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Carvalho EO, Fernandes MM, Ivanova K, Rodriguez-Lejarraga P, Tzanov T, Ribeiro C, Lanceros-Mendez S. Multifunctional piezoelectric surfaces enhanced with layer-by-layer coating for improved osseointegration and antibacterial performance. Colloids Surf B Biointerfaces 2024; 243:114123. [PMID: 39079183 DOI: 10.1016/j.colsurfb.2024.114123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/17/2024]
Abstract
Implant failure is primarily caused by poor osseointegration and bacterial colonization, which demands readmissions and revision surgeries to correct it. A novel approach involves engineering multifunctional interfaces using piezoelectric polyvinylidene fluoride (PVDF) materials, which mimic bone tissue's electroactive properties to promote bone integration and provide antibacterial functionality when mechanically stimulated. In this study, PVDF films were coated with antibacterial essential oil nanoparticles and antibiofilm enzymes using a layer-by-layer (LBL) approach to ensure antibacterial properties even without mechanical stimulation. The experimental results confirmed the LBL build-up and demonstrated notable antibiofilm properties against Pseudomonas aeruginosa and Staphylococcus aureus while enhancing pre-osteoblast cell proliferation under mechanical dynamic conditions in a bioreactor that replicated the real-life environment of implants within the body. The findings highlight the potential of PVDF-coated surfaces to prevent biofilm formation and boost cell proliferation through the piezoelectric effect, paving the way for advanced implantable devices with improved osseointegration and antibacterial performance.
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Affiliation(s)
- E O Carvalho
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET - Laboratory of Physics for Materials and Emergent Technologies, University of Minho, Braga, 4710-057, Portugal; IB-S - Institute for Research and Innovation on Bio-Sustainability, University of Minho, Braga, 4710-057, Portugal.
| | - M M Fernandes
- LABBELS-Associate Laborator, Braga, Guimarães, Portugal; Centre for MicroElectroMechanics Systems (CMEMS), University of Minho, Guimarães 4710-057, Portugal
| | - K Ivanova
- Group of Molecular and Industrial Biotechnology, Department of Chemical Engineering, Universitat Politècnica de Catalunya, Rambla Sant Nebridi 22, Terrassa 08222, Spain
| | - P Rodriguez-Lejarraga
- BCMaterials, Basque Center Centre for Materials, Applications, and Nanostructures, UPV/EHU Science Park, Leioa 48940, Spain
| | - T Tzanov
- Group of Molecular and Industrial Biotechnology, Department of Chemical Engineering, Universitat Politècnica de Catalunya, Rambla Sant Nebridi 22, Terrassa 08222, Spain
| | - C Ribeiro
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET - Laboratory of Physics for Materials and Emergent Technologies, University of Minho, Braga, 4710-057, Portugal; IB-S - Institute for Research and Innovation on Bio-Sustainability, University of Minho, Braga, 4710-057, Portugal
| | - S Lanceros-Mendez
- Physics Centre of Minho and Porto Universities (CF-UM-UP) and LaPMET - Laboratory of Physics for Materials and Emergent Technologies, University of Minho, Braga, 4710-057, Portugal; BCMaterials, Basque Center Centre for Materials, Applications, and Nanostructures, UPV/EHU Science Park, Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain.
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2
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Babar S, Baloch A, Qasim M, Wang J, Wang X, Li Y, Khalid S, Jiang C. Unearthing the soil-bacteria nexus to enhance potassium bioavailability for global sustainable agriculture: A mechanistic preview. Microbiol Res 2024; 288:127885. [PMID: 39236472 DOI: 10.1016/j.micres.2024.127885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 08/02/2024] [Accepted: 08/25/2024] [Indexed: 09/07/2024]
Abstract
Established as a plant macronutrient, potassium (K) substantially bestows plant growth and thus, global food production. It is absorbed by plants as potassium cation (K+) from soil solution, which is enriched through slow-release from soil minerals or addition of soluble fertilizers. Contribution of bioavailable K+ from soil is usually insignificant (< 2 %), although the earth's crust is rich in K-bearing minerals. However, K is fixed largely in interlayer spaces of K-bearing minerals, which can be released by K-solubilizing bacteria (KSB) such as Bacillus, Pseudomonas, Enterobacter, and Acidithiobacillus. The underlying mechanisms of K dissolution by KSB include acidolysis, ion exchange reactions, chelation, complexolysis, and release of various organic and inorganic acids such as citric, oxalic, acetic, gluconic, and tartaric acids. These acids cause disintegration of K-bearing minerals and bring K+ into soil solution that becomes available to the plants. Current literature review updates the scientific information about microbial species, factors, and mechanisms governing the bio-intrusion of K-bearing minerals. Moreover, it explores the potential of KSB not only for K-solubilization but also to enhance bioavailability of phosphorus, nitrogen, and micronutrients, as well as its other beneficial impact on plant growth. Thus, in the context of sustainable agricultural production and global food security, utilization of KSB may facilitate plant nutrient availability, conserve natural resources, and reduce environmental impacts caused by chemical fertilizers.
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Affiliation(s)
- Saba Babar
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Amanullah Baloch
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Qasim
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Jiyuan Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiangling Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yuxuan Li
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Sarmand Khalid
- Key Laboratory of Horticulture Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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3
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Wang J, Wang Y, Lu S, Lou H, Wang X, Wang W. The protective role of potassium in the adaptation of Pseudomonas protegens SN15-2 to hyperosmotic stress. Microbiol Res 2024; 289:127887. [PMID: 39277942 DOI: 10.1016/j.micres.2024.127887] [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: 06/10/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/17/2024]
Abstract
Pseudomonas protegens is an important biocontrol agent with the ability to suppress plant pathogens and promote plant growth. P. protegens' ability to endure hyperosmotic stress is crucial to its effectiveness as a biocontrol agent. This study elucidated potassium's role and mechanism of action in enabling the hyperosmotic tolerance of P. protegens. Potassium was observed to significantly improve the growth of P. protegens under hyperosmotic conditions. Four functionally redundant potassium transporters, KdpA1, KdpA2, TrkH, and Kup, were identified in P. protegens, of which KdpA2 and TrkH were particularly important for its growth under hyperosmotic conditions. Potassium enhanced the biofilm formation and cell membrane stability of P. protegens under hyperosmotic conditions. In addition, we revealed that K+ stimulates the expression of several genes related to DNA damage repair in P. protegens under hyperosmotic conditions. Further experiments revealed that the DNA repair-related recG induced by potassium contributes to P. protegens' hyperosmotic tolerance. We also found that the sigma factor RpoN participates in the hyperosmotic adaptation of P. protegens. Furthermore, we revealed that the opuCABCD operon, whose expression is induced by potassium through RpoN, serves as the key pathway through which betaine, choline, and carnitine improve the hyperosmotic tolerance of P. protegens.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shouquan Lu
- Shanghai Shuyin Intelligent Technology Co., LTD, Shanghai, China
| | - Haibo Lou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - XiaoBing Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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4
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Werum V, Ehrmann M. Transcriptome responses of Lactococcus paracarnosus to different gas compositions and co-culture with Brochothrix thermosphacta. Int J Food Microbiol 2024; 421:110803. [PMID: 38908220 DOI: 10.1016/j.ijfoodmicro.2024.110803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
Lactococcus (Lc.) paracarnosus and the phylogenetically closely related Lc. carnosus species are common members of the microbiota in meat stored under modified atmosphere and at low temperature. The effect of these strains on meat spoilage is controversially discussed. While some strains are known to cause spoilage, others are being studied for their potential to suppress the growth of spoilage and pathogenic bacteria. In this study, Lc. paracarnosus DSM 111017T was selected based on a previous study for its ability to suppress the growth of meat spoilers, including Brochothrix thermosphacta. The mechanism by which this bioprotective strain inhibits competing bacteria and how it contributes to spoilage are not yet known. To answer these two questions, we investigated the effect of four different headspace gas mixtures (simulated air (21 % O2/79 % N2); HiOx-MAP (70 % O2/30 % CO2); nonOx-MAP (70 % N2/ 30 % CO2); simulated vacuum (100 % N2) and the presence of Brochothrix (B.) thermosphacta TMW 2.2101 on the growth and transcriptional response of Lc. paracarnosus DSM 111017T when cultured on a meat simulation agar surface at 4 °C. Analysis of genes specifically upregulated by the gas mixtures used revealed metabolic pathways that may lead to different levels of spoilage metabolites production. We propose that under elevated oxygen levels, Lc. paracarnosus preferentially converts pyruvate from glucose and glycerol to uncharged acetoin/diacetyl instead of lactate to counteract acid stress. Due to the potential production of a buttery off-flavour, the strain may not be suitable as a protective culture in meat packaged under high‑oxygen conditions. 70 % N2/ 30 % CO2, simulated vacuum- and the presence of Lc. paracarnosus inhibited the growth of B. thermosphacta TMW 2.2101. However, B. thermosphacta did not affect gene regulation of metabolic pathways in Lc. paracarnosus, and genes previously predicted to be involved in B. thermosphacta growth suppression were not regulated at the transcriptional level. In conclusion, the study indicates that the gas mixture used in packaging significantly affects the metabolism and spoilage potential of Lc. paracarnosus and its ability to inhibit B. thermosphacta growth.
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Affiliation(s)
- Victoria Werum
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Matthias Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354 Freising, Germany.
