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Bientz V, Lanois A, Ginibre N, Pagès S, Ogier JC, George S, Rialle S, Brillard J. OxyR is required for oxidative stress resistance of the entomopathogenic bacterium Xenorhabdus nematophila and has a minor role during the bacterial interaction with its hosts. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001481. [PMID: 39058385 PMCID: PMC11281485 DOI: 10.1099/mic.0.001481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
Xenorhabdus nematophila is a Gram-negative bacterium, mutualistically associated with the soil nematode Steinernema carpocapsae, and this nemato-bacterial complex is parasitic for a broad spectrum of insects. The transcriptional regulator OxyR is widely conserved in bacteria and activates the transcription of a set of genes that influence cellular defence against oxidative stress. It is also involved in the virulence of several bacterial pathogens. The aim of this study was to identify the X. nematophila OxyR regulon and investigate its role in the bacterial life cycle. An oxyR mutant was constructed in X. nematophila and phenotypically characterized in vitro and in vivo after reassociation with its nematode partner. OxyR plays a major role during the X. nematophila resistance to oxidative stress in vitro. Transcriptome analysis allowed the identification of 59 genes differentially regulated in the oxyR mutant compared to the parental strain. In vivo, the oxyR mutant was able to reassociate with the nematode as efficiently as the control strain. These nemato-bacterial complexes harbouring the oxyR mutant symbiont were able to rapidly kill the insect larvae in less than 48 h after infestation, suggesting that factors other than OxyR could also allow X. nematophila to cope with oxidative stress encountered during this phase of infection in insect. The significantly increased number of offspring of the nemato-bacterial complex when reassociated with the X. nematophila oxyR mutant compared to the control strain revealed a potential role of OxyR during this symbiotic stage of the bacterial life cycle.
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Affiliation(s)
| | - Anne Lanois
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France
| | | | - Sylvie Pagès
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France
| | | | - Simon George
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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2
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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Park HJ, Jeong HW, Lee C, Lee MR, Choi H, Kim E, Bang IS. Val43 residue of NsrR is crucial for the nitric oxide response of Salmonella Typhimurium. Microbiol Spectr 2024; 12:e0302423. [PMID: 38054720 PMCID: PMC10783083 DOI: 10.1128/spectrum.03024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/30/2023] [Indexed: 12/07/2023] Open
Abstract
ABSTRACT In pathogenic bacteria, the flavohemoglobin Hmp is crucial in metabolizing the cytotoxic levels of nitric oxide (NO) produced in phagocytic cells, contributing to bacterial virulence. Hmp expression is predominantly regulated by the Rrf2 family transcription repressor NsrR in an NO-dependent manner; however, the underlying molecular mechanism in enterobacteria remains poorly understood. In this study, we identified Val43 of Salmonella Typhimurium NsrR (StNsrR) as a critical amino acid residue for regulating Hmp expression. The Val43-to-Ala-substituted mutant NsrR isolated through random and site-directed mutagenesis showed high binding affinity to the target DNA irrespective of NO exposure, resulting in a severe reduction in hmp transcription and slow NO metabolism in Salmonella under NO-producing conditions. Conversely, the Val43-to-Glu-substituted NsrR caused effects similar to nsrR null mutation, which directed hmp transcription and NO metabolism in a constitutive way. Comparative analysis of the primary sequences of NsrR and another NO-sensing Rrf2 family regulator, IscR, from diverse bacteria, revealed that Val43 of enterobacterial NsrR corresponds to Ala in Pseudomonas aeruginosa or Streptomyces coelicolor NsrR and Glu in enterobacterial IscR, all of which are located in the DNA recognition helix α3. The predicted structure of StNsrR in complex with the hmp DNA suggests dissimilar spatial stoichiometry in the interactions of Val43 and its substituted residues with the target DNA, consistent with the observed phenotypic changes in StNsrR Val43 mutants. Our findings highlight the discriminative roles of the NsrR recognition helix in regulating species-specific target gene expression, facilitating effective NO detoxification strategies in bacteria across diverse environments. IMPORTANCE The precise regulation of flavohemoglobin Hmp expression by NsrR is critical for bacterial fitness, as excessive Hmp expression in the absence of NO can disturb bacterial redox homeostasis. While the molecular structure of Streptomyces coelicolor NsrR has been recently identified, the specific molecular structures of NsrR proteins in enterobacteria remain unknown. Our discovery of the crucial role of Val43 in the DNA recognition helix α3 of Salmonella NsrR offers valuable insights into the Hmp modulation under NO stress. Furthermore, the observed amino acid polymorphisms in the α3 helices of NsrR proteins across different bacterial species suggest the diverse evolution of NsrR structure and gene regulation in response to varying levels of NO pressure within their ecological niches.
