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Liao M, Gong H, Liu H, Shen K, Ge T, King S, Schweins R, McBain AJ, Hu X, Lu JR. Combination of a pH-responsive peptide amphiphile and a conventional antibiotic in treating Gram-negative bacteria. J Colloid Interface Sci 2024; 659:397-412. [PMID: 38183806 DOI: 10.1016/j.jcis.2023.12.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/16/2023] [Accepted: 12/24/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Clinical treatments ofgastric infections using antibiotics suffer from the undesired killing of commensal bacteria and emergence of antibiotic resistance. It is desirable to develop pH-responsive antimicrobial peptides (AMPs) that kill pathogenic bacteria such as H. pyloriand resistant E. coli under acidic environment with minimal impact to commensal bacteria whilst not causing antibiotic resistance. EXPERIMENTS Using a combined approach of cell assays, molecular dynamics (MD) simulations and membrane models facilitating biophysical and biochemical measurements including small angle neutron scattering (SANS), we have characterized the pH-responsive physiochemical properties and antimicrobial performance of two amphiphilic AMPs, GIIKDIIKDIIKDI-NH2 and GIIKKIIDDIIKKI-NH2 (denoted as 3D and 2D, respectively), that were designed by selective substitutions of cationic residues of Lys (K) in the extensively studied AMP G(IIKK)3I-NH2 with anionic residue Asp (D). FINDINGS Whilst 2D kept non-ordered coils across the entire pH range studied, 3D displayed a range of secondary structures when pH was shifted from basic to acidic, with distinct self-assembly into nanofibers in aqueous environment. Further experimental and modeling studies revealed that the AMPs interacted differently with the inner and outer membranes of Gram-negative bacteria in a pH-responsive manner and that the structural features characterized by membrane leakage and intramembrane nanoaggregates revealed from fluorescence spectroscopy and SANS were well linked to antimicrobial actions. Different antimicrobial efficacies of 2D and 3D were underlined by the interplay between their ability to bind to the outer membrane lipid LPS (lipopolysaccharide), outer membrane permeability change and inner membrane depolarization and leakage. Furthermore, AMP's binding with the inner membrane under acidic condition caused both the dissipation of membrane potential (Δψ) and the continuous dissipation of transmembrane ΔpH, with Δψ and ΔpH being the key components of the proton motive force. Combinations of antibiotic (Minocycline) with the pH-responsive AMP generated the synergistic effects against Gram-negative bacteria only under acidic condition. These features are crucial to target applications to gastric infections, anti-acne and wound healing.
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Affiliation(s)
- Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Huayang Liu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Kangcheng Shen
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Tianhao Ge
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Stephen King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | | | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Jian R Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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152
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Chmykh Y, Nadeau JL. The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates. J Microsc 2024; 294:36-51. [PMID: 38230460 DOI: 10.1111/jmi.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging. It was found that FLIM enabled discrimination of SYTO 9 labelled cells from background, but that the lifetime of SYTO 9 was shorter in cells on minerals than in pure culture under our conditions. Photosynthetic microorganisms were easily observed using both FLIM and confocal. Unlabelled, nonpigmented bacteria showed weak signals that were difficult to distinguish from background when minerals were present, though cellular autofluorescence consistent with NAD(P)H could be seen in pure cultures, and phasor analysis permitted detection on rocks. Gypsum and marble samples showed similar autofluorescence profiles, with little autofluorescence in the yellow-to-red range. Lifetime or time-gated imaging may prove a useful tool for environmental microbiology. LAY DESCRIPTION: The standard method of bacterial enumeration is to label the cells with a fluorescent dye and count them under high-power fluorescence microscopy. However, this can be difficult when the cells are embedded in soil and rock due to fluorescence from the surrounding minerals and dye binding to ambiguous features of the substrate. The use of fluorescence lifetime imaging (FLIM) can disambiguate these signals and allow for improved detection of bacteria in environmental samples.
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Affiliation(s)
- Yekaterina Chmykh
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jay L Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
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153
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Firrincieli A, Tornatore E, Piacenza E, Cappelletti M, Saiano F, Pavia FC, Alduina R, Zannoni D, Presentato A. The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion. Chemosphere 2024; 354:141712. [PMID: 38484991 DOI: 10.1016/j.chemosphere.2024.141712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
The effects of oxyanions selenite (SeO32-) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized.
