most closely related to CRP TFs known to sense carbon sources in well-studied organisms. However, we predict that in autotrophic Brocadia, this TF most likely regulates a diverse set of functions, including a response to stress during the cyclic aerobic/anoxic conditions. Overall, this analysis allowed us to define a meta-regulon of the PNA microbiome that explains functions and interactions of the most active community members. IMPORTANCE Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions. We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles. Our results indicated that, for some members of the community, prior knowledge is sufficient for high-confidence assignments of TF function, whereas other community members have CRP/FNR TFs for which inferences of function are limited by lack of prior knowledge. This study provides a framework to begin elucidating meta-regulons in microbiomes, where pure cultures are not available for traditional transcriptional regulation studies. Defining the meta-regulon can help in optimizing microbiome performance.
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Phenn J, Pané-Farré J, Meukow N, Klein A, Troitzsch A, Tan P, Fuchs S, Wagner GE, Lichtenegger S, Steinmetz I, Kohler C. RegAB Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence. PLoS Pathog 2021; 17:e1009604. [PMID: 34048488 PMCID: PMC8191878 DOI: 10.1371/journal.ppat.1009604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/10/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei, the etiological agent of melioidosis in humans and animals, often occupies environmental niches and infection sites characterized by limited concentrations of oxygen. Versatile genomic features enable this pathogen to maintain its physiology and virulence under hypoxia, but the crucial regulatory networks employed to switch from oxygen dependent respiration to alternative terminal electron acceptors (TEA) like nitrate, remains poorly understood. Here, we combined a Tn5 transposon mutagenesis screen and an anaerobic growth screen to identify a two-component signal transduction system with homology to RegAB. We show that RegAB is not only essential for anaerobic growth, but also for full virulence in cell lines and a mouse infection model. Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. Of the 20 identified regulators, NarX/L and a FNR homolog were selected for further analyses and a role in adaptation to anaerobic conditions was demonstrated. Growth experiments identified nitrate and intermediates of the denitrification process as the likely signal activateing RegAB, NarX/L, and probably of the downstream regulators Dnr or NsrR homologs. While deletions of individual genes involved in the denitrification process demonstrated their important role in anaerobic fitness, they showed no effect on virulence. This further highlights the central role of RegAB as the master regulator of anaerobic metabolism in B. pseudomallei and that the complete RegAB-mediated response is required to achieve full virulence. In summary, our analysis of the RegAB-dependent modulon and its interconnected regulons revealed a key role for RegAB of B. pseudomallei in the coordination of the response to hypoxic conditions and virulence, in the environment and the host.
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Affiliation(s)
- Julia Phenn
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nikolai Meukow
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Annelie Klein
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Anne Troitzsch
- Department for Microbial Physiology and Molecular Biology, University Greifswald, Greifswald, Germany
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, Republic of Singapore
- Duke-NUS Medical School Singapore, Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
| | - Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Sabine Lichtenegger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Ivo Steinmetz
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Ganesh I, Gwon DA, Lee JW. Gas-Sensing Transcriptional Regulators. Biotechnol J 2020; 15:e1900345. [PMID: 32362055 DOI: 10.1002/biot.201900345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Indexed: 11/10/2022]
Abstract
Gas molecules are ubiquitous in the environment and are used as nutrient and energy sources for living organisms. Many organisms, therefore, have developed gas-sensing systems to respond efficiently to changes in the atmospheric environment. In microorganisms and plants, two-component systems (TCSs) and transcription factors (TFs) are two primary mechanisms to sense gas molecules. In this review, gas-sensing transcriptional regulators, TCSs, and TFs, focusing on protein structures, mechanisms of gas molecule interaction, DNA binding regions of transcriptional regulators, signal transduction mechanisms, and gene expression regulation are discussed. At first, transcriptional regulators that directly sense gas molecules with the help of a prosthetic group is described and then gas-sensing systems that indirectly recognize the presence of gas molecules is explained. Overall, this review provides a comprehensive understanding of gas-sensing transcriptional regulators in microorganisms and plants, and proposes a future perspective on the use of gas-sensing transcriptional regulators.
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Affiliation(s)
- Irisappan Ganesh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
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Rinaldo S, Giardina G, Mantoni F, Paone A, Cutruzzolà F. Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms. FEMS Microbiol Lett 2019; 365:4834012. [PMID: 29401255 DOI: 10.1093/femsle/fny029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.