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5
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Hu J, Yao J, Lei C, Sun X. c-di-AMP accumulation impairs toxin expression of Bacillus anthracis by down-regulating potassium importers. Microbiol Spectr 2024; 12:e0378623. [PMID: 38899864 PMCID: PMC11302148 DOI: 10.1128/spectrum.03786-23] [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: 10/31/2023] [Accepted: 04/20/2024] [Indexed: 06/21/2024] Open
Abstract
The Gram-positive bacterium Bacillus anthracis is the causative agent of anthrax and a bioterrorism threat worldwide. As a crucial second messenger in many bacterial species, cyclic di-AMP (c-di-AMP) modulates various key processes for bacterial homeostasis and pathogenesis. Overaccumulation of c-di-AMP alters cellular growth and reduces anthrax toxin expression as well as virulence in Bacillus anthracis by unresolved underlying mechanisms. In this report, we discovered that c-di-AMP binds to a series of receptors involved in potassium uptake in B. anthracis. By analyzing Kdp and Ktr mutants for osmotic stress, gene expression, and anthrax toxin expression, we also showed that c-di-AMP inhibits Kdp operon expression through binding to the KdpD and ydaO riboswitch; up-regulating intracellular potassium promotes anthrax toxin expression in c-di-AMP accumulated B. anthracis. Decreased anthrax toxin expression at high c-di-AMP occurs through the inhibition of potassium uptake. Understanding the molecular basis of how potassium uptake affects anthrax toxin has the potential to provide new insight into the control of B. anthracis.IMPORTANCEThe bacterial second messenger cyclic di-AMP (c-di-AMP) is a conserved global regulator of potassium homeostasis. How c-di-AMP regulates bacterial virulence is unknown. With this study, we provide a link between potassium uptake and anthrax toxin expression in Bacillus anthracis. c-di-AMP accumulation might inhibit anthrax toxin expression by suppressing potassium uptake.
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Affiliation(s)
- Jia Hu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Junmin Yao
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengfeng Lei
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiulian Sun
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
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Viola V, D’Angelo A, Vertuccio L, Catauro M. Metakaolin-Based Geopolymers Filled with Industrial Wastes: Improvement of Physicochemical Properties through Sustainable Waste Recycling. Polymers (Basel) 2024; 16:2118. [PMID: 39125144 PMCID: PMC11313737 DOI: 10.3390/polym16152118] [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: 05/30/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
The increasing global demand for cement significantly impacts greenhouse gas emissions and resource consumption, necessitating sustainable alternatives. This study investigates fresh geopolymer (GP) pastes incorporating 20 wt.% of five industrial wastes-suction dust, red mud from alumina production, electro-filter dust, and extraction sludges from food supplement production and from partially stabilized industrial waste-as potential replacements for traditional cement. Consistent synthesis methods are used to prepare the geopolymers, which are characterized for their physicochemical, mechanical, and biological properties. Ionic conductivity and pH measurements together with integrity tests, thermogravimetry analysis (TGA), and leaching analysis are used to confirm the stability of the synthesized geopolymers. Fourier-transform Infrared (FT-IR) spectroscopy is used to follow geopolymerization occurrences. Results for ionic conductivity, pH, and integrity revealed that the synthesized GPs were macroscopically stable. TGA revealed that the main mass losses were ascribable to water dehydration and to water entrapped in the geopolymer networks. Only the GP filled with the powder of the red mud coming from alumina production experienced a mass loss of 23% due to a partial waste degradation. FT-IR showed a red shift in the main Si-O-(Si or Al) absorption band, indicating successful geopolymer network formations. Additionally, most of the GPs filled with the wastes exhibited higher compressive strength (37.8-58.5 MPa) compared to the control (22 MPa). Only the GP filled with the partially stabilized industrial waste had a lower mechanical strength as its structure was highly porous because of gas formation during geopolymerization reactions. Despite the high compressive strength (58.5 MPa) of the GP filled with suction dust waste, the concentration of Sb leached was 25 ppm, which limits its use. Eventually, all samples also demonstrated effective antimicrobial activity against Escherichia coli and Staphylococcus aureus due to the alkaline environment and the presence of metal cations able to react with the bacterial membranes. The findings revealed the possibility of recycling these wastes within several application fields.
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Affiliation(s)
| | - Antonio D’Angelo
- Department of Engineering, University of Campania “Luigi Vanvitelli”, Via Roma 29, I-81031 Aversa, Italy; (V.V.); (L.V.); (M.C.)
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Vanyan L, Trchounian K. Glucose concentration is determinant for the functioning of hydrogenase 1 and hydrogenase 2 in regulating the proton and potassium fluxes in Escherichia coli at pH 7.5. Biochimie 2024:S0300-9084(24)00172-X. [PMID: 39038731 DOI: 10.1016/j.biochi.2024.07.013] [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: 02/14/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
This study examines how FOF1-ATPase, hydrogenases (Hyd-1 and Hyd-2), and potassium transport systems (TrkA) interact to maintain the proton motive force (pmf) in E. coli during fermentation of different glucose concentrations (2 g L-1 and 8 g L-1). Our findings indicate that mutants lacking the hyaA-hyaC genes exhibited a 30 % increase in total proton flux compared to the wild type when grown with 2 g L-1 glucose. This has been observed during assays where similar glucose levels were supplemented. Disruptions in proton pumping, particularly in hyaB and hyaC single mutants, led to increased potassium uptake. The hyaB mutant showed a threefold increase in the contribution of FOF1-ATPase to proton flux, suggesting a significant role for Hyd-1 in proton translocation. In the hybC mutant grown in 2 g L-1 glucose conditions, DCCD-sensitive fluxes decreased by 70 %, indicating critical role of Hyd-2 in proton transport and FOF1 function. When cells were grown with 8 g L-1 glucose, the 2H+/1K+ ratio was significantly disturbed in both wild type and mutants. Despite these perturbances, mutants with disruptions in Hyd-1 and Hyd-2 maintained constant FOF1 function, suggesting that this enzyme remains stable in glucose-rich environments. These results provide valuable insights into how Hyd-1 and Hyd-2 contribute to the regulation of ion transport, particularly proton translocation, in response to glucose concentration. Our study uncovered potential complementary mechanisms between Hyd-1 and Hyd-2 subunits, suggesting a complex interplay between these enzymes via metabolic cross talk with FOF1 in response to glucose concentrations to maintain pmf.
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Affiliation(s)
- Liana Vanyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 1 A. Manoogian str., 0025, Yerevan, Armenia.
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8
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Ahn S, Choi DHS, Weerawongwiwat V, Kim JH, Sukhoom A, Kim W. Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand. Int J Syst Evol Microbiol 2024; 74:006458. [PMID: 38995165 PMCID: PMC11316597 DOI: 10.1099/ijsem.0.006458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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9
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 PMCID: PMC11332354 DOI: 10.1128/mmbr.00181-23] [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] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J. Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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10
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Brissac T, Guyonnet C, Sadouni A, Hernández-Montoya A, Jacquemet E, Legendre R, Sismeiro O, Trieu-Cuot P, Lanotte P, Tazi A, Firon A. Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B Streptococcus. MICROLIFE 2024; 5:uqae014. [PMID: 38993744 PMCID: PMC11238645 DOI: 10.1093/femsml/uqae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we first report ß-lactam tolerance due to the inactivation of the c-di-AMP phosphodiesterase GdpP. Mechanistically, tolerance depends on antagonistic regulation by the repressor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB osmolyte transporter and the AmaP/Asp23/GlsB cell envelope stress complex. The BusR transcriptional response is synergistic with the simultaneous allosteric inhibition of potassium and osmolyte transporters by c-di-AMP, which individually contribute to low-level ß-lactam tolerance. Genome-wide transposon mutagenesis confirms the role of GdpP and highlights functional interactions between a lysozyme-like hydrolase, the KhpAB RNA chaperone and the protein S immunomodulator in the response of GBS to ß-lactam. Overall, we demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response at the transcriptional and post-translational levels to cell wall weakening caused by ß-lactam activity, and reveal additional mechanisms that could foster resistance.
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Affiliation(s)
- Terry Brissac
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Cécile Guyonnet
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Aymane Sadouni
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Ariadna Hernández-Montoya
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Elise Jacquemet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Odile Sismeiro
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Patrick Trieu-Cuot
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Philippe Lanotte
- Université de Tours, INRAE, UMR 1282 ISP, 3700, Tours, France
- CHRU de Tours, Service de Bactériologie-Virologie, 37044, Tours, France
| | - Asmaa Tazi
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Arnaud Firon
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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11
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Gulati A, Kokane S, Perez-Boerema A, Alleva C, Meier PF, Matsuoka R, Drew D. Structure and mechanism of the K +/H + exchanger KefC. Nat Commun 2024; 15:4751. [PMID: 38834573 PMCID: PMC11150392 DOI: 10.1038/s41467-024-49082-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Intracellular potassium (K+) homeostasis is fundamental to cell viability. In addition to channels, K+ levels are maintained by various ion transporters. One major family is the proton-driven K+ efflux transporters, which in gram-negative bacteria is important for detoxification and in plants is critical for efficient photosynthesis and growth. Despite their importance, the structure and molecular basis for K+-selectivity is poorly understood. Here, we report ~3.1 Å resolution cryo-EM structures of the Escherichia coli glutathione (GSH)-gated K+ efflux transporter KefC in complex with AMP, AMP/GSH and an ion-binding variant. KefC forms a homodimer similar to the inward-facing conformation of Na+/H+ antiporter NapA. By structural assignment of a coordinated K+ ion, MD simulations, and SSM-based electrophysiology, we demonstrate how ion-binding in KefC is adapted for binding a dehydrated K+ ion. KefC harbors C-terminal regulator of K+ conductance (RCK) domains, as present in some bacterial K+-ion channels. The domain-swapped helices in the RCK domains bind AMP and GSH and they inhibit transport by directly interacting with the ion-transporter module. Taken together, we propose that KefC is activated by detachment of the RCK domains and that ion selectivity exploits the biophysical properties likewise adapted by K+-ion-channels.