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Affiliation(s)
- Hee Jeong Park
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, Republic of Korea
| | - Hye Won Jeong
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, Republic of Korea
| | - Choa Lee
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, Republic of Korea
| | - Mi Rae Lee
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, Republic of Korea
| | - Hojung Choi
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Eungseok Kim
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Iel Soo Bang
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, Republic of Korea
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Stark GF, Martin RM, Smith LE, Wei B, Hellweger FL, Bullerjahn GS, McKay RML, Boyer GL, Wilhelm SW. Microcystin aids in cold temperature acclimation: Differences between a toxic Microcystis wildtype and non-toxic mutant. HARMFUL ALGAE 2023; 129:102531. [PMID: 37951605 PMCID: PMC10640677 DOI: 10.1016/j.hal.2023.102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023]
Abstract
For Microcystis aeruginosa PCC 7806, temperature decreases from 26 °C to 19 °C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin provided M. aeruginosa PCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, reactive oxygen species damage, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strain M. aeruginosa PCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19 °C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e., making microcystin) vs the shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents.
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Affiliation(s)
- Gwendolyn F Stark
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - Laura E Smith
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - Bofan Wei
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research, The University of Windsor, Windsor, ON, Canada
| | - Gregory L Boyer
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA.
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Chen L, Liu R, Li S, Wu M, Yu H, Ge Q. Metabolism of hydrogen peroxide by Lactobacillus plantarum NJAU-01: A proteomics study. Food Microbiol 2023; 112:104246. [PMID: 36906310 DOI: 10.1016/j.fm.2023.104246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/08/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
This study aimed to investigate the time-course effect of Lactobacillus plantarum NJAU-01 in scavenging exogenous hydrogen peroxide (H2O2). The results showed that L. plantarum NJAU-01 at 107 CFU/mL was able to eliminate a maximum of 4 mM H2O2 within a prolonged lag phase and resume to proliferate during the following culture. Redox state in the start-lag phase (0 h, without the addition of H2O2), indicated by glutathione and protein sulfhydryl, was impaired in the lag phase (3 h and 12 h) and then gradually recovered during subsequent growing stages (20 h and 30 h). By using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and proteomics analysis, a total of 163 proteins such as PhoP family transcriptional regulator, glutamine synthetase, peptide methionine sulfoxide reductase, thioredoxin reductase, ribosomal proteins, acetolactate synthase, ATP binding subunit ClpX, phosphoglycerate kinase, UvrABC system protein A and UvrABC system protein B were identified as differential proteins across the entire growth phase. Those proteins were mainly involved in H2O2 sensing, protein synthesis, repairing proteins and DNA lesions, amino sugar and nucleotide sugar metabolism. Our data suggest that biomolecules of L. plantarum NJAU-01 are oxidized to passively consume H2O2 and are restored by the enhanced protein and/or gene repair systems.
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Affiliation(s)
- Lei Chen
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Rui Liu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China.
| | - Suyun Li
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Mangang Wu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Hai Yu
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China
| | - Qingfeng Ge
- College of Food Science and Engineering, Yangzhou University, Industrial Engineering Center for Huaiyang Cuisine of Jiangsu Province, Yangzhou, 225127, China.