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Affiliation(s)
- Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Federico Mantoni
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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Belvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP. Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR. Acta Crystallogr D Struct Biol 2019; 75:437-450. [PMID: 30988260 PMCID: PMC6465984 DOI: 10.1107/s205979831900264x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain. It is shown that heme bound to HcpR exhibits heme iron as a hexacoordinate system in the absence of nitric oxide (NO) and that upon nitrosylation it transitions to a pentacoordinate system. Finally, small-angle X-ray scattering experiments on full-length HcpR reveal that the C-terminal DNA-binding domain of HcpR has a high degree of interdomain flexibility.
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Affiliation(s)
- B. Ross Belvin
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Faik N. Musayev
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - John Burgner
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J. Neel Scarsdale
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Janina P. Lewis
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
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Abstract
SIGNIFICANCE The molecule nitric oxide (NO) has been shown to regulate behaviors in bacteria, including biofilm formation. NO detection and signaling in bacteria is typically mediated by hemoproteins such as the bis-(3',5')-cyclic dimeric adenosine monophosphate-specific phosphodiesterase YybT, the transcriptional regulator dissimilative nitrate respiration regulator, or heme-NO/oxygen binding (H-NOX) domains. H-NOX domains are well-characterized primary NO sensors that are capable of detecting nanomolar NO and influencing downstream signal transduction in many bacterial species. However, many bacteria, including the human pathogen Pseudomonas aeruginosa, respond to nanomolar concentrations of NO but do not contain an annotated H-NOX domain, indicating the existence of an additional nanomolar NO-sensing protein (NosP). Recent Advances: A newly discovered bacterial hemoprotein called NosP may also act as a primary NO sensor in bacteria, in addition to, or in place of, H-NOX. NosP was first described as a regulator of a histidine kinase signal transduction pathway that is involved in biofilm formation in P. aeruginosa. CRITICAL ISSUES The molecular details of NO signaling in bacteria are still poorly understood. There are still many bacteria that are NO responsive but do encode either H-NOX or NosP domains in their genomes. Even among bacteria that encode H-NOX or NosP, many questions remain. FUTURE DIRECTIONS The molecular mechanisms of NO regulation in many bacteria remain to be established. Future studies are required to gain knowledge about the mechanism of NosP signaling. Advancements on structural and molecular understanding of heme-based sensors in bacteria could lead to strategies to alleviate or control bacterial biofilm formation or persistent biofilm-related infections.
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Affiliation(s)
| | - Lisa-Marie Nisbett
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Bezalel Bacon
- 2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York
| | - Elizabeth Boon
- 1 Department of Chemistry, Stony Brook University , Stony Brook, New York.,2 Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York.,3 Institute of Chemical Biology and Drug Design, Stony Brook University , Stony Brook, New York
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Bueno E, Robles EF, Torres MJ, Krell T, Bedmar EJ, Delgado MJ, Mesa S. Disparate response to microoxia and nitrogen oxides of the Bradyrhizobium japonicum napEDABC, nirK and norCBQD denitrification genes. Nitric Oxide 2017; 68:137-149. [DOI: 10.1016/j.niox.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/27/2017] [Accepted: 02/02/2017] [Indexed: 01/25/2023]
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Ebert M, Schweyen P, Bröring M, Laass S, Härtig E, Jahn D. Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napD promoter affinity. J Biol Chem 2017; 292:15468-15480. [PMID: 28765283 DOI: 10.1074/jbc.m117.798728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/24/2017] [Indexed: 12/27/2022] Open
Abstract
Under oxygen-limiting conditions, the marine bacterium Dinoroseobacter shibae DFL12T generates energy via denitrification, a respiratory process in which nitric oxide (NO) is an intermediate. Accumulation of NO may cause cytotoxic effects. The response to this nitrosative (NO-triggered) stress is controlled by the Crp/Fnr-type transcriptional regulator DnrF. We analyzed the response to NO and the mechanism of NO sensing by the DnrF regulator. Using reporter gene fusions and transcriptomics, here we report that DnrF selectively repressed nitrate reductase (nap) genes, preventing further NO formation. In addition, DnrF induced the expression of the NO reductase genes (norCB), which promote NO consumption. We used UV-visible and EPR spectroscopy to characterize heme binding to DnrF and subsequent NO coordination. DnrF detects NO via its bound heme cofactor. We found that the dimeric DnrF bound one molecule of heme per subunit. Purified recombinant apo-DnrF bound its target promoter sequences (napD, nosR2, norC, hemA, and dnrE) in electromobility shift assays, and we identified a specific palindromic DNA-binding site 5'-TTGATN4ATCAA-3' in these target sequences via mutagenesis studies. Most importantly, successive addition of heme as well as heme and NO to purified recombinant apo-DnrF protein increased affinity of the holo-DnrF for its specific binding motif in the napD promoter. On the basis of these results, we propose a model for the DnrF-mediated NO stress response of this marine bacterium.