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Affiliation(s)
- Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via San Camillo de Lellis snc, 01100, Viterbo, Italy.
| | - Enrico Tornatore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Elena Piacenza
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Filippo Saiano
- Department of Agricultural, Food and Forestry Sciences (SAAF), University of Palermo, Viale delle Scienze Ed. 4, 90128, Palermo, Italy.
| | - Francesco Carfì Pavia
- Department of Engineering, University of Palermo, Viale delle Scienze Ed. 8, 90128, Palermo, Italy.
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Alessandro Presentato
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128, Palermo, Italy.
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154
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Otto M, Papastefanou P, Fahse L. Pressure from insect-resistant maize on protected butterflies and moths. Conserv Biol 2024; 38:e14222. [PMID: 37990833 DOI: 10.1111/cobi.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/31/2023] [Accepted: 09/21/2023] [Indexed: 11/23/2023]
Abstract
Intensification in agriculture affects many insect species, including butterflies. Insect-resistant crops, such as Bt (Bacillus thuringiensis) maize, which produces a toxin active against Lepidoptera, are an alternative to insecticide sprays. Genetically modified crops are regulated in most countries and require an environmental risk assessment. In the European Union, such assessments include the use of simulation models to predict the effects on nontarget Lepidoptera (NTL). To support the assessment of protected NTL, we extended an individual-based, stochastic, spatially explicit mathematical model (LepiX) to include a wider range of exposure scenarios, a species-sensitivity distribution, and an option for repeated exposure of individuals. We applied the model to transgenic maize DAS-1507, which expresses a high concentration of Bt toxin in pollen that may be consumed by NTL larvae on their host plants nearby. Even in the most conservative scenario without repeated exposure, mortality estimates for highly sensitive species ranged from 41% to 6% at distances of 10-1000 m from the nearest maize field. Repeated exposure can cause additional mortality and thus is relevant for the overall risk assessment. Uncertainties in both exposure and ecotoxicity estimates strongly influenced the predicted mortalities. Care should be taken to include these uncertainties in the model scenarios used for decision-making. In accordance with other modeling results, our simulations demonstrated that mean mortality may not be safe for protected species. With its high pollen expression, DAS-1507 maize may pose risks to sensitive and protected butterfly and moth species that may be difficult to manage. High expression of Bt toxin in pollen is unnecessary for controlling target pests. Consequently, we suggest that Bt maize with high pollen expression not be cultivated in regions where protected butterflies are to be conserved.
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Affiliation(s)
- Mathias Otto
- Federal Agency for Nature Conservation (BfN), Bonn, Germany
| | - Phillip Papastefanou
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Lorenz Fahse
- Institute for Environmental Sciences, University of Koblenz-Landau, Renamed Rhineland-Palatinate Technical University Kaiserlautern, Landau, Germany
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155
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Waheed Iqbal M, Tang X, Riaz T, Mahmood S, Zhang Y, Zhao M, Yun J, Li J, Qi X. Exploiting the biocatalytic potential of co-expressed l-fucose isomerase and d-tagatose 3-epimerase for the biosynthesis of 6-deoxy-l-sorbose. Bioorg Chem 2024; 145:107189. [PMID: 38350272 DOI: 10.1016/j.bioorg.2024.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
6-Deoxy-l-sorbose (6-DLS) is an imperative rare sugar employed in food, agriculture, pharmaceutical and cosmetic industeries. However, it is a synthetic and very expensive rare sugars, previously synthesized by chemo-enzymatic methods through a long chain of chemical processes. Recently, enzymatic synthesis of rare sugars has attracted a lot of attention due to its advantages over synthetic methods. In this work, a promising approach for the synthesis of 6-DLS from an inexpensive sugar l-fucose was identified. The genes for l-fucose isomerase from Paenibacillus rhizosphaerae (Pr-LFI) and genes for d-tagatose-3-epimerase from Caballeronia fortuita (Cf-DTE) have been used for cloning and co-expression in Escherichia coli, developed a recombinant plasmid harboring pANY1-Pr-LFI/Cf-DTE vector. The recombinant co-expression system exhibited an optimum activity at 50 °C of temperature and pH 6.5 in the presence of Co2+ metal ion which inflated the catalytic activity by 6.8 folds as compared to control group with no metal ions. The recombinant co-expressed system was stable up to more than 50 % relative activity after 12 h and revealed a melting temperature (Tm) of 63.38 °C exhibiting half-life of 13.17 h at 50 °C. The co-expression system exhibited, 4.93, 11.41 and 16.21 g/L of 6-DLS production from initial l-fucose concentration of 30, 70 and 100 g/L, which equates to conversion yield of 16.44 %, 16.30 % and 16.21 % respectively. Generally, this study offers a promising strategy for the biological production of 6-DLS from an inexpensive substrate l-fucose in slightly acidic conditions with the aid of co-expression system harboring Pr-LFI and CF-DTE genes.