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Affiliation(s)
- Ashutosh Gulati
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Surabhi Kokane
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Annemarie Perez-Boerema
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Claudia Alleva
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Pascal F Meier
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Rei Matsuoka
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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12
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Saha KK, Mandal S, Barman A, Mondal S, Chatterjee S, Mandal NC. Genomic insight of phosphate solubilization and plant growth promotion of two taxonomically distinct winter crops by Enterobacter sp. DRP3. J Appl Microbiol 2024; 135:lxae146. [PMID: 38877666 DOI: 10.1093/jambio/lxae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
AIMS Study of rhizospheric microbiome-mediated plant growth promotional attributes currently highlighted as a key tool for the development of suitable bio-inoculants for sustainable agriculture purposes. In this context, we have conducted a detailed study regarding the characterization of phosphate solubilizing potential by plant growth-promoting bacteria that have been isolated from the rhizosphere of a pteridophyte Dicranopteris sp., growing on the lateritic belt of West Bengal. METHODS AND RESULTS We have isolated three potent bacterial strains, namely DRP1, DRP2, and DRP3 from the rhizoids-region of Dicranopteris sp. Among the isolated strains, DRP3 is found to have the highest phosphate solubilizing potentiality and is able to produce 655.89 and 627.58 µg ml-1 soluble phosphate by solubilizing tricalcium phosphate (TCP) and Jordan rock phosphate, respectively. This strain is also able to solubilize Purulia rock phosphate moderately (133.51 µg ml-1). Whole-genome sequencing and further analysis of the studied strain revealed the presence of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase gdh gene along with several others that were well known for their role in phosphate solubilization. Further downstream, quantitative reverse transcriptase PCR-based expression study revealed 1.59-fold upregulation of PQQ-dependent gdh gene during the solubilization of TCP. Root colonization potential of the studied strain on two taxonomically distinct winter crops viz. Cicer arietinum and Triticum aestivum has been checked by using scanning electron microscopy. Other biochemical analyses for plant growth promotion traits including indole acetic acid production (132.02 µg ml-1), potassium solubilization (3 mg l-1), biofilm formation, and exopolymeric substances productions (1.88-2.03 µg ml-1) also has been performed. CONCLUSION This study highlighted the active involvement of PQQ-dependent gdh gene during phosphate solubilization from any Enterobacter group. Moreover, our study explored different roadmaps for sustainable farming methods and the preservation of food security without endangering soil health in the future.
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Affiliation(s)
- Kunal Kumar Saha
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Subhrangshu Mandal
- Stress Physiology and Environmental Microbiology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sangita Mondal
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
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13
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Rubin-Blum M, Makovsky Y, Rahav E, Belkin N, Antler G, Sisma-Ventura G, Herut B. Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106497. [PMID: 38631226 DOI: 10.1016/j.marenvres.2024.106497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024]
Abstract
Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.
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Affiliation(s)
- Maxim Rubin-Blum
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
| | - Yizhaq Makovsky
- The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel; The Hatter Department of Marine Technologies, Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Natalia Belkin
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gilad Antler
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; The Interuniversity Institute for Marine Sciences, Eilat, Israel
| | - Guy Sisma-Ventura
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Barak Herut
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel
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14
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Babayan A, Vassilian A, Poladyan A, Trchounian K. Role of the Escherichia coli FocA and FocB formate channels in controlling proton/potassium fluxes and hydrogen production during osmotic stress in energy-limited, stationary phase fermenting cells. Biochimie 2024; 221:91-98. [PMID: 38307245 DOI: 10.1016/j.biochi.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
Escherichia coli FocA and FocB formate channels export formate or import it for further disproportionation by the formate hydrogenlyase (FHL) complex to H2 and CO2. Here, we show that under pH and osmotic stress FocA and FocB play important roles in regulating proton and potassium fluxes and couple this with H2 production in stationary-phase cells. Using whole-cell assays with glucose as electron donor, a focB mutant showed a 50 % decrease in VH2, while N'N'-dicyclohexylcarbodiimide (DCCD) treatment of osmotically stressed cells underlined the role of FOF1 ATPase in H2 production. At pH 7.5 and under osmotic stress FocB contributed to the proton flux but not to the potassium flux. At pH 5.5 both formate channels contributed to the proton and potassium fluxes. Particulalry, a focA mutant had 40 % lower potassium flux whereas the proton flux increased approximately two-fold. Moreover, at pH 5.5H2 production was totally inhibited by DCCD in the focA mutant. Taken together, our results suggest that depending on external pH, the formate channels play an important role in osmoregulation by helping to balance proton/potassium fluxes and H2 production, and thus assist the proton FOF1-ATPase in maintenance of ion gradients in fermenting stationary-phase cells.
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Affiliation(s)
- A Babayan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - A Vassilian
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - A Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - K Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia.
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15
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Chiang WT, Chang YK, Hui WH, Chang SW, Liao CY, Chang YC, Chen CJ, Wang WC, Lai CC, Wang CH, Luo SY, Huang YP, Chou SH, Horng TL, Hou MH, Muench SP, Chen RS, Tsai MD, Hu NJ. Structural basis and synergism of ATP and Na + activation in bacterial K + uptake system KtrAB. Nat Commun 2024; 15:3850. [PMID: 38719864 PMCID: PMC11078986 DOI: 10.1038/s41467-024-48057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na+ activates KtrAB and the Na+ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na+, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na+ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K+ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na+ in activating BsKtrAB is likely applicable to Na+-activated K+ channels in central nervous system.
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Affiliation(s)
- Wesley Tien Chiang
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Wei-Han Hui
- Department of Civil Engineering, National Taiwan University, Taipei, 106319, Taiwan
| | - Shu-Wei Chang
- Department of Civil Engineering, National Taiwan University, Taipei, 106319, Taiwan
- Department of Biomedical Engineering, National Taiwan University, Taipei, 10663, Taiwan
| | - Chen-Yi Liao
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Yi-Chuan Chang
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30092, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402202, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, 406040, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Siou-Ying Luo
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Ya-Ping Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Shan-Ho Chou
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Tzyy-Leng Horng
- Department of Applied Mathematics, Feng Chia University, Taichung, 407102, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ren-Shiang Chen
- Department of Life Science, Tunghai University, Taichung, 407224, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan.
| | - Nien-Jen Hu
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan.
- Ph.D Program in Translational Medicine, National Chung Hsing University, Taichung, 402202, Taiwan.
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16
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Rocha R, Jorge JMP, Teixeira-Duarte CM, Figueiredo-Costa IR, Cereija TB, Ferreira-Teixeira PF, Herzberg C, Stülke J, Morais-Cabral JH. c-di-AMP determines the hierarchical organization of bacterial RCK proteins. Proc Natl Acad Sci U S A 2024; 121:e2318666121. [PMID: 38652747 PMCID: PMC11067040 DOI: 10.1073/pnas.2318666121] [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: 10/25/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
In bacteria, intracellular K+ is involved in the regulation of membrane potential, cytosolic pH, and cell turgor as well as in spore germination, environmental adaptation, cell-to-cell communication in biofilms, antibiotic sensitivity, and infectivity. The second messenger cyclic-di-AMP (c-di-AMP) has a central role in modulating the intracellular K+ concentration in many bacterial species, controlling transcription and function of K+ channels and transporters. However, our understanding of how this regulatory network responds to c-di-AMP remains poor. We used the RCK (Regulator of Conductance of K+) proteins that control the activity of Ktr channels in Bacillus subtilis as a model system to analyze the regulatory function of c-di-AMP with a combination of in vivo and in vitro functional and structural characterization. We determined that the two RCK proteins (KtrA and KtrC) are neither physiologically redundant or functionally equivalent. KtrC is the physiologically dominant RCK protein in the regulation of Ktr channel activity. In explaining this hierarchical organization, we found that, unlike KtrA, KtrC is very sensitive to c-di-AMP inactivation and lack of c-di-AMP regulation results in RCK protein toxicity, most likely due to unregulated K+ flux. We also found that KtrC can assemble with KtrA, conferring c-di-AMP regulation to the functional KtrA/KtrC heteromers and potentially compensating KtrA toxicity. Altogether, we propose that the central role of c-di-AMP in the control of the K+ machinery, by modulating protein levels through gene transcription and by regulating protein activity, has determined the evolutionary selection of KtrC as the dominant RCK protein, shaping the hierarchical organization of regulatory components of the K+ machinery.