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Affiliation(s)
- Matthias Ebert
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig
| | - Peter Schweyen
- the Institute for Inorganic and Analytical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig
| | - Martin Bröring
- the Institute for Inorganic and Analytical Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig
| | - Sebastian Laass
- the Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, and
| | - Elisabeth Härtig
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
| | - Dieter Jahn
- the Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, D-38106 Braunschweig, Germany
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Ebert M, Laaß S, Thürmer A, Roselius L, Eckweiler D, Daniel R, Härtig E, Jahn D. FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae. Front Microbiol 2017; 8:642. [PMID: 28473807 PMCID: PMC5398030 DOI: 10.3389/fmicb.2017.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/29/2017] [Indexed: 11/14/2022] Open
Abstract
The heterotrophic marine bacterium Dinoroseobacter shibae utilizes aerobic respiration and anaerobic denitrification supplemented with aerobic anoxygenic photosynthesis for energy generation. The aerobic to anaerobic transition is controlled by four Fnr/Crp family regulators in a unique cascade-type regulatory network. FnrL is utilizing an oxygen-sensitive Fe-S cluster for oxygen sensing. Active FnrL is inducing most operons encoding the denitrification machinery and the corresponding heme biosynthesis. Activation of gene expression of the high oxygen affinity cbb3-type and repression of the low affinity aa3-type cytochrome c oxidase is mediated by FnrL. Five regulator genes including dnrE and dnrF are directly controlled by FnrL. Multiple genes of the universal stress protein (USP) and cold shock response are further FnrL targets. DnrD, most likely sensing NO via a heme cofactor, co-induces genes of denitrification, heme biosynthesis, and the regulator genes dnrE and dnrF. DnrE is controlling genes for a putative Na+/H+ antiporter, indicating a potential role of a Na+ gradient under anaerobic conditions. The formation of the electron donating primary dehydrogenases is coordinated by FnrL and DnrE. Many plasmid encoded genes were DnrE regulated. DnrF is controlling directly two regulator genes including the Fe-S cluster biosynthesis regulator iscR, genes of the electron transport chain and the glutathione metabolism. The genes for nitrate reductase and CO dehydrogenase are repressed by DnrD and DnrF. Both regulators in concert with FnrL are inducing the photosynthesis genes. One of the major denitrification operon control regions, the intergenic region between nirS and nosR2, contains one Fnr/Dnr binding site. Using regulator gene mutant strains, lacZ-reporter gene fusions in combination with promoter mutagenesis, the function of the single Fnr/Dnr binding site for FnrL-, DnrD-, and partly DnrF-dependent nirS and nosR2 transcriptional activation was shown. Overall, the unique regulatory network of the marine bacterium D. shibae for the transition from aerobic to anaerobic growth composed of four Crp/Fnr family regulators was elucidated.
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Affiliation(s)
- Matthias Ebert
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Sebastian Laaß
- Institute for Molecular Biosciences, Goethe-University FrankfurtFrankfurt, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Louisa Roselius
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Denitsa Eckweiler
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University GöttingenGöttingen, Germany
| | - Elisabeth Härtig
- Institute of Microbiology, Technische Universität BraunschweigBraunschweig, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology, Technische Universität BraunschweigBraunschweig, Germany
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Abstract
The formation of the organized bacterial community called biofilm is a crucial event in bacterial physiology. Given that biofilms are often refractory to antibiotics and disinfectants to which planktonic bacteria are susceptible, their formation is also an industrially and medically relevant issue. Pseudomonas aeruginosa, a well-known human pathogen causing acute and chronic infections, is considered a model organism to study biofilms. A large number of environmental cues control biofilm dynamics in bacterial cells. In particular, the dispersal of individual cells from the biofilm requires metabolic and morphological reprogramming in which the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) plays a central role. The diatomic gas nitric oxide (NO), a well-known signaling molecule in both prokaryotes and eukaryotes, is able to induce the dispersal of P. aeruginosa and other bacterial biofilms by lowering c-di-GMP levels. In this review, we summarize the current knowledge on the molecular mechanisms connecting NO sensing to the activation of c-di-GMP-specific phosphodiesterases in P. aeruginosa, ultimately leading to c-di-GMP decrease and biofilm dispersal.