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He Y, Wang Y, Ma X, Zhao L, Guan J, Zhao J, Yu W, Li Y, Ni W, Gao Z. Resistance to Cefiderocol Involved Expression of PER-1 β-Lactamase and Downregulation of Iron Transporter System in Carbapenem-Resistant Acinetobacter baumannii. Infect Drug Resist 2022; 15:7177-7187. [PMID: 36514799 PMCID: PMC9741825 DOI: 10.2147/idr.s392241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Background Cefiderocol (CFDC) is a promising antimicrobial agent against multidrug resistant Gram-negative bacteria. However, CFDC resistance has emerged in carbapenem-resistant Acinetobacter baumannii (CR-AB) but the underlying mechanisms remain unclear. Methods Whole-genome sequencing and transcriptome sequencing were performed on CFDC-non-susceptible and CFDC-susceptible isolates. Two different recombinant plasmids was electro-transformed into the E. coli BL21 strain to determine the impact of blaPER and the combined impact of blaPER-1 and blaOXA-23 on CFDC resistance. Results Fifty-five CR-AB isolates with minimum inhibitory concentrations (MICs) ranged from 0.06 mg/L to >256 mg/L were sequenced, including 47 CFDC-non-susceptible and eight CFDC-susceptible isolates. Two CFDC-non-susceptible isolates belonged to ST104 whereas the remaining isolates belonged to ST2, and blaPER-1 was present only in CFDC-non-susceptible isolates. Amino acid substitutions were noted in penicillin-binding proteins (PBPs) in four CFDC-susceptible isolates, with slightly elevated MICs. The MICs of recombinant E. coli BL21 carrying the blaPER-1 gene increased 64-fold and recombinant E. coli BL21 carrying both the blaPER-1 and blaOXA-23 genes increased 8-fold but both remained within the susceptibility range. Transcriptome sequencing of 17 CFDC-non-susceptible isolates and eight CFDC-susceptible isolates revealed that transcriptional levels of various iron transport proteins, such as fiu, feoA, and feoB, and the energy transduction system, TonB-ExbB-ExbD, were relatively downregulated in CFDC-non-susceptible isolates. GO enrichment analysis revealed that the upregulated genes in CFDC-non-susceptible isolates were mainly associated with redox homeostasis and stress response. Besides, the expression levels of the blaOXA-23 and exbD genes were negatively correlated with the MICs. Conclusion PER-1 production, iron transport system downregulation, and mutations in PBPs may synergistically impart high-level resistance to CFDC in CR-AB.
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Affiliation(s)
- Yukun He
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Yifan Wang
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Xinqian Ma
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Lili Zhao
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Jie Guan
- Clinical Laboratory, Peking University First Hospital, Beijing, People’s Republic of China
| | - Jin Zhao
- Department of Respiratory Diseases, Air Force Medical Center, Chinese People’s Liberation Army, Beijing, People’s Republic of China
| | - Wenyi Yu
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Yanjun Li
- Clinical Laboratory, The Sixth Medical Center of PLA General Hospital, Beijing, People’s Republic of China
| | - Wentao Ni
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China,Correspondence: Wentao Ni; Zhancheng Gao, Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China, Email ;
| | - Zhancheng Gao
- Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
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Growth fitness, heme uptake and genomic variants in mutants of oxygen-tolerant Lacticaseibacillus casei and Lactiplantibacillus plantarum strains. Microbiol Res 2022; 262:127096. [DOI: 10.1016/j.micres.2022.127096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/04/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022]
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Optimization of a Method for Detecting Intracellular Sulfane Sulfur Levels and Evaluation of Reagents That Affect the Levels in Escherichia coli. Antioxidants (Basel) 2022; 11:antiox11071292. [PMID: 35883783 PMCID: PMC9311597 DOI: 10.3390/antiox11071292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Sulfane sulfur is a class of compounds containing zero-valent sulfur. Most sulfane sulfur compounds are reactive and play important signaling roles. Key enzymes involved in the production and metabolism of sulfane sulfur have been characterized; however, little is known about how to change intracellular sulfane sulfur (iSS) levels. To accurately measure iSS, we optimized a previously reported method, in which reactive iSS reacts with sulfite to produce thiosulfate, a stable sulfane sulfur compound, before detection. With the improved method, several factors were tested to influence iSS in Escherichia coli. Temperature, pH, and osmotic pressure showed little effect. At commonly used concentrations, most tested oxidants, including hydrogen peroxide, tert-butyl hydroperoxide, hypochlorous acid, and diamide, did not affect iSS, but carbonyl cyanide m-chlorophenyl hydrazone increased iSS. For reductants, 10 mM dithiothreitol significantly decreased iSS, but tris(2-carboxyethyl)phosphine did not. Among different sulfur-bearing compounds, NaHS, cysteine, S2O32− and diallyl disulfide increased iSS, of which only S2O32− did not inhibit E. coli growth at 10 mM or less. Thus, with the improved method, we have identified reagents that may be used to change iSS in E. coli and other organisms, providing tools to further study the physiological functions of iSS.