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Affiliation(s)
- Rita Rocha
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto4200-135, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto4200-135, Portugal
| | - João M. P. Jorge
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto4200-135, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto4200-135, Portugal
| | - Celso M. Teixeira-Duarte
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto4200-135, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto4200-135, Portugal
| | | | - Tatiana B. Cereija
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto4200-135, Portugal
| | | | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen37073, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen37073, Germany
| | - João H. Morais-Cabral
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto4200-135, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto4200-135, Portugal
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17
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Ruppelt D, Trollmann MFW, Dema T, Wirtz SN, Flegel H, Mönnikes S, Grond S, Böckmann RA, Steinem C. The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes. Nat Commun 2024; 15:3521. [PMID: 38664456 PMCID: PMC11045845 DOI: 10.1038/s41467-024-47803-6] [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: 06/13/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Recently, a novel cyclo-heptapeptide composed of alternating D,L-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential. However, the precise mode of action of this new class of fibupeptides remains largely elusive. Here, we disclose the mechanism by which lugdunin rapidly destabilizes the bacterial membrane potential using an in vitro approach. The peptide strongly partitions into lipid compositions resembling Gram-positive bacterial membranes but less in those harboring the eukaryotic membrane component cholesterol. Upon insertion, lugdunin forms hydrogen-bonded antiparallel β-sheets by the formation of peptide nanotubes, as demonstrated by ATR-FTIR spectroscopy and molecular dynamics simulations. These hydrophilic nanotubes filled with a water wire facilitate not only the translocation of protons but also of monovalent cations as demonstrated by voltage-clamp experiments on black lipid membranes. Collectively, our results provide evidence that the natural fibupeptide lugdunin acts as a peptidic channel that is spontaneously formed by an intricate stacking mechanism, leading to the dissipation of a bacterial cell's membrane potential.
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Affiliation(s)
- Dominik Ruppelt
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Marius F W Trollmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Sebastian N Wirtz
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Hendrik Flegel
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Sophia Mönnikes
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany.
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
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18
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Ahn S, Weerawongwiwat V, Lee Y, Choi DHS, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast. Curr Microbiol 2024; 81:150. [PMID: 38647555 DOI: 10.1007/s00284-024-03681-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024]
Abstract
A Gram-stain-negative, aerobic, rod-shaped, motile, flagellated bacterial strain, designated as CAU 1639T, was isolated from the tidal flat sediment on the Yellow Sea in the Republic of Korea. Growth of the isolate was observed at 20-37 °C, at pH 5.0-10.5 and with 0-7% (w/v) NaCl. The genomic DNA G + C content was 60.8%. Phylogenetic analysis, grounded on 16S rRNA gene sequencing, revealed that strain CAU 1639T was closely related to species within the genus Roseibium. It shared the highest similarity with Roseibium album CECT 5095T, followed by Roseibium aggregatum IAM 12614T and Roseibium salinum Cs25T, with 16S rRNA gene sequence similarity ranging from 98.0-98.4%. It was observed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values ranged between 72.5-79.5 and 20.0-22.9%, respectively. The polyphasic taxonomic analysis reveals that strain CAU 1639T represents a novel species in the genus Roseibium with the proposed name Roseibium sediminicola sp. nov. The type strain is CAU 1639T (= KCTC 82430T = MCCC 1K06081T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Yunjeong Lee
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jung-Sook Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea.
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19
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Silberberg JM, Ketter S, Böhm PJN, Jordan K, Wittenberg M, Grass J, Hänelt I. KdpD is a tandem serine histidine kinase that controls K + pump KdpFABC transcriptionally and post-translationally. Nat Commun 2024; 15:3223. [PMID: 38622146 PMCID: PMC11018627 DOI: 10.1038/s41467-024-47526-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Two-component systems, consisting of a histidine kinase and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a histidine kinase of the KdpDE two-component system, which controls production of the potassium pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high potassium levels, using not its C-terminal histidine kinase domain but an N-terminal atypical serine kinase domain. Sequence analysis of KdpDs from different species highlights that some KdpDs are much shorter than others. We show that, while Escherichia coli KdpD's atypical serine kinase domain responds directly to potassium levels, a shorter version from Deinococcus geothermalis is controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial potassium homeostasis.
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Affiliation(s)
- Jakob M Silberberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Sophie Ketter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Paul J N Böhm
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Kristin Jordan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Marcel Wittenberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Julia Grass
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany.
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20
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Okabe S, Kamizono A, Zhang L, Kawasaki S, Kobayashi K, Oshiki M. Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5357-5371. [PMID: 38491939 DOI: 10.1021/acs.est.3c07324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
The salinity tolerance and osmoadaptation strategies in four phylogenetically distant anammox species, Brocadia, Jettenia, Kuenenia, and Scalindua, were investigated by using highly enriched cell cultures. The first-emerged "Ca. Scalindua sp." showed optimum growth at 1.5-3% salinity and was tolerant to ∼10% salinity (a slight halophile). The second-emerged "Ca. Kuenenia stuttgartiensis" was tolerant to ∼6% salinity with optimum growth at 0.25-1.5% (a halotolerant). These early-emerged "Ca. Scalindua sp." and ″Ca. K. stuttgartiensis" rapidly accumulated K+ ions and simultaneously synthesized glutamate as a counterion. Subsequently, part of the glutamate was replaced by trehalose. In contrast, the late-emerged "Ca. B. sinica" and "Ca. J. caeni" were unable to accumulate sufficient amounts of K+─glutamate and trehalose, resulting in a significant decrease in activity even at 1-2% salinity (nonhalophiles). In addition, the external addition of glutamate may increase anammox activity at high salinity. The species-dependent salinity tolerance and osmoadaptation strategies were consistent with the genetic potential required for the biosynthesis and transport of these osmolytes and the evolutionary history of anammox bacteria: Scalindua first emerged in marine environments and then Kuenenia and other two species gradually expanded their habitat to estuaries, freshwater, and terrestrial environments, while Brocadia and Jettenia likely lost their ability to accumulate K+─glutamate.
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Affiliation(s)
- Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akimichi Kamizono
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Seiya Kawasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Kanae Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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21
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Nikolaidou C, Mola M, Papakostas S, Aschonitis VG, Monokrousos N, Kougias PG. The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-32850-9. [PMID: 38517633 DOI: 10.1007/s11356-024-32850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.
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Affiliation(s)
- Charitini Nikolaidou
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Magkdi Mola
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Spiros Papakostas
- Department of Science and Technology, International Hellenic University, 57001, Thessaloniki, Greece
| | - Vassilis G Aschonitis
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
| | - Nikolaos Monokrousos
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Panagiotis G Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece.
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22
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Wan J, Dai L, Xiao H, Zhang W, Zhang R, Xie T, Jia Y, Gao X, Huang J, Liu F. Biological characteristics of mechanosensitive channels MscS and MscL in Actinobacillus pleuropneumoniae. J Bacteriol 2024; 206:e0042923. [PMID: 38391161 PMCID: PMC10955882 DOI: 10.1128/jb.00429-23] [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: 12/14/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Actinobacillus pleuropneumoniae is an important respiratory pathogen that can cause porcine contagious pleuropneumonia (PCP), resulting in significant economic losses in swine industry. Microorganisms are subjected to drastic changes in environmental osmolarity. In order to alleviate the drastic rise or fall of osmolarity, cells activate mechanosensitive channels MscL and MscS through tension changes. MscL not only regulates osmotic pressure but also has been reported to secrete protein and uptake aminoglycoside antibiotic. However, MscL and MscS, as the most common mechanosensitive channels, have not been characterized in A. pleuropneumoniae. In this study, the osmotic shock assay showed that MscL increased sodium adaptation by regulating cell length. The results of MIC showed that deletion of mscL decreased the sensitivity of A. pleuropneumoniae to multiple antibiotics, while deletion of mscS rendered A. pleuropneumoniae hypersensitive to penicillin. Biofilm assay demonstrated that MscL contributed the biofilm formation but MscS did not. The results of animal assay showed that MscL and MscS did not affect virulence in vivo. In conclusion, MscL is essential for sodium hyperosmotic tolerance, biofilm formation, and resistance to chloramphenicol, erythromycin, penicillin, and oxacillin. On the other hand, MscS is only involved in oxacillin resistance.IMPORTANCEBacterial resistance to the external environment is a critical function that ensures the normal growth of bacteria. MscL and MscS play crucial roles in responding to changes in both external and internal environments. However, the function of MscL and MscS in Actinobacillus pleuropneumoniae has not yet been reported. Our study shows that MscL plays a significant role in osmotic adaptation, antibiotic resistance, and biofilm formation of A. pleuropneumoniae, while MscS only plays a role in antibiotic resistance. Our findings provide new insights into the functional characteristics of MscL and MscS in A. pleuropneumoniae. MscL and MscS play a role in antibiotic resistance and contribute to the development of antibiotics for A. pleuropneumoniae.