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Affiliation(s)
- Muhammad Waheed Iqbal
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xinrui Tang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Tahreem Riaz
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Shahid Mahmood
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yufei Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Mei Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Junhua Yun
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China.
| | - Jia Li
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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156
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Mariner BL, Rodriguez AS, Heath OC, McCormick MA. Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors. GeroScience 2024; 46:1755-1773. [PMID: 37749371 PMCID: PMC10828360 DOI: 10.1007/s11357-023-00938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
We have recently shown that multiple tRNA synthetase inhibitors can greatly increase lifespan in multiple models by acting through the conserved transcription factor ATF4. Here, we show that these compounds, and several others of the same class, can greatly upregulate mammalian ATF4 in cells in vitro, in a dose dependent manner. Further, RNASeq analysis of these cells pointed toward changes in protein turnover. In subsequent experiments here we show that multiple tRNA synthetase inhibitors can greatly upregulate activity of the ubiquitin proteasome system (UPS) in cells in an ATF4-dependent manner. The UPS plays an important role in the turnover of many damaged or dysfunctional proteins in an organism. Increasing UPS activity has been shown to enhance the survival of Huntington's disease cell models, but there are few known pharmacological enhancers of the UPS. Additionally, we see separate ATF4 dependent upregulation of macroautophagy upon treatment with tRNA synthetase inhibitors. Protein degradation is an essential cellular process linked to many important human diseases of aging such as Alzheimer's disease and Huntington's disease. These drugs' ability to enhance proteostasis more broadly could have wide-ranging implications in the treatment of important age-related neurodegenerative diseases.
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Affiliation(s)
- Blaise L Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA
| | - Antonio S Rodriguez
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Olivia C Heath
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA.
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157
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Zhu Z, Ding J, Du R, Zhang Z, Guo J, Li X, Jiang L, Chen G, Bu Q, Tang N, Lu L, Gao X, Li W, Li S, Zeng G, Liang J. Systematic tracking of nitrogen sources in complex river catchments: Machine learning approach based on microbial metagenomics. Water Res 2024; 253:121255. [PMID: 38341971 DOI: 10.1016/j.watres.2024.121255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Tracking nitrogen pollution sources is crucial for the effective management of water quality; however, it is a challenging task due to the complex contaminative scenarios in the freshwater systems. The contaminative pattern variations can induce quick responses of aquatic microorganisms, making them sensitive indicators of pollution origins. In this study, the soil and water assessment tool, accompanied by a detailed pollution source database, was used to detect the main nitrogen pollution sources in each sub-basin of the Liuyang River watershed. Thus, each sub-basin was assigned to a known class according to SWAT outputs, including point source pollution-dominated area, crop cultivation pollution-dominated area, and the septic tank pollution-dominated area. Based on these outputs, the random forest (RF) model was developed to predict the main pollution sources from different river ecosystems using a series of input variable groups (e.g., natural macroscopic characteristics, river physicochemical properties, 16S rRNA microbial taxonomic composition, microbial metagenomic data containing taxonomic and functional information, and their combination). The accuracy and the Kappa coefficient were used as the performance metrics for the RF model. Compared with the prediction performance among all the input variable groups, the prediction performance of the RF model was significantly improved using metagenomic indices as inputs. Among the metagenomic data-based models, the combination of the taxonomic information with functional information of all the species achieved the highest accuracy (0.84) and increased median Kappa coefficient (0.70). Feature importance analysis was used to identify key features that could serve as indicators for sudden pollution accidents and contribute to the overall function of the river system. The bacteria Rhabdochromatium marinum, Frankia, Actinomycetia, and Competibacteraceae were the most important species, whose mean decrease Gini indices were 0.0023, 0.0021, 0.0019, and 0.0018, respectively, although their relative abundances ranged only from 0.0004 to 0.1 %. Among the top 30 important variables, functional variables constituted more than half, demonstrating the remarkable variation in the microbial functions among sites with distinct pollution sources and the key role of functionality in predicting pollution sources. Many functional indicators related to the metabolism of Mycobacterium tuberculosis, such as K24693, K25621, K16048, and K14952, emerged as significant important factors in distinguishing nitrogen pollution origins. With the shortage of pollution source data in developing regions, this suggested approach offers an economical, quick, and accurate solution to locate the origins of water nitrogen pollution using the metagenomic data of microbial communities.
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Affiliation(s)
- Ziqian Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Junjie Ding
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Ran Du
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zehua Zhang
- Center for Economics, Finance, and Management Studies, Hunan University, Changsha 410082, PR China
| | - Jiayin Guo
- School of Resources and Environment, Hunan University of Technology and Business, Changsha 410205, PR China
| | - Xiaodong Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Longbo Jiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Gaojie Chen
- School of Mathematics, Hunan University, Changsha 410082, PR China
| | - Qiurong Bu
- National Engineering Research Centre of Advanced Technologies and Equipment for Water Environmental Pollution Monitoring, Changsha 410205, PR China
| | - Ning Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Lan Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiang Gao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Weixiang Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Shuai Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jie Liang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
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158
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Ouyang MY, Wang S, Nie WH, Wang PH, Liao WX, Liu XH, Lin SS, Lin RP, Chen GY, Zhu B, Shen J. Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant. Int J Syst Evol Microbiol 2024; 74. [PMID: 38607367 DOI: 10.1099/ijsem.0.006321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.
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Affiliation(s)
- Ming-Yan Ouyang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wen-Han Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Pei-Hong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wei-Xue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiao-Hui Liu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Si-Si Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Rong-Peng Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Gong-You Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jian Shen
- People's Hospital, Hangzhou 310014, Zhejiang, PR China
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159
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Eckel F, Sinzinger K, Van Opdenbosch D, Schieder D, Sieber V, Zollfrank C. Influence of microbial biomass content on biodegradation and mechanical properties of poly(3-hydroxybutyrate) composites. Biodegradation 2024; 35:209-224. [PMID: 37402058 PMCID: PMC10881657 DOI: 10.1007/s10532-023-10038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Biodegradation rates and mechanical properties of poly(3-hydroxybutyrate) (PHB) composites with green algae and cyanobacteria were investigated for the first time. To the authors knowledge, the addition of microbial biomass led to the biggest observed effect on biodegradation so far. The composites with microbial biomass showed an acceleration of the biodegradation rate and a higher cumulative biodegradation within 132 days compared to PHB or the biomass alone. In order to determine the causes for the faster biodegradation, the molecular weight, the crystallinity, the water uptake, the microbial biomass composition and scanning electron microscope images were assessed. The molecular weight of the PHB in the composites was lower than that of pure PHB while the crystallinity and microbial biomass composition were the same for all samples. A direct correlation of water uptake and crystallinity with biodegradation rate could not be observed. While the degradation of molecular weight of PHB during sample preparation contributed to the improvement of biodegradation, the main reason was attributed to biostimulation by the added biomass. The resulting enhancement of the biodegradation rate appears to be unique in the field of polymer biodegradation. The tensile strength was lowered, elongation at break remained constant and Young's modulus was increased compared to pure PHB.
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Affiliation(s)
- Felix Eckel
- Chair for Biogenic Polymers, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany
| | - Korbinian Sinzinger
- Chair for Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany
| | - Daniel Van Opdenbosch
- Chair for Biogenic Polymers, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany
| | - Doris Schieder
- Chair for Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany
| | - Volker Sieber
- Chair for Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany
| | - Cordt Zollfrank
- Chair for Biogenic Polymers, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, Straubing, 94315, Germany.
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160
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Schubert A, Griesmüller C, Gersdorff N, Bürgers R, Wiechens B, Wassmann T. Antibacterial coating of orthodontic elastomeric ligatures with silver and bismuth nanofilms by magnetron sputtering: A feasibility study. Clin Exp Dent Res 2024; 10:e864. [PMID: 38433291 PMCID: PMC10909824 DOI: 10.1002/cre2.864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/11/2024] [Accepted: 01/20/2024] [Indexed: 03/05/2024] Open
Abstract
OBJECTIVES Magnetron sputtering was evaluated to equip surfaces of orthodontic elastomeric ligatures with silver and bismuth nanofilms. MATERIAL AND METHODS Antibacterial properties were evaluated by the adhesion of Streptococcus mutans. Polyurethane-based elastomeric ligatures were coated with silver and bismuth nanofilms via direct current magnetron sputtering. Surface roughness (Ra ) and surface-free energy (SFE) were assessed. Coated specimens were incubated with S. mutans for 2 h. Adhering bacteria were visualized by Hoechst staining and quantified by an ATP-based luminescence assay. One-way analysis of variance with Tukey post hoc testing and Pearson correlation analysis were performed (p < .05) to relate bacterial adhesion to surface roughness and surface-free energy. RESULTS Elastomeric ligatures were successfully coated with silver and bismuth nanofilms. Ra was significantly reduced by silver coating. Silver and bismuth coatings showed significantly higher SFE than controls. Adhesion of S. mutans was significantly decreased by silver coating. No correlation between bacterial adhesion and SFE was found. Correlation between bacterial adhesion and Ra was positive but not statistically significant. CONCLUSIONS Magnetron sputtering proved to be a feasible method to equip orthodontic elastomeric ligatures with silver and bismuth nanofilms. Silver coatings of elastomeric ligatures may reduce white spots and carious lesions in orthodontic patients. Future research is required to stabilize coatings.
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Affiliation(s)
- Andrea Schubert
- Department of ProsthodonticsUniversity Medical Center GoettingenGoettingenGermany
| | - Carolin Griesmüller
- Department of ProsthodonticsUniversity Medical Center GoettingenGoettingenGermany
| | - Nikolaus Gersdorff
- Department of ProsthodonticsUniversity Medical Center GoettingenGoettingenGermany
| | - Ralf Bürgers
- Department of ProsthodonticsUniversity Medical Center GoettingenGoettingenGermany
| | - Bernhard Wiechens
- Department of OrthodonticsUniversity Medical Center GoettingenGoettingenGermany
| | - Torsten Wassmann
- Department of ProsthodonticsUniversity Medical Center GoettingenGoettingenGermany
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161
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Hollender M, Sałek M, Karlicki M, Karnkowska A. Single-cell genomics revealed Candidatus Grellia alia sp. nov. as an endosymbiont of Eutreptiella sp. (Euglenophyceae). Protist 2024; 175:126018. [PMID: 38325049 DOI: 10.1016/j.protis.2024.126018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Abstract
Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing intracellular bacteria in some strains. Here, we perform a comprehensive molecular analysis of a previously identified endosymbiont in the Eutreptiella sp. CCMP3347 using a single cell approach and bulk culture sequencing. The genome reconstruction of this endosymbiont allowed the description of a new endosymbiont Candidatus Grellia alia sp. nov. from the family Midichloriaceae. Comparative genomics revealed a remarkably complete conjugative type IV secretion system present in three copies on the plasmid sequences of the studied endosymbiont, a feature missing in the closely related Grellia incantans. This study addresses the challenge of limited host cultures with endosymbionts by showing that the genomes of endosymbionts reconstructed from single host cells have the completeness and contiguity that matches or exceeds those coming from bulk cultures. This paves the way for further studies of endosymbionts in euglenids and other protist groups. The research also provides the opportunity to study the diversity of endosymbionts in natural populations.
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Affiliation(s)
- Metody Hollender
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Marta Sałek
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland.
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162
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Emilia N, Pia SV, Tiina HP, Antti N, Anniina V, Anneli R, Michael L, Natalia RS. In vitro protein digestion and carbohydrate colon fermentation of microbial biomass samples from bacterial, filamentous fungus and yeast sources. Food Res Int 2024; 182:114146. [PMID: 38519176 DOI: 10.1016/j.foodres.2024.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
This study evaluated the nutritional quality of different microbial biomass samples by assessing their protein digestibility and carbohydrate fermentability in the colon using in vitro methods. Four microbial samples were produced: one hydrogen-oxidizing bacterial strain (Nocardioides nitrophenolicus KGS-27), two strains of filamentous fungi (Rhizopus oligosporus and Paecilomyces variotii), and one yeast strain (Rhodotorula babjevae). The microorganisms were grown in bioreactors, harvested and dried before analysis. The commercial fungal product Quorn was used as a reference. The protein digestibility of the microbial samples was analysed using the INFOGEST in vitro model, followed by quantification of N-terminal amine groups. An in vitro faecal fermentation experiment was also performed to evaluate the degradation of carbohydrates in microbial biomass samples and formation of short-chain fatty acids (SCFA). The fungal biomass samples had higher protein hydrolysis (60-75 %) than the bacterial sample (12 %) and Quorn (45 %), while the yeast biomass had the highest protein digestibility (85 %). Heat-treatment of the biomass significantly reduced its protein digestibility. Total dietary fibre (DF) content of fungal biomass was 31 - 43 %(DW), mostly insoluble, whereas the bacterial biomass contained mainly soluble DF (total DF: 25.7 %, of which 23.5 % were soluble and 2.2 % insoluble). After 24 h of colonic in vitro fermentation, SCFA production from the biomass of Paecilomyces, Quorn and Rhodotorula was similar to that of wheat bran, while 17 % and 32 % less SCFA were produced from the biomass of Rhizopus and the bacterial strain, respectively. Further studies are needed to clarify the reasons for the observed differences in protein digestibility and DF fermentability, especially regarding the cell wall structures and role of post-processing.
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Affiliation(s)
- Nordlund Emilia
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland.
| | | | | | - Nyyssölä Antti
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
| | - Valtonen Anniina
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland; Nordic Umami Company Ltd., Karamalmintie 2, 02630 Espoo, Finland(1)
| | - Ritala Anneli
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
| | - Lienemann Michael
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
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163
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Neira JL, López-Redondo ML, Cámara-Artigas A, Marina A, Contreras A. Structure and dynamics of the cyanobacterial regulator SipA. Arch Biochem Biophys 2024; 754:109943. [PMID: 38395125 DOI: 10.1016/j.abb.2024.109943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter () of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - María Luisa López-Redondo
- Unidad Regulación de La Síntesis de Proteínas, Instituto de Biomedicina de Valencia (CSIC), 46010, Valencia, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- CeiA3, 04120, Almería, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC) and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 46010, Valencia, Spain
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164
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Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol 2024; 26:e16619. [PMID: 38649189 DOI: 10.1111/1462-2920.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Abstract
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
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Affiliation(s)
- Megan Gross
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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165
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Yang Y, Chen Z, Zhou J, Jiang S, Wang G, Wan L, Yu J, Jiang M, Wang Y, Hu J, Liu X, Wang Y. Anti-PD-1 treatment protects against seizure by suppressing sodium channel function. CNS Neurosci Ther 2024; 30:e14504. [PMID: 37904722 PMCID: PMC11017438 DOI: 10.1111/cns.14504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
AIMS Although programmed cell death protein 1 (PD-1) typically serves as a target for immunotherapies, a few recent studies have found that PD-1 is expressed in the nervous system and that neuronal PD-1 might play a crucial role in regulating neuronal excitability. However, whether brain-localized PD-1 is involved in seizures and epileptogenesis is still unknown and worthy of in-depth exploration. METHODS The existence of PD-1 in human neurons was confirmed by immunohistochemistry, and PD-1 expression levels were measured by real-time quantitative PCR (RT-qPCR) and western blotting. Chemoconvulsants, pentylenetetrazol (PTZ) and cyclothiazide (CTZ), were applied for the establishment of in vivo (rodents) and in vitro (primary hippocampal neurons) models of seizure, respectively. SHR-1210 (a PD-1 monoclonal antibody) and sodium stibogluconate (SSG, a validated inhibitor of SH2-containing protein tyrosine phosphatase-1 [SHP-1]) were administrated to investigate the impact of PD-1 pathway blockade on epileptic behaviors of rodents and epileptiform discharges of neurons. A miRNA strategy was applied to determine the impact of PD-1 knockdown on neuronal excitability. The electrical activities and sodium channel function of neurons were determined by whole-cell patch-clamp recordings. The interaction between PD-1 and α-6 subunit of human voltage-gated sodium channel