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtíková V, Martínková M. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-redox sensors. Chem Rev 2015; 115:6491-533. [PMID: 26021768 DOI: 10.1021/acs.chemrev.5b00018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Toru Shimizu
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
- §Research Center for Compact Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Sendai 983-8551, Japan
| | - Dongyang Huang
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fang Yan
- †Department of Cell Biology and Genetics and Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Martin Stranava
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Martina Bartosova
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Veronika Fojtíková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
| | - Markéta Martínková
- ‡Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague 2 128 43, Czech Republic
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Luebke JL, Giedroc DP. Cysteine sulfur chemistry in transcriptional regulators at the host-bacterial pathogen interface. Biochemistry 2015; 54:3235-49. [PMID: 25946648 DOI: 10.1021/acs.biochem.5b00085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hosts employ myriad weapons to combat invading microorganisms as an integral feature of the host-bacterial pathogen interface. This interface is dominated by highly reactive small molecules that collectively induce oxidative stress. Successful pathogens employ transcriptional regulatory proteins that sense these small molecules directly or indirectly via a change in the ratio of reduced to oxidized low-molecular weight (LMW) thiols that collectively comprise the redox buffer in the cytoplasm. These transcriptional regulators employ either a prosthetic group or reactive cysteine residue(s) to effect changes in the transcription of genes that encode detoxification and repair systems that is driven by regulator conformational switching between high-affinity and low-affinity DNA-binding states. Cysteine harbors a highly polarizable sulfur atom that readily undergoes changes in oxidation state in response to oxidative stress to produce a range of regulatory post-translational modifications (PTMs), including sulfenylation (S-hydroxylation), mixed disulfide bond formation with LMW thiols (S-thiolation), di- and trisulfide bond formation, S-nitrosation, and S-alkylation. Here we discuss several examples of structurally characterized cysteine thiol-specific transcriptional regulators that sense changes in cellular redox balance, focusing on the nature of the cysteine PTM itself and the interplay of small molecule oxidative stressors in mediating a specific transcriptional response.
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Affiliation(s)
- Justin L Luebke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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16
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Structural basis of functional diversification of the HD-GYP domain revealed by the Pseudomonas aeruginosa PA4781 protein, which displays an unselective bimetallic binding site. J Bacteriol 2015; 197:1525-35. [PMID: 25691523 DOI: 10.1128/jb.02606-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED The intracellular level of the bacterial secondary messenger cyclic di-3',5'-GMP (c-di-GMP) is determined by a balance between its biosynthesis and degradation, the latter achieved via dedicated phosphodiesterases (PDEs) bearing a characteristic EAL or HD-GYP domain. We here report the crystal structure of PA4781, one of the three Pseudomonas aeruginosa HD-GYP proteins, which we have previously characterized in vitro. The structure shows a bimetallic active site whose metal binding mode is different from those of both HD-GYP PDEs characterized so far. Purified PA4781 does not contain iron in the active site as for other HD-GYPs, and we show that it binds to a wide range of transition metals with similar affinities. Moreover, the structural features of PA4781 indicate that this is preferentially a pGpG binding protein, as we previously suggested. Our results point out that the structural features of HD-GYPs are more complex than predicted so far and identify the HD-GYP domain as a conserved scaffold which has evolved to preferentially interact with a partner GGDEF but which harbors different functions obtained through diversification of the active site. IMPORTANCE In bacteria, the capability to form biofilms, responsible for increased pathogenicity and antibiotic resistance, is almost universally stimulated by the second messenger cyclic di-GMP (c-di-GMP). To design successful strategies for targeting biofilm formation, a detailed characterization of the enzymes involved in c-di-GMP metabolism is crucial. We solved the structure of the HD-GYP domain of PA4781 from Pseudomonas aeruginosa, involved in c-di-GMP degradation. This is the third structure of this class of phosphodiesterases to be solved, and with respect to its homologues, it shows significant differences both in the nature and in the binding mode of the coordinated metals, indicating that HD-GYP proteins are able to fine-tune their function, thereby increasing the chances of the microorganism to adapt to different environmental needs.