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Affiliation(s)
- Jiajia Wan
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Lu Dai
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Huasong Xiao
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Wendie Zhang
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Rui Zhang
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Tingting Xie
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Yizhen Jia
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Xuejun Gao
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
| | - Jing Huang
- College of Arts and Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Feng Liu
- College of Animal Science and Technology, Yangtze University, Jingzhou, Hubei, China
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23
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Gao J, Zhou K, Li H, Li Y, Yang K, Wang W. Intermittent proton bursts of single lactic acid bacteria. Chem Sci 2024; 15:3516-3523. [PMID: 38455010 PMCID: PMC10915832 DOI: 10.1039/d3sc06238d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
Lactic acid bacteria are a kind of probiotic microorganisms that efficiently convert carbohydrates to lactic acids, thus playing essential roles in fermentation and food industry. While conventional wisdom often suggests continuous release of protons from bacteria during acidification, here we developed a methodology to measure the dynamics of proton release at the single bacteria level, and report on the discovery of a proton burst phenomenon, i.e., the intermittent efflux of protons, of single Lactobacillus plantarum bacteria. When placing an individual bacterium in an oil-sealed microwell, efflux and accumulation of protons consequently reduced the pH in the confined extracellular medium, which was monitored with fluorescent pH indicators in a high-throughput and real-time manner. In addition to the slow and continuous proton release behavior (as expected), stochastic and intermittent proton burst events were surprisingly observed with a typical timescale of several seconds. It was attributed to the regulatory response of bacteria by activating H+-ATPase to compensate the stochastic and transient depolarizations of membrane potential. These findings not only revealed an unprecedented proton burst phenomenon in lactic acid bacteria, but also shed new lights on the intrinsic roles of H+-ATPase in membrane potential homeostasis, with implications for both fermentation industry and bacterial electrophysiology.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kai Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kairong Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
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24
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Warsi OM, Upterworth LM, Breidenstein A, Lustig U, Mikkelsen K, Nagy T, Szatmari D, Ingmer H, Andersson DI. Staphylococcus aureus mutants resistant to the feed-additive monensin show increased virulence and altered purine metabolism. mBio 2024; 15:e0315523. [PMID: 38214510 PMCID: PMC10865815 DOI: 10.1128/mbio.03155-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Ionophores are antibacterial compounds that affect bacterial growth by changing intracellular concentrations of the essential cations, sodium and potassium. They are extensively used in animal husbandry to increase productivity and reduce infectious diseases, but our understanding of the potential for and effects of resistance development to ionophores is poorly known. Thus, given their widespread global usage, it is important to determine the potential negative consequences of ionophore use on human and animal health. In this study, we demonstrate that exposure to the ionophore monensin can select for resistant mutants in the human and animal pathogen Staphylococcus aureus, with a majority of the resistant mutants showing increased growth rates in vitro and/or in mice. Whole-genome sequencing and proteomic analysis of the resistant mutants show that the resistance phenotype is associated with de-repression of de novo purine synthesis, which could be achieved through mutations in different transcriptional regulators including mutations in the gene purR, the repressor of the purine de novo synthesis pathway. This study shows that mutants with reduced susceptibility to the ionophore monensin can be readily selected and highlights an unexplored link between ionophore resistance, purine metabolism, and fitness in pathogenic bacteria.IMPORTANCEThis study demonstrates a novel link between ionophore resistance, purine metabolism, and virulence/fitness in the key human and animal pathogen Staphylococcus aureus. The results show that mutants with reduced susceptibility to the commonly used ionophore monensin can be readily selected and that the reduced susceptibility observed is associated with an increased expression of the de novo purine synthesis pathway. This study increases our understanding of the impact of the use of animal feed additives on both human and veterinary medicine.
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Affiliation(s)
- Omar M. Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lina M. Upterworth
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Annika Breidenstein
- Department of Medical Chemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamás Nagy
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Dávid Szatmari
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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25
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Upadhyaya C, Patel H, Patel I, Ahir P, Upadhyaya T. Development of Biological Coating from Novel Halophilic Exopolysaccharide Exerting Shelf-Life-Prolonging and Biocontrol Actions for Post-Harvest Applications. Molecules 2024; 29:695. [PMID: 38338439 PMCID: PMC10856335 DOI: 10.3390/molecules29030695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The literature presents the preserving effect of biological coatings developed from various microbial sources. However, the presented work exhibits its uniqueness in the utilization of halophilic exopolysaccharides as food coating material. Moreover, such extremophilic exopolysaccharides are more stable and economical production is possible. Consequently, the aim of the presented research was to develop a coating material from marine exopolysaccharide (EPS). The significant EPS producers having antagonistic attributes against selected phytopathogens were screened from different marine water and soil samples. TSIS01 isolate revealed the maximum antagonism well and EPS production was selected further and characterized as Bacillus tequilensis MS01 by 16S rRNA analysis. EPS production was optimized and deproteinized EPS was assessed for biophysical properties. High performance thin layer chromatography (HPTLC) analysis revealed that EPS was a heteropolymer of glucose, galactose, mannose, and glucuronic acid. Fourier transform infrared spectroscopy, X-ray diffraction, and UV-visible spectra validated the presence of determined sugars. It showed high stability at a wide range of temperatures, pH and incubation time, ≈1.63 × 106 Da molecular weight, intermediate solubility index (48.2 ± 3.12%), low water holding capacity (12.4 ± 1.93%), and pseudoplastic rheologic shear-thinning comparable to xanthan gum. It revealed antimicrobial potential against human pathogens and antioxidants as well as anti-inflammatory potential. The biocontrol assay of EPS against phytopathogens revealed the highest activity against Alternaria solani. The EPS-coated and control tomato fruits were treated with A. solani suspension to check the % disease incidence, which revealed a significant (p < 0.001) decline compared to uncoated controls. Moreover, it revealed shelf-life prolonging action on tomatoes comparable to xanthan gum and higher than chitosan. Consequently, the presented marine EPS was elucidated as a potent coating material to mitigate post-harvest losses.
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Affiliation(s)
- Chandni Upadhyaya
- School of Sciences, P. P. Savani University, Surat 394125, Gujarat, India
| | - Hiren Patel
- School of Sciences, P. P. Savani University, Surat 394125, Gujarat, India
- School of Agriculture, P. P. Savani University, Surat 394125, Gujarat, India
| | - Ishita Patel
- Shree P. M. Patel Institute of Integrated M. Sc. in Biotechnology, Sardar Patel University, Anand 388001, Gujarat, India
| | - Parth Ahir
- Shree P. M. Patel Institute of P. G. Studies in Research and Sciences, Sardar Patel University, Anand 388001, Gujarat, India
| | - Trushit Upadhyaya
- Chandubhai S. Patel Institute of Technology, Charotar University of Science & Technology, Changa, Anand 388421, Gujarat, India;
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26
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König P, Averhoff B, Müller V. K + homeostasis is important for survival of Acinetobacter baumannii ATCC 19606 in the nosocomial environment. Int Microbiol 2024; 27:303-310. [PMID: 37338636 PMCID: PMC10830791 DOI: 10.1007/s10123-023-00389-3] [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: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Pathogenic bacteria have developed several mechanisms to thrive within the hostile environment of the human host, but it is often disregarded that their survival outside this niche is crucial for their successful transmission. Acinetobacter baumannii is very well adapted to both the human host and the hospital environment. The latter is facilitated by multifactorial mechanisms including its outstanding ability to survive on dry surfaces, its high metabolic diversity, and, of course, its remarkable osmotic resistance. As a first response to changing osmolarities, bacteria accumulate K+ in high amount to counterbalance the external ionic strength. Here, we addressed whether K+ uptake is involved in the challenges imposed by the harsh conditions outside its host and how K+ import influences the antibiotic resistance of A. baumannii. For this purpose, we used a strain lacking all major K+ importer ∆kup∆trk∆kdp. Survival of this mutant was strongly impaired under nutrient limitation in comparison to the wild type. Furthermore, we found that not only the resistance against copper but also against the disinfectant chlorhexidine was reduced in the triple mutant compared to the wild type. Finally, we revealed that the triple mutant is highly susceptible to a broad range of antibiotics and antimicrobial peptides. By studying mutants, in which the K+ transporter were deleted individually, we provide evidence that this effect is a consequence of the altered K+ uptake machinery. Conclusively, this study provides supporting information on the relevance of K+ homeostasis in the adaptation of A. baumannii to the nosocomial environment.
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Affiliation(s)
- Patricia König
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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27
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Kojima D, Tanaka S, Kurosaki A, Zhiyu X, Ito M. Isolation and Cs + resistance mechanism of Escherichia coli strain ZX-1. Front Microbiol 2024; 14:1340033. [PMID: 38304862 PMCID: PMC10831881 DOI: 10.3389/fmicb.2023.1340033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024] Open
Abstract
This research aims to elucidate the physiological mechanisms behind the accidental acquisition of high-concentration cesium ions (Cs+) tolerance of Escherichia coli and apply this understanding to develop bioremediation technologies. Bacterial Cs+ resistance has attracted attention, but its physiological mechanism remains largely unknown and poorly understood. In a prior study, we identified the Cs+/H+ antiporter TS_CshA in Microbacterium sp. TS-1, resistant to high Cs+ concentrations, exhibits a low Cs+ affinity with a Km value of 370 mM at pH 8.5. To enhance bioremediation efficacy, we conducted random mutagenesis of TS_cshA using Error-Prone PCR, aiming for higher-affinity mutants. The mutations were inserted downstream of the PBAD promoter in the pBAD24 vector, creating a mutant library. This was then transformed into E. coli-competent cells. As a result, we obtained a Cs+-resistant strain, ZX-1, capable of thriving in 400 mM CsCl-a concentration too high for ordinary E. coli. Unlike the parent strain Mach1™, which struggled in 300 mM CsCl, ZX-1 showed robust growth even in 700 mM CsCl. After 700 mM CsCl treatment, the 70S ribosome of Mach1™ collapsed, whereas ZX-1 and its derivative ΔZX-1/pBR322ΔAp remained stable. This means that the ribosomes of ZX-1 are more stable to high Cs+. The inverted membrane vesicles from strain ZX-1 showed an apparent Km value of 28.7 mM (pH 8.5) for Cs+/H+ antiport activity, indicating an approximately 12.9-fold increase in Cs+ affinity. Remarkably, the entire plasmid isolated from ZX-1, including the TS_cshA region, was mutation-free. Subsequent whole-genome analysis of ZX-1 identified multiple SNPs on the chromosome that differed from those in the parent strain. No mutations in transporter-related genes were identified in ZX-1. However, three mutations emerged as significant: genes encoding the ribosomal bS6 modification enzyme RimK, the phage lysis regulatory protein LysB, and the flagellar base component protein FlgG. These mutations are hypothesized to affect post-translational modifications, influencing the Km value of TS_CshA and accessory protein expression. This study unveils a novel Cs+ resistance mechanism in ZX-1, enhancing our understanding of Cs+ resistance and paving the way for developing technology to recover radioactive Cs+ from water using TS_CshA-expressing inverted membrane vesicles.
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Affiliation(s)
- Daiki Kojima
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Shunsuke Tanaka
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Ayane Kurosaki
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Xiong Zhiyu
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe, Saitama, Japan
- Bio-Resilience Research Project (BRRP), Toyo University, Oura-gun, Gunma, Japan
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28
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Zhao D, Zhang S, Chen J, Zhao J, An P, Xiang H. Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea. THE ISME JOURNAL 2024; 18:wrad033. [PMID: 38366248 PMCID: PMC10873845 DOI: 10.1093/ismejo/wrad033] [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: 10/08/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 02/18/2024]
Abstract
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Sichuan Normal University, Sichuan 610068, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Benavente D, Saiz-Jimenez C, Sanchez-Moral S. Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls. Microbiol Res 2023; 277:127511. [PMID: 37852679 DOI: 10.1016/j.micres.2023.127511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, 28805 Madrid, Spain.
| | | | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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Zhu X, Baranowski E, Hao Z, Li X, Zhao G, Dong Y, Chen Y, Hu C, Chen H, Citti C, Wang A, Guo A. An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis. Front Microbiol 2023; 14:1250368. [PMID: 38098652 PMCID: PMC10720645 DOI: 10.3389/fmicb.2023.1250368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Nucleotide second messengers play an important role in bacterial adaptation to environmental changes. Recent evidence suggests that some of these regulatory molecular pathways were conserved upon the degenerative evolution of the wall-less mycoplasmas. We have recently reported the occurrence of a phosphodiesterase (PDE) in the ruminant pathogen Mycoplasma bovis, which was involved in c-di-AMP metabolism. In the present study, we demonstrate that the genome of this mycoplasma species encodes a PDE of the GdpP family with atypical DHH domains. Characterization of M. bovis GdpP (MbovGdpP) revealed a multifunctional PDE with unusual nanoRNase and single-stranded DNase activities. The alarmone ppGpp was found unable to inhibit c-di-NMP degradation by MbovGdpP but efficiently blocked its nanoRNase activity. Remarkably, MbovGdpP was found critical for the osmotic tolerance of M. bovis under K+ and Na+ conditions. Transcriptomic analyses further revealed the biological importance of MbovGdpP in tRNA biosynthesis, pyruvate metabolism, and several steps in genetic information processing. This study is an important step in understanding the role of PDE and nucleotide second messengers in the biology of a minimal bacterial pathogen.
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Affiliation(s)
- Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xixi Li
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaqi Dong
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
| | | | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
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Herzberg C, Meißner J, Warneke R, Stülke J. The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis. MICROLIFE 2023; 4:uqad043. [PMID: 37954098 PMCID: PMC10636490 DOI: 10.1093/femsml/uqad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023]
Abstract
The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis as well as in many bacteria and archaea. Bacillus subtilis possesses three diadenylate cyclases and two phosphodiesterases that synthesize and degrade the molecule, respectively. Among the second messengers, c-di-AMP is unique since it is essential for B. subtilis on the one hand but toxic upon accumulation on the other. This role as an "essential poison" is related to the function of c-di-AMP in the control of potassium homeostasis. C-di-AMP inhibits the expression and activity of potassium uptake systems by binding to riboswitches and transporters and activates the activity of potassium exporters. In this way, c-di-AMP allows the adjustment of uptake and export systems to achieve a balanced intracellular potassium concentration. C-di-AMP also binds to two dedicated signal transduction proteins, DarA and DarB. Both proteins seem to interact with other proteins in their apo state, i.e. in the absence of c-di-AMP. For DarB, the (p)ppGpp synthetase/hydrolase Rel and the pyruvate carboxylase PycA have been identified as targets. The interactions trigger the synthesis of the alarmone (p)ppGpp and of the acceptor molecule for the citric acid cycle, oxaloacetate, respectively. In the absence of c-di-AMP, many amino acids inhibit the growth of B. subtilis. This feature can be used to identify novel players in amino acid homeostasis. In this review, we discuss the different functions of c-di-AMP and their physiological relevance.
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Affiliation(s)
- Christina Herzberg
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Janek Meißner
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
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Gevorgyan H, Abaghyan T, Mirumyan M, Yenkoyan K, Trchounian K. Propionic and valproic acids have an impact on bacteria viability, proton flux and ATPase activity. J Bioenerg Biomembr 2023; 55:397-408. [PMID: 37700074 DOI: 10.1007/s10863-023-09983-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Short-chain fatty acids like propionic (PPA) and valproic acids (VP) can alter gut microbiota, which is suggested to play a role in development of autism spectrum disorders (ASD). In this study we investigated the role of various concentrations of PPA and VP in gut enteric gram-negative Escherichia coli K12 and gram-positive Enterococcus hirae ATCC 9790 bacteria growth properties, ATPase activity and proton flux. The specific growth rate (µ) was 0.24 h-1 and 0.82 h-1 in E. coli and E. hirae, respectively. Different concentrations of PPA reduced the value of µ similarly in both strains. PPA affects membrane permeability only in E. hirae. PPA decreased DCCD-sensitive ATPase activity in the presence of K+ ions by 20% in E. coli and 40% in E. hirae suggesting the importance of the FOF1-K+ transport system in the regulation of PPA-disrupted homeostasis. Moreover, the H+ flux during PPA consumption could be the protective mechanism for enteric bacteria. VP has a selective effect on the µ depending on bacteria. The overwhelming effect of VP was detected on the K+-promoted ATPase activity in E. hirae. Taken together it can be suggested that PPA and VP have a disruptive effect on E. coli and E. hirae growth, viability, bioenergetic and biochemical properties, which are connected with the alteration of FOF1-ATPase activity and H+ flux rate or direction.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
| | - Tamara Abaghyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Margarita Mirumyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Konstantin Yenkoyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia.
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia.
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia.
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Chen L, Wang C, Su J. Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis. Microorganisms 2023; 11:2401. [PMID: 37894061 PMCID: PMC10609351 DOI: 10.3390/microorganisms11102401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.
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Affiliation(s)
- Liping Chen
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Chenglong Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jianyu Su
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
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34
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Wan J, Zhang R, Jia Y, Xie T, Dai L, Yao Q, Zhang W, Xiao H, Gao X, Huang J, Bei W, Liu F. The two-component system CpxAR is required for the high potassium stress survival of Actinobacillus pleuropneumoniae. Front Microbiol 2023; 14:1259935. [PMID: 37822748 PMCID: PMC10562621 DOI: 10.3389/fmicb.2023.1259935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Actinobacillus pleuropneumoniae is an important respiratory pathogen, which can cause porcine contagious pleuropneumonia and lead to great economic losses to worldwide swine industry. High potassium is an adverse environment for bacteria, which is not conducive to providing turgor pressure for cell growth and division. Two-component system CpxAR is an important regulatory system of bacteria in response to environmental changes, which is involved in a variety of biological activities, such as antibiotic resistance, periplasmic protein folding, peptidoglycan metabolism and so on. Methods However, little is known about the role of CpxAR in high potassium stress in A. pleuropneumoniae. Here, we showed that CpxAR is critical for cell division of A. pleuropneumoniae under high potassium (K+) stress. Results qRT-PCR analysis found that CpxAR positively regulated the cell division genes ftsEX. In addition, we also demonstrated that CpxR-P could directly bind the promoter region of the cell division gene ftsE by EMSA. Discussion In conclusion, our results described a mechanism where CpxAR adjusts A. pleuropneumoniae survival under high-K+ stress by upregulating the expression of the cell division proteins FtsE and FtsX. These findings are the first to directly demonstrate CpxAR-mediated high-K+ tolerance, and to investigate the detailed molecular mechanism.
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Affiliation(s)
- Jiajia Wan
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Rui Zhang
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Yizhen Jia
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Tingting Xie
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Lu Dai
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Qing Yao
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Wendie Zhang
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Huasong Xiao
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Xuejun Gao
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Jing Huang
- College of Arts and Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Liu
- College of Animal Sciences, Yangtze University, Jingzhou, Hubei, China
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35
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Benyamin MS, Perisin MP, Hellman CA, Schwalm ND, Jahnke JP, Sund CJ. Modeling control and transduction of electrochemical gradients in acid-stressed bacteria. iScience 2023; 26:107140. [PMID: 37404371 PMCID: PMC10316662 DOI: 10.1016/j.isci.2023.107140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.
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Affiliation(s)
- Marcus S. Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Matthew P. Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Caleb A. Hellman
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Nathan D. Schwalm
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Justin P. Jahnke
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Christian J. Sund
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
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36
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Fuss MF, Wieferig JP, Corey RA, Hellmich Y, Tascón I, Sousa JS, Stansfeld PJ, Vonck J, Hänelt I. Cyclic di-AMP traps proton-coupled K + transporters of the KUP family in an inward-occluded conformation. Nat Commun 2023; 14:3683. [PMID: 37344476 DOI: 10.1038/s41467-023-38944-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Cyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. In Bacillus subtilis, the K+/H+ symporter KimA of the KUP family is inactivated by c-di-AMP. KimA sustains survival at potassium limitation at low external pH by mediating potassium ion uptake. However, at elevated intracellular K+ concentrations, further K+ accumulation would be toxic. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K+ binding site and therefore traps KimA in an inward-occluded conformation.
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Affiliation(s)
- Michael F Fuss
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Philip Wieferig
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Yvonne Hellmich
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Igor Tascón
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- UCB Pharma, UCB Biopharma UK, Slough, SL1 3WE, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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VanderWal AR, Park JU, Polevoda B, Nicosia JK, Vargas AMM, Kellogg EH, O’Connell MR. Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense. Science 2023; 380:410-415. [PMID: 37104586 PMCID: PMC10228660 DOI: 10.1126/science.abm1184] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Type VI CRISPR-Cas systems use RNA-guided ribonuclease (RNase) Cas13 to defend bacteria against viruses, and some of these systems encode putative membrane proteins that have unclear roles in Cas13-mediated defense. We show that Csx28, of type VI-B2 systems, is a transmembrane protein that assists to slow cellular metabolism upon viral infection, increasing antiviral defense. High-resolution cryo-electron microscopy reveals that Csx28 forms an octameric pore-like structure. These Csx28 pores localize to the inner membrane in vivo. Csx28's antiviral activity in vivo requires sequence-specific cleavage of viral messenger RNAs by Cas13b, which subsequently results in membrane depolarization, slowed metabolism, and inhibition of sustained viral infection. Our work suggests a mechanism by which Csx28 acts as a downstream, Cas13b-dependent effector protein that uses membrane perturbation as an antiviral defense strategy.
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Affiliation(s)
- Arica R. VanderWal
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, USA
| | - Bogdan Polevoda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Julia K. Nicosia
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Adrian M. Molina Vargas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | | | - Mitchell R. O’Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
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Rasmussen T. The Potassium Efflux System Kef: Bacterial Protection against Toxic Electrophilic Compounds. MEMBRANES 2023; 13:465. [PMID: 37233526 PMCID: PMC10224563 DOI: 10.3390/membranes13050465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Kef couples the potassium efflux with proton influx in gram-negative bacteria. The resulting acidification of the cytosol efficiently prevents the killing of the bacteria by reactive electrophilic compounds. While other degradation pathways for electrophiles exist, Kef is a short-term response that is crucial for survival. It requires tight regulation since its activation comes with the burden of disturbed homeostasis. Electrophiles, entering the cell, react spontaneously or catalytically with glutathione, which is present at high concentrations in the cytosol. The resulting glutathione conjugates bind to the cytosolic regulatory domain of Kef and trigger activation while the binding of glutathione keeps the system closed. Furthermore, nucleotides can bind to this domain for stabilization or inhibition. The binding of an additional ancillary subunit, called KefF or KefG, to the cytosolic domain is required for full activation. The regulatory domain is termed K+ transport-nucleotide binding (KTN) or regulator of potassium conductance (RCK) domain, and it is also found in potassium uptake systems or channels in other oligomeric arrangements. Bacterial RosB-like transporters and K+ efflux antiporters (KEA) of plants are homologs of Kef but fulfill different functions. In summary, Kef provides an interesting and well-studied example of a highly regulated bacterial transport system.
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Affiliation(s)
- Tim Rasmussen
- Rudolf Virchow Center and Biocenter, Institute of Biochemistry II, Julius-Maximilians-Universität Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
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39
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Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
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40
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Acciarri G, Gizzi FO, Torres Manno MA, Stülke J, Espariz M, Blancato VS, Magni C. Redundant potassium transporter systems guarantee the survival of Enterococcus faecalis under stress conditions. Front Microbiol 2023; 14:1117684. [PMID: 36846772 PMCID: PMC9945522 DOI: 10.3389/fmicb.2023.1117684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Enterococcus is able to grow in media at pH from 5.0 to 9.0 and a high concentration of NaCl (8%). The ability to respond to these extreme conditions requires the rapid movement of three critical ions: proton (H+), sodium (Na+), and potassium (K+). The activity of the proton F0F1 ATPase and the sodium Na+ V0V1 type ATPase under acidic or alkaline conditions, respectively, is well established in these microorganisms. The potassium uptake transporters KtrI and KtrII were described in Enterococcus hirae, which were associated with growth in acidic and alkaline conditions, respectively. In Enterococcus faecalis, the presence of the Kdp (potassium ATPase) system was early established. However, the homeostasis of potassium in this microorganism is not completely explored. In this study, we demonstrate that Kup and KimA are high-affinity potassium transporters, and the inactivation of these genes in E. faecalis JH2-2 (a Kdp laboratory natural deficient strain) had no effect on the growth parameters. However, in KtrA defective strains (ΔktrA, ΔkupΔktrA) an impaired growth was observed under stress conditions, which was restored to wild type levels by external addition of K+ ions. Among the multiplicity of potassium transporters identify in the genus Enterococcus, Ktr channels (KtrAB and KtrAD), and Kup family symporters (Kup and KimA) are present and may contribute to the particular resistance of these microorganisms to different stress conditions. In addition, we found that the presence of the Kdp system in E. faecalis is strain-dependent, and this transporter is enriched in strains of clinical origin as compared to environmental, commensal, or food isolates.
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Affiliation(s)
- Giuliana Acciarri
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina
| | - Fernán O. Gizzi
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina
| | - Mariano A. Torres Manno
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Área Bioinformática, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Jörg Stülke
- Department of General Microbiology, Georg August University, Göttingen, Germany
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Área Bioinformática, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Víctor S. Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los Alimentos, FBioyF, UNR–Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los Alimentos, FBioyF, UNR–Municipalidad de Granadero Baigorria, Rosario, Argentina,*Correspondence: Christian Magni, ✉
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41
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Sensitive bacterial V m sensors revealed the excitability of bacterial V m and its role in antibiotic tolerance. Proc Natl Acad Sci U S A 2023; 120:e2208348120. [PMID: 36623202 PMCID: PMC9934018 DOI: 10.1073/pnas.2208348120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
As an important free energy source, the membrane voltage (Vm) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial Vm sensors which allow single-cell recording of bacterial Vm dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically "excitable" and "resting" states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial Vm are observed, which are regulated by Na+/K+ ratio of the medium and facilitate increased antibiotic tolerance. In the electrically resting state, bacterial Vm displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment. Our findings demonstrate the potential of our newly developed voltage sensors to reveal the underpinning connections between bacterial Vm and antibiotic tolerance.
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42
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Higgins JA, Ramos DS, Gili S, Spetea C, Kanoski S, Ha D, McDonough AA, Youn JH. Stable potassium isotopes (41K/39K) track transcellular and paracellular potassium transport in biological systems. Front Physiol 2022; 13:1016242. [PMID: 36388124 PMCID: PMC9644202 DOI: 10.3389/fphys.2022.1016242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 12/04/2022] Open
Abstract
As the most abundant cation in archaeal, bacterial, and eukaryotic cells, potassium (K+) is an essential element for life. While much is known about the machinery of transcellular and paracellular K transport–channels, pumps, co-transporters, and tight-junction proteins—many quantitative aspects of K homeostasis in biological systems remain poorly constrained. Here we present measurements of the stable isotope ratios of potassium (41K/39K) in three biological systems (algae, fish, and mammals). When considered in the context of our current understanding of plausible mechanisms of K isotope fractionation and K+ transport in these biological systems, our results provide evidence that the fractionation of K isotopes depends on transport pathway and transmembrane transport machinery. Specifically, we find that passive transport of K+ down its electrochemical potential through channels and pores in tight-junctions at favors 39K, a result which we attribute to a kinetic isotope effect associated with dehydration and/or size selectivity at the channel/pore entrance. In contrast, we find that transport of K+ against its electrochemical gradient via pumps and co-transporters is associated with less/no isotopic fractionation, a result that we attribute to small equilibrium isotope effects that are expressed in pumps/co-transporters due to their slower turnover rate and the relatively long residence time of K+ in the ion pocket. These results indicate that stable K isotopes may be able to provide quantitative constraints on transporter-specific K+ fluxes (e.g., the fraction of K efflux from a tissue by channels vs. co-transporters) and how these fluxes change in different physiological states. In addition, precise determination of K isotope effects associated with K+ transport via channels, pumps, and co-transporters may provide unique constraints on the mechanisms of K transport that could be tested with steered molecular dynamic simulations.
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Affiliation(s)
- John A. Higgins
- Department of Geosciences, Princeton University, Princeton, NJ, United States
- *Correspondence: John A. Higgins,
| | - Danielle Santiago Ramos
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Stefania Gili
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Scott Kanoski
- Department of Human and Evolutionary Biology, University of Southern California, Los Angeles, CA, United States
| | - Darren Ha
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Alicia A. McDonough
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Jang H. Youn
- Department of Physiology and Neuroscience, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
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43
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Kikuchi K, Galera-Laporta L, Weatherwax C, Lam JY, Moon EC, Theodorakis EA, Garcia-Ojalvo J, Süel GM. Electrochemical potential enables dormant spores to integrate environmental signals. Science 2022; 378:43-49. [PMID: 36201591 PMCID: PMC10593254 DOI: 10.1126/science.abl7484] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The dormant state of bacterial spores is generally thought to be devoid of biological activity. We show that despite continued dormancy, spores can integrate environmental signals over time through a preexisting electrochemical potential. Specifically, we studied thousands of individual Bacillus subtilis spores that remain dormant when exposed to transient nutrient pulses. Guided by a mathematical model of bacterial electrophysiology, we modulated the decision to exit dormancy by genetically and chemically targeting potassium ion flux. We confirmed that short nutrient pulses result in step-like changes in the electrochemical potential of persistent spores. During dormancy, spores thus gradually release their stored electrochemical potential to integrate extracellular information over time. These findings reveal a decision-making mechanism that operates in physiologically inactive cells.
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Affiliation(s)
- Kaito Kikuchi
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Colleen Weatherwax
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Jamie Y Lam
- Department of Chemistry and Biochemistry, University of California San Diego; La Jolla, CA 92093, USA
| | - Eun Chae Moon
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Emmanuel A Theodorakis
- Department of Chemistry and Biochemistry, University of California San Diego; La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra; 08003 Barcelona, Spain
- Senior author
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
- San Diego Center for Systems Biology, University of California San Diego; La Jolla, CA 92093-0380, USA
- Center for Microbiome Innovation, University of California San Diego; La Jolla, CA 92093-0380, USA
- Senior author
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44
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White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na + riboswitches regulate genes for diverse physiological processes in bacteria. Nat Chem Biol 2022; 18:878-885. [PMID: 35879547 PMCID: PMC9337991 DOI: 10.1038/s41589-022-01086-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
Abstract
Organisms presumably have mechanisms to monitor and physiologically adapt to changes in cellular Na+ concentrations. Only a single bacterial protein has previously been demonstrated to selectively sense Na+ and regulate gene expression. Here we report a riboswitch class, previously called the 'DUF1646 motif', whose members selectively sense Na+ and regulate the expression of genes relevant to sodium biology. Many proteins encoded by Na+-riboswitch-regulated genes are annotated as metal ion transporters, whereas others are involved in mitigating osmotic stress or harnessing Na+ gradients for ATP production. Na+ riboswitches exhibit dissociation constants in the low mM range, and strongly reject all other alkali and alkaline earth ions. Likewise, only Na+ triggers riboswitch-mediated transcription and gene expression changes. These findings reveal that some bacteria use Na+ riboswitches to monitor, adjust and exploit Na+ concentrations and gradients, and in some instances collaborate with c-di-AMP riboswitches to coordinate gene expression during osmotic stress.
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Affiliation(s)
- Neil White
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Anna Sun
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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45
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Ivanova A, Ivanova K, Fiandra L, Mantecca P, Catelani T, Natan M, Banin E, Jacobi G, Tzanov T. Antibacterial, Antibiofilm, and Antiviral Farnesol-Containing Nanoparticles Prevent Staphylococcus aureus from Drug Resistance Development. Int J Mol Sci 2022; 23:ijms23147527. [PMID: 35886883 PMCID: PMC9321328 DOI: 10.3390/ijms23147527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
Multidrug antimicrobial resistance is a constantly growing health care issue associated with increased mortality and morbidity, and huge financial burden. Bacteria frequently form biofilm communities responsible for numerous persistent infections resistant to conventional antibiotics. Herein, novel nanoparticles (NPs) loaded with the natural bactericide farnesol (FSL NPs) are generated using high-intensity ultrasound. The nanoformulation of farnesol improved its antibacterial properties and demonstrated complete eradication of Staphylococcus aureus within less than 3 h, without inducing resistance development, and was able to 100% inhibit the establishment of a drug-resistant S. aureus biofilm. These antibiotic-free nano-antimicrobials also reduced the mature biofilm at a very low concentration of the active agent. In addition to the outstanding antibacterial properties, the engineered nano-entities demonstrated strong antiviral properties and inhibited the spike proteins of SARS-CoV-2 by up to 83%. The novel FSL NPs did not cause skin tissue irritation and did not induce the secretion of anti-inflammatory cytokines in a 3D skin tissue model. These results support the potential of these bio-based nano-actives to replace the existing antibiotics and they may be used for the development of topical pharmaceutic products for controlling microbial skin infections, without inducing resistance development.
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Affiliation(s)
- Aleksandra Ivanova
- Group of Molecular and Industrial Biotechnology, Chemical Engineering, Universitat Politécnica de Catalunya, 08222 Terrassa, Spain; (A.I.); (K.I.)
| | - Kristina Ivanova
- Group of Molecular and Industrial Biotechnology, Chemical Engineering, Universitat Politécnica de Catalunya, 08222 Terrassa, Spain; (A.I.); (K.I.)
| | - Luisa Fiandra
- Department of Earth and Environmental Sciences, Research Center POLARIA, Universita degli Studi di Milano-Bicocca, 20900 Milano, Italy; (L.F.); (P.M.)
| | - Paride Mantecca
- Department of Earth and Environmental Sciences, Research Center POLARIA, Universita degli Studi di Milano-Bicocca, 20900 Milano, Italy; (L.F.); (P.M.)
| | - Tiziano Catelani
- Interdepartmental Microscopy Platform, University of Milano-Bicocca, 20126 Milano, Italy;
| | - Michal Natan
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.N.); (E.B.); (G.J.)
| | - Ehud Banin
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.N.); (E.B.); (G.J.)
| | - Gila Jacobi
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.N.); (E.B.); (G.J.)
| | - Tzanko Tzanov
- Group of Molecular and Industrial Biotechnology, Chemical Engineering, Universitat Politécnica de Catalunya, 08222 Terrassa, Spain; (A.I.); (K.I.)
- Correspondence:
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46
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Bioremediation potential of hexavalent chromium-resistant Arthrobacter globiformis 151B: study of the uptake of cesium and other alkali ions. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:745-758. [PMID: 35768673 DOI: 10.1007/s10123-022-00258-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/04/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
Abstract
Cesium (Cs+) enters environments largely because of global release into the environment from weapons testing and accidents such as Fukushima Daiichi and Chernobyl nuclear waste. Even at low concentrations, Cs+ is highly toxic to ecological receptors because of its physicochemical similarity to macronutrient potassium (K+). We investigated the uptake and accumulation of Cs+ by Arthrobacter globiformis strain 151B in reference to three similar alkali metal cations rubidium (Rb+), sodium (Na+), and potassium (K+). The impact of hexavalent chromium (Cr+6) as a co-contaminant was also evaluated. A. globiformis 151B accumulated Cs+ and Cr6+ in a time-dependent fashion. In contrast, the uptake and accumulation of Rb+ did not exhibit any trends. An exposure to Cs+, Rb+, and Cr+6 triggered a drastic increase in K+ and Na+ uptake by the bacterial cells. That was followed by the efflux of K+ and Na+, suggesting a Cs+ "substitution." Two-dimensional gel-electrophoresis of bacterial cell proteomes with the following mass-spectrometry of differentially expressed bands revealed that incubation of bacterial cells with Cs+ induced changes in the expression of proteins involved in the maintenance of cellular homeostasis and reactive oxygen species removal. The ability of A. globiformis 151B to mediate the uptake and accumulation of cesium and hexavalent chromium suggests that it possesses wide-range bioremediation potential.
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47
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Zhou H, Zhao D, Zhang S, Xue Q, Zhang M, Yu H, Zhou J, Li M, Kumar S, Xiang H. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ Microbiol 2022; 24:2239-2258. [PMID: 35048500 DOI: 10.1111/1462-2920.15899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.
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Affiliation(s)
- Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Manqi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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48
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Ruiz-Castilla FJ, Ruiz Pérez FS, Ramos-Moreno L, Ramos J. Candida albicans Potassium Transporters. Int J Mol Sci 2022; 23:ijms23094884. [PMID: 35563275 PMCID: PMC9105532 DOI: 10.3390/ijms23094884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/10/2022] Open
Abstract
Potassium is basic for life. All living organisms require high amounts of intracellular potassium, which fulfils multiple functions. To reach efficient potassium homeostasis, eukaryotic cells have developed a complex and tightly regulated system of transporters present both in the plasma membrane and in the membranes of internal organelles that allow correct intracellular potassium content and distribution. We review the information available on the pathogenic yeast Candida albicans. While some of the plasma membrane potassium transporters are relatively well known and experimental data about their nature, function or regulation have been published, in the case of most of the transporters present in intracellular membranes, their existence and even function have just been deduced because of their homology with those present in other yeasts, such as Saccharomyces cerevisiae. Finally, we analyse the possible links between pathogenicity and potassium homeostasis. We comment on the possibility of using some of these transporters as tentative targets in the search for new antifungal drugs.
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Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
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Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
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Inactivation of a New Potassium Channel Increases Rifampicin Resistance and Induces Collateral Sensitivity to Hydrophilic Antibiotics in Mycobacterium smegmatis. Antibiotics (Basel) 2022; 11:antibiotics11040509. [PMID: 35453260 PMCID: PMC9025972 DOI: 10.3390/antibiotics11040509] [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: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/10/2022] Open
Abstract
Rifampicin is a critical first-line antibiotic for treating mycobacterial infections such as tuberculosis, one of the most serious infectious diseases worldwide. Rifampicin resistance in mycobacteria is mainly caused by mutations in the rpoB gene; however, some rifampicin-resistant strains showed no rpoB mutations. Therefore, alternative mechanisms must explain this resistance in mycobacteria. In this work, a library of 11,000 Mycobacterium smegmatis mc2 155 insertion mutants was explored to search and characterize new rifampicin-resistance determinants. A transposon insertion in the MSMEG_1945 gene modified the growth rate, pH homeostasis and membrane potential in M. smegmatis, producing rifampicin resistance and collateral susceptibility to other antitubercular drugs such as isoniazid, ethionamide and aminoglycosides. Our data suggest that the M. smegmatis MSMEG_1945 protein is an ion channel, dubbed MchK, essential for maintaining the cellular ionic balance and membrane potential, modulating susceptibility to antimycobacterial agents. The functions of this new gene point once again to potassium homeostasis impairment as a proxy to resistance to rifampicin. This study increases the known repertoire of mycobacterial ion channels involved in drug susceptibility/resistance to antimycobacterial drugs and suggests novel intervention opportunities, highlighting ion channels as druggable pathways.
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