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Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts. Adv Microb Physiol 2022; 80:85-155. [PMID: 35489794 DOI: 10.1016/bs.ampbs.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial pathogens have sophisticated systems that allow them to survive in hosts in which innate immunity is the frontline of defense. One of the substances produced by infected hosts is nitric oxide (NO) that together with its derived species leads to the so-called nitrosative stress, which has antimicrobial properties. In this review, we summarize the current knowledge on targets and protective systems that bacteria have to survive host-generated nitrosative stress. We focus on bacterial pathogens that pose serious health concerns due to the growing increase in resistance to currently available antimicrobials. We describe the role of nitrosative stress as a weapon for pathogen eradication, the detoxification enzymes, protein/DNA repair systems and metabolic strategies that contribute to limiting NO damage and ultimately allow survival of the pathogen in the host. Additionally, this systematization highlights the lack of available data for some of the most important human pathogens, a gap that urgently needs to be addressed.
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Li B, Jo M, Liu J, Tian J, Canfield R, Bridwell-Rabb J. Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT. Commun Biol 2022; 5:275. [PMID: 35347217 PMCID: PMC8960804 DOI: 10.1038/s42003-022-03226-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H2O2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H2O2-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H2O2. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H2O2-consumption assays. Furthermore, an entrance channel for H2O2 was identified and key residues implicated in H2O2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation. The DNA binding and H2O2 sensing mechanisms are revealed for RexT, a transcriptional regulator found in cyanobacteria of the Nostocales order.
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Zhou Y, Pu Q, Chen J, Hao G, Gao R, Ali A, Hsiao A, Stock AM, Goulian M, Zhu J. Thiol-based functional mimicry of phosphorylation of the two-component system response regulator ArcA promotes pathogenesis in enteric pathogens. Cell Rep 2021; 37:110147. [PMID: 34936880 PMCID: PMC8728512 DOI: 10.1016/j.celrep.2021.110147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
Pathogenic bacteria can rapidly respond to stresses such as reactive oxygen species (ROS) using reversible redox-sensitive oxidation of cysteine thiol (-SH) groups in regulators. Here, we use proteomics to profile reversible ROS-induced thiol oxidation in Vibrio cholerae, the etiologic agent of cholera, and identify two modified cysteines in ArcA, a regulator of global carbon oxidation that is phosphorylated and activated under low oxygen. ROS abolishes ArcA phosphorylation but induces the formation of an intramolecular disulfide bond that promotes ArcA-ArcA interactions and sustains activity. ArcA cysteines are oxidized in cholera patient stools, and ArcA thiol oxidation drives in vitro ROS resistance, colonization of ROS-rich guts, and environmental survival. In other pathogens, such as Salmonella enterica, oxidation of conserved cysteines of ArcA orthologs also promotes ROS resistance, suggesting a common role for ROS-induced ArcA thiol oxidation in modulating ArcA activity, allowing for a balance of expression of stress- and pathogenesis-related genetic programs.
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Affiliation(s)
- Yitian Zhou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qinqin Pu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiandong Chen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guijuan Hao
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Afsar Ali
- Department of Environmental and Global Health, College of Public Health and Health Professions and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Ansel Hsiao
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Lushchak VI, Lushchak O. Interplay between reactive oxygen and nitrogen species in living organisms. Chem Biol Interact 2021; 349:109680. [PMID: 34606757 DOI: 10.1016/j.cbi.2021.109680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/06/2021] [Accepted: 09/29/2021] [Indexed: 01/16/2023]
Abstract
In living organisms most oxygen consumed is reduced to water via four-electron reduction. However, few percentages of oxygen are reduced by consecutive one electron mechanisms giving rise to superoxide anion radical, (O2•-), hydrogen peroxide (H2O2) and hydroxyl radical (HO•) and their derivatives collectively called reactive oxygen species (ROS). Nitric oxide (•NO) is produced at oxidation of arginine by nitric oxide synthase (NOS) or at reduction of nitrites by diverse reductases. Interaction of •NO with O2•- results in formation of peroxinitrite (ONOO-), a powerful oxidant. Additionally, H2O2 can interact with •NO resulting in HO• production. Nitric oxide and its derivatives are collectively called reactive nitrogen species (RNS) and together with ROS they form a group of so-called reactive oxygen/nitrogen species (RONS). Nonspecific effects of RONS are related to their interaction with various components of living organisms, whereas specific effects are based mainly on interaction with specific proteins containing [Fe-S]-clusters and thiol groups of cysteine residues. Most early ROS studies were mainly focused on their deleterious effects, whereas now more delicate mechanisms of their involvement in signaling and toxic processes are under inspection. Studies of RNS activities in biological systems started from their vasodilating effects which lead to discovery of activation of soluble guanylate cyclase. Interestingly, at low ROS and RNS concentrations signaling effects prevail, whereas at their high concentrations they affect biological systems inhibiting due to massive oxidation of cellular components.
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Affiliation(s)
- Volodymyr I Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine; I. Horbachevsky Ternopil National Medical University, 1 m. Voli, Ternopil, 46002, Ukraine; Research and Development University, 13a Shota Rustaveli Str., Ivano-Frankivsk, 76000, Ukraine.
| | - Oleh Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk, 76018, Ukraine; Research and Development University, 13a Shota Rustaveli Str., Ivano-Frankivsk, 76000, Ukraine.
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Ye Q, Lee C, Shin E, Lee SJ. Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis. Antioxidants (Basel) 2021; 10:antiox10101623. [PMID: 34679757 PMCID: PMC8533066 DOI: 10.3390/antiox10101623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/11/2023] Open
Abstract
The transposition of insertion sequence elements was evaluated among different Deinococcus geothermalis lineages, including the wild-type, a cystine importer-disrupted mutant, a complemented strain, and a cystine importer-overexpressed strain. Cellular growth reached early exponential growth at OD600 2.0 and late exponential growth at OD600 4.0. Exposing the cells to hydrogen peroxide (80–100 mM) resulted in the transposition of insertion sequences (ISs) in genes associated with the carotenoid biosynthesis pathway. Particularly, ISDge7 (an IS5 family member) and ISDge5 (an IS701 family member) from the cystine importer-disrupted mutant were transposed into phytoene desaturase (dgeo_0524) via replicative transposition. Further, the cystine importer-overexpressed strain Δdgeo_1985R showed transposition of both ISDge2 and ISDge5 elements. In contrast, IS transposition was not detected in the complementary strain. Interestingly, a cystine importer-overexpressing strain exhibited streptomycin resistance, indicating that point mutation occurred in the rpsL (dgeo_1873) gene encoding ribosomal protein S12. qRT-PCR analyses were then conducted to evaluate the expression of oxidative stress response genes, IS elements, and low-molecular-weight thiol compounds such as mycothiol and bacillithiol. Nevertheless, the mechanisms that trigger IS transposition in redox imbalance conditions remain unclear. Here, we report that the active transposition of different IS elements was affected by intracellular redox imbalances caused by cystine importer deficiencies or overexpression.
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Qiu X, Gao T, Yang J, Wang E, Liu L, Yuan H. Water-Soluble Humic Materials Modulating Metabolism and Triggering Stress Defense in Sinorhizobium fredii. Microbiol Spectr 2021; 9:e0029321. [PMID: 34479412 PMCID: PMC8552645 DOI: 10.1128/spectrum.00293-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments. In-depth understanding of these mechanisms can allow for better developing and utilizing of bacteria with various biological functions. In this study, we found that water-soluble humic materials (WSHM), a well-known environment-friendly plant growth biostimulant, significantly promoted the free-living growth and survival of Sinorhizobium fredii CCBAU45436 in a bell-shaped, dose-dependent manner, along with more-efficient carbon source consumption and relief of medium acidification. By using RNA-Seq analysis, a total of 1,136 genes significantly up-/downregulated by external addition of WSHM were identified under test conditions. These differentially expressed genes (DEGs) were enriched in functional categories related to carbon/nitrogen metabolism, cellular stress response, and genetic information processing. Further protein-protein interaction (PPI) network analysis and reverse genetic engineering indicated that WSHM might reprogram the transcriptome through inhibiting the expression of key hub gene rsh, which encodes a bifunctional enzyme catalyzing synthesis and hydrolysis of the "magic spot" (p)ppGpp. In addition, the root colonization and viability in soil of S. fredii CCBAU45436 were increased by WSHM. These findings provide us with new insights into how WSHM benefit bacterial adaptations and demonstrate great application value to be a unique inoculant additive. IMPORTANCE Sinorhizobium fredii CCBAU45436 is a highly effective, fast-growing rhizobium that can establish symbiosis with multiple soybean cultivars. However, it is difficult to maintain the high-density effective viable cells in the rhizobial inoculant for the stressful conditions during production, storage, transport, and application. Here, we showed that WSHM greatly increased the viable cells of S. fredii CCBAU45436 in culture, modulating metabolism and triggering stress defense. The root colonization and viability in soil of S. fredii CCBAU45436 were also increased by WSHM. Our results shed new insights into the effects of WSHM on bacteria and the importance of metabolism and stress defense during the bacteria's whole life. In addition, the functional mechanism of WSHM may provide candidate genes for improving environmental adaptability and application potential of bacteria through genetic engineering.
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Affiliation(s)
- Xiaoqian Qiu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tongguo Gao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Liang Liu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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Baković J, Yu BYK, Silva D, Baczynska M, Peak-Chew SY, Switzer A, Burchell L, Wigneshweraraj S, Vandanashree M, Gopal B, Filonenko V, Skehel M, Gout I. Redox Regulation of the Quorum-sensing Transcription Factor AgrA by Coenzyme A. Antioxidants (Basel) 2021; 10:antiox10060841. [PMID: 34070323 PMCID: PMC8228455 DOI: 10.3390/antiox10060841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 12/23/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is an aggressive opportunistic pathogen of prominent virulence and antibiotic resistance. These characteristics are due in part to the accessory gene regulator (agr) quorum-sensing system, which allows for the rapid adaptation of S. aureus to environmental changes and thus promotes virulence and the development of pathogenesis. AgrA is the agr system response regulator that binds to the P2 and P3 promoters and upregulates agr expression. In this study, we reveal that S. aureus AgrA is modified by covalent binding of CoA (CoAlation) in response to oxidative or metabolic stress. The sites of CoAlation were mapped by liquid chromatography tandem mass spectrometry (LC-MS/MS) and revealed that oxidation-sensing Cys199 is modified by CoA. Surface plasmon resonance (SPR) analysis showed an inhibitory effect of CoAlation on the DNA-binding activity, as CoAlated AgrA had significantly lower affinity towards the P2 and P3 promoters than non-CoAlated AgrA. Overall, this study provides novel insights into the mode of transcriptional regulation in S. aureus and further elucidates the link between the quorum-sensing and oxidation-sensing roles of the agr system.
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Affiliation(s)
- Jovana Baković
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (J.B.); (B.Y.K.Y.); (D.S.); (M.B.)
| | - Bess Yi Kun Yu
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (J.B.); (B.Y.K.Y.); (D.S.); (M.B.)
| | - Daniel Silva
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (J.B.); (B.Y.K.Y.); (D.S.); (M.B.)
| | - Maria Baczynska
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (J.B.); (B.Y.K.Y.); (D.S.); (M.B.)
| | - Sew Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK; (S.Y.P.-C.); (M.S.)
| | - Amy Switzer
- Section of Microbiology, Faculty of Medicine and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; (A.S.); (L.B.); (S.W.)
| | - Lynn Burchell
- Section of Microbiology, Faculty of Medicine and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; (A.S.); (L.B.); (S.W.)
| | - Sivaramesh Wigneshweraraj
- Section of Microbiology, Faculty of Medicine and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; (A.S.); (L.B.); (S.W.)
| | | | - Balasubramanian Gopal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; (M.V.); (B.G.)
| | - Valeriy Filonenko
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, 143 Kyiv, Ukraine;
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK; (S.Y.P.-C.); (M.S.)
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; (J.B.); (B.Y.K.Y.); (D.S.); (M.B.)
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, 143 Kyiv, Ukraine;
- Correspondence: ; Tel.: +0044-2076794482; Fax: +0044-2076797193
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Śmiga M, Olczak T. PgRsp Is a Novel Redox-Sensing Transcription Regulator Essential for Porphyromonas gingivalis Virulence. Microorganisms 2019; 7:microorganisms7120623. [PMID: 31795139 PMCID: PMC6955866 DOI: 10.3390/microorganisms7120623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Porphyromonas gingivalis is one of the etiological agents of chronic periodontitis. Both heme and oxidative stress impact expression of genes responsible for its survival and virulence. Previously we showed that P. gingivalis ferric uptake regulator homolog affects expression of a gene encoding a putative Crp/Fnr superfamily member, termed P. gingivalis redox-sensing protein (PgRsp). Although PgRsp binds heme and shows the highest similarity to proteins assigned to the CooA family, it could be a member of a novel, separate family of proteins with unknown function. Expression of the pgrsp gene is autoregulated and iron/heme dependent. Genes encoding proteins engaged in the oxidative stress response were upregulated in the pgrsp mutant (TO11) strain compared with the wild-type strain. The TO11 strain showed higher biomass production, biofilm formation, and coaggregation ability with Tannerella forsythia and Prevotella intermedia. We suggest that PgRsp may regulate production of virulence factors, proteases, Hmu heme acquisition system, and FimA protein. Moreover, we observed growth retardation of the TO11 strain under oxidative conditions and decreased survival ability of the mutant cells inside macrophages. We conclude that PgRsp protein may play a role in the oxidative stress response using heme as a ligand for sensing changes in redox status, thus regulating the alternative pathway of the oxidative stress response alongside OxyR.
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Pérez-Amigot D, Taleb V, Boneta S, Anoz-Carbonell E, Sebastián M, Velázquez-Campoy A, Polo V, Martínez-Júlvez M, Medina M. Towards the competent conformation for catalysis in the ferredoxin-NADP + reductase from the Brucella ovis pathogen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148058. [PMID: 31394095 DOI: 10.1016/j.bbabio.2019.148058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.
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Affiliation(s)
- Daniel Pérez-Amigot
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Víctor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sergio Boneta
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Aragon Institute for Health Research (IIS-Aragon), Zaragoza 50009, Spain; Biomedical Research Networking Center in Digestive and Hepatic Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Víctor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
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