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Lobato L, Bouzhir-Sima L, Yamashita T, Wilson MT, Vos MH, Liebl U. Dynamics of the heme-binding bacterial gas-sensing dissimilative nitrate respiration regulator (DNR) and activation barriers for ligand binding and escape. J Biol Chem 2014; 289:26514-26524. [PMID: 25037216 DOI: 10.1074/jbc.m114.571398] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
DNR (dissimilative nitrate respiration regulator) is a heme-binding transcription factor that is involved in the regulation of denitrification in Pseudomonas aeruginosa. In the ferrous deoxy state, the heme is 6-coordinate; external NO and CO can replace an internal ligand. Using fluorescence anisotropy, we show that high-affinity sequence-specific DNA binding occurs only when the heme is nitrosylated, consistent with the proposed function of DNR as NO sensor and transcriptional activator. This role is moreover supported by the NO "trapping" properties revealed by ultrafast spectroscopy that are similar to those of other heme-based NO sensor proteins. Dissociated CO-heme pairs rebind in an essentially barrierless way. This process competes with migration out of the heme pocket. The latter process is thermally activated (Ea ∼ 7 kJ/mol). This result is compared with other heme proteins, including the homologous CO sensor/transcription factor CooA, variants of the 5-coordinate mycobacterial sensor DosT and the electron transfer protein cytochrome c. This comparison indicates that thermal activation of ligand escape from the heme pocket is specific for systems where an external ligand replaces an internal one. The origin of this finding and possible implications are discussed.
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Affiliation(s)
- Laura Lobato
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France
| | - Taku Yamashita
- Laboratory of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan, and
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester C04 3SQ, United Kingdom
| | - Marten H Vos
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, 91128 Palaiseau, France,; INSERM U696, 91128 Palaiseau, France,.
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Distal-proximal crosstalk in the heme binding pocket of the NO sensor DNR. Biometals 2014; 27:763-73. [PMID: 25007853 DOI: 10.1007/s10534-014-9770-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/25/2014] [Indexed: 01/10/2023]
Abstract
In the opportunistic pathogen Pseudomonas aeruginosa the denitrification process is triggered by nitric oxide (NO) and plays a crucial role for the survival in chronic infection sites as a microaerobic-anaerobic biofilm. This respiratory pathway is transcriptionally induced by DNR, an heme-based gas sensor which positively responds to NO. Molecular details of the NO sensing mechanism employed by DNR are now emerging: we recently reported an in vitro study which dissected, for the first time, the heme-iron environment and identified one of the heme axial ligand (i.e. His187), found to be crucial to respond to NO. Nevertheless, the identification of the second heme axial ligand has been unsuccessful, given that a peculiar phenomenon of ligand switching around the heme-iron presumably occurs in DNR. The unusual heme binding properties of DNR could be due to the remarkable flexibility in solution of DNR itself, which, in turns, is crucial for the sensing activity; protein flexibility and dynamics indeed represent a common strategy employed by heme-based redox sensors, which present features deeply different from those of "canonical" hemeproteins. The capability of DNR to deeply rearrange around the heme-iron as been here demonstrated by means of spectroscopic characterization of the H167A/H187A DNR double mutant, which shows unusual kinetics of binding of NO and CO. Moreover, we show that the alteration (such as histidines mutations) of the distal side of the heme pocket is perceived by the proximal one, possibly via the DNR protein chain.
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Stern AM, Zhu J. An introduction to nitric oxide sensing and response in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2014; 87:187-220. [PMID: 24581392 DOI: 10.1016/b978-0-12-800261-2.00005-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nitric oxide (NO) is a radical gas that has been intensively studied for its role as a bacteriostatic agent. NO reacts in complex ways with biological molecules, especially metal centers and other radicals, to generate other bioactive compounds that inhibit enzymes, oxidize macromolecules, and arrest bacterial growth. Bacteria encounter not only NO derived from the host during infection but also NO derived from other bacteria and inorganic sources. The transcriptional responses used by bacteria to respond to NO are diverse but usually involve an iron-containing transcription factor that binds NO and alters its affinity for either DNA or factors involved in transcription, leading to the production of enzymatic tolerance systems. Some of these systems, such as flavohemoglobin and flavorubredoxin, directly remove NO. Some do not but are still important for NO tolerance through other mechanisms. The targets of NO that are protected by these systems include many metabolic pathways such as the tricarboxylic acid cycle and branched chain amino acid synthesis. This chapter discusses these topics and others and serves as a general introduction to microbial NO biology.
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