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Guesmi S, Ghedira K, Pujic P, Najjari A, Miotello G, Cherif A, Narumi I, Armengaud J, Normand P, Sghaier H. Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10. Res Microbiol 2024:104230. [PMID: 39089347 DOI: 10.1016/j.resmic.2024.104230] [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: 09/17/2023] [Revised: 07/03/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
In this paper, we investigated the effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, Kocuria rhizophila PT10, isolated from the rhizosphere of the desert plant Panicum turgidum using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS). Overall, 1,487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids. Also, one of the more significant findings to emerge from this study is the SOS response of stressed PT10. Moreover, a comparison of top hits radio-modulated proteins of cold-acclimated PT10 with proteomics data from gamma-irradiated Deinococcus deserti showed that stressed PT10 has a specific response characterised by a high over-abundance of two transcriptional regulators, NemA, GatD, and UdgB.
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Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute (INAT), Avenue Charles Nicolle, Mahrajène, 1082, Tunis, Tunisia; Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia.
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, 13, Place Pasteur, Tunis, 1002, Tunisia.
| | - Petar Pujic
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France.
| | - Afef Najjari
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092, Tunis, Tunisia.
| | - Guylaine Miotello
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols sur Cèze, France.
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
| | - Issay Narumi
- Radiation Microbiology Laboratory, Department of Life Sciences, Faculty of Life Sciences, Toyo University, 48-1 Oka, Asaka, Saitama 351-8510, Japan.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols sur Cèze, France.
| | - Philippe Normand
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, 69622 Villeurbanne, Cedex, INRA, UMR1418, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory ″Energy and Matter for Development of Nuclear Sciences″ (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia; Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Peng F, Ye M, Liu Y, Liu J, Lan Y, Luo A, Zhang T, Jiang Z, Song H. Comparative genomics reveals response of Rhodococcus pyridinivorans B403 to phenol after evolution. Appl Microbiol Biotechnol 2022; 106:2751-2761. [DOI: 10.1007/s00253-022-11858-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/24/2022]
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Bispo M, Suhani S, van Dijl JM. Empowering antimicrobial photodynamic therapy of Staphylococcus aureus infections with potassium iodide. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 225:112334. [PMID: 34678616 DOI: 10.1016/j.jphotobiol.2021.112334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/26/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022]
Abstract
Infections caused by the Gram-positive bacterium Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), impose a great burden on global healthcare systems. Thus, there is an urgent need for alternative approaches to fight staphylococcal infections, such as targeted antimicrobial photodynamic therapy (aPDT). We recently reported that targeted aPDT with the S. aureus-specific immunoconjugate 1D9-700DX can be effectively applied to eradicate MRSA. Nonetheless, the efficacy of aPDT in the human body may be diminished by powerful antioxidant activities. In particular, we observed that the efficacy of aPDT with 1D9-700DX towards MRSA was reduced in human plasma. Here we show that this antagonistic effect can be attributed to human serum albumin, which represents the largest pool of free thiols in plasma for trapping reactive oxygen species. Importantly, we also show that our targeted aPDT approach with 1D9-700DX can be empowered by the non-toxic inorganic salt potassium iodide (KI), which reacts with the singlet oxygen produced upon aPDT, resulting in the formation of free iodine. The targeted iodine formation allows full eradication of MRSA (more than 6-log reduction) without negatively affecting other non-targeted bacterial species or human cells. Altogether, we show that the addition of KI allows a drastic reduction of both the amount of the immunoconjugate 1D9-700DX and the irradiation time needed for effective elimination of MRSA by aPDT in the presence of human serum albumin.
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Affiliation(s)
- Mafalda Bispo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Sabrina Suhani
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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Woo K, Kim DH, Oh MH, Park HS, Choi CH. N-3-Hydroxy Dodecanoyl-DL-homoserine Lactone (OH-dDHL) Triggers Apoptosis of Bone Marrow-Derived Macrophages through the ER- and Mitochondria-Mediated Pathways. Int J Mol Sci 2021; 22:ijms22147565. [PMID: 34299184 PMCID: PMC8305837 DOI: 10.3390/ijms22147565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
Quorum sensing of Acinetobacter nosocomialis for cell-to-cell communication produces N-3-hydroxy dodecanoyl-DL-homoserine lactone (OH-dDHL) by an AnoR/I two-component system. However, OH-dDHL-driven apoptotic mechanisms in hosts have not been clearly defined. Here, we investigated the induction of apoptosis signaling pathways in bone marrow-derived macrophages treated with synthetic OH-dDHL. Moreover, the quorum-sensing system for virulence regulation was evaluated in vivo using wild-type and anoI-deletion mutant strains. OH-dDHL decreased the viability of macrophage and epithelial cells in dose- and time-dependent manners. OH-dDHL induced Ca2+ efflux and caspase-12 activation by ER stress transmembrane protein (IRE1 and ATF6a p50) aggregation and induced mitochondrial dysfunction through reactive oxygen species (ROS) production, which caused cytochrome c to leak. Pretreatment with a pan-caspase inhibitor reduced caspase-3, -8, and -9, which were activated by OH-dDHL. Pro-inflammatory cytokine and paraoxonase-2 (PON2) gene expression were increased by OH-dDHL. We showed that the anoI-deletion mutant strains have less intracellular invasion compared to the wild-type strain, and their virulence, such as colonization and dissemination, was decreased in vivo. Consequently, these findings revealed that OH-dDHL, as a virulence factor, contributes to bacterial infection and survival as well as the modification of host responses in the early stages of infection.
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Affiliation(s)
- Kyungho Woo
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea; (K.W.); (D.H.K.); (H.S.P.)
| | - Dong Ho Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea; (K.W.); (D.H.K.); (H.S.P.)
| | - Man Hwan Oh
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
| | - Ho Sung Park
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea; (K.W.); (D.H.K.); (H.S.P.)
| | - Chul Hee Choi
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea; (K.W.); (D.H.K.); (H.S.P.)
- Correspondence: ; Tel.: +82-42-580-8246
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Abstract
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.
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da Cruz Nizer WS, Inkovskiy V, Overhage J. Surviving Reactive Chlorine Stress: Responses of Gram-Negative Bacteria to Hypochlorous Acid. Microorganisms 2020; 8:E1220. [PMID: 32796669 PMCID: PMC7464077 DOI: 10.3390/microorganisms8081220] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 01/29/2023] Open
Abstract
Sodium hypochlorite (NaOCl) and its active ingredient, hypochlorous acid (HOCl), are the most commonly used chlorine-based disinfectants. HOCl is a fast-acting and potent antimicrobial agent that interacts with several biomolecules, such as sulfur-containing amino acids, lipids, nucleic acids, and membrane components, causing severe cellular damage. It is also produced by the immune system as a first-line of defense against invading pathogens. In this review, we summarize the adaptive responses of Gram-negative bacteria to HOCl-induced stress and highlight the role of chaperone holdases (Hsp33, RidA, Cnox, and polyP) as an immediate response to HOCl stress. We also describe the three identified transcriptional regulators (HypT, RclR, and NemR) that specifically respond to HOCl. Besides the activation of chaperones and transcriptional regulators, the formation of biofilms has been described as an important adaptive response to several stressors, including HOCl. Although the knowledge on the molecular mechanisms involved in HOCl biofilm stimulation is limited, studies have shown that HOCl induces the formation of biofilms by causing conformational changes in membrane properties, overproducing the extracellular polymeric substance (EPS) matrix, and increasing the intracellular concentration of cyclic-di-GMP. In addition, acquisition and expression of antibiotic resistance genes, secretion of virulence factors and induction of the viable but nonculturable (VBNC) state has also been described as an adaptive response to HOCl. In general, the knowledge of how bacteria respond to HOCl stress has increased over time; however, the molecular mechanisms involved in this stress response is still in its infancy. A better understanding of these mechanisms could help understand host-pathogen interactions and target specific genes and molecules to control bacterial spread and colonization.
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Affiliation(s)
| | | | - Joerg Overhage
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada; (W.S.d.C.N.); (V.I.)
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Ray A, Edmonds KA, Palmer LD, Skaar EP, Giedroc DP. Staphylococcus aureus Glucose-Induced Biofilm Accessory Protein A (GbaA) Is a Monothiol-Dependent Electrophile Sensor. Biochemistry 2020; 59:2882-2895. [PMID: 32697076 DOI: 10.1021/acs.biochem.0c00347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Staphylococcus aureus is a commensal pathogen that has evolved to protect itself from unfavorable conditions by forming complex community structures termed biofilms. The regulation of the formation of these structures is multifactorial and in S. aureus involves a number of transcriptional regulators. GbaA (glucose-induced biofilm accessory protein A) is a tetracycline repressor (TetR) family regulator that harbors two conserved Cys residues (C55 and C104) and impacts the regulation of formation of poly-N-acetylglucosamine-based biofilms in many methicillin-resistant S. aureus (MRSA) strains. Here, we show that GbaA-regulated transcription of a divergently transcribed operon in a MRSA strain can be induced by potent electrophiles, N-ethylmaleimide and methylglyoxal. Strikingly, induction of transcription in cells requires C55 or C104, but not both. These findings are consistent with in vitro small-angle X-ray scattering, chemical modification, and DNA operator binding experiments, which reveal that both reduced and intraprotomer (C55-C104) disulfide forms of GbaA have very similar overall structures and each exhibits a high affinity for the DNA operator, while DNA binding is strongly inhibited by derivatization of one or the other Cys residues via formation of a mixed disulfide with bacillithiol disulfide or a monothiol derivatization adduct with NEM. While both Cys residues are reactive toward electrophiles, C104 in the regulatory domain is the more reactive thiolate. These characteristics enhance the inducer specificity of GbaA and would preclude sensing of generalized cellular oxidative stress via disulfide bond formation. The implications of the findings for GbaA function in MRSA strains are discussed.
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Affiliation(s)
- Abhinaba Ray
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Lauren D Palmer
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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Domingo G, Villa F, Vannini C, Garuglieri E, Onelli E, Bracale M, Cappitelli F. Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium. Front Microbiol 2019; 10:2709. [PMID: 31866956 PMCID: PMC6906586 DOI: 10.3389/fmicb.2019.02709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023] Open
Abstract
Among all the food-related nanoparticles consumed every day, silver nanoparticles (AgNPs) have become one of the most commonly utilized because of their antimicrobial properties. Despite their common use, the effects of sublethal concentrations of AgNPs, especially on gut biofilms, have been poorly investigated. To address this issue, we investigated in vitro the proteomic response of a monospecies Escherichia coli gut biofilm to chronic and acute exposures in sublethal concentrations of AgNPs. We used a new gel- and label-free proteomic approach based on shotgun nanoflow liquid chromatography-tandem mass spectrometry. This approach allows a quantification of the whole proteome at a dynamic range that is higher than the traditional proteomic investigation. To assess all different possible exposure scenarios, we compared the biofilm proteome of four treatments: (i) untreated cells for the control treatment, (ii) cells treated with 1 μg/ml AgNPs for 24 h for the acute treatment, (iii) cells grown with 1 μg/ml AgNPs for 96 h for the chronic treatment, and (iv) cells grown in the presence of 1 μg/ml AgNPs for 72 h and then further treated for 24 h with 10 μg/ml AgNPs for the chronic + acute treatment. Among the 1,917 proteins identified, 212 were significantly differentially expressed proteins. Several pathways were altered including biofilm formation, bacterial adhesion, stress response to reactive oxygen species, and glucose utilization.
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Affiliation(s)
- Guido Domingo
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Candida Vannini
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Elisa Garuglieri
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Onelli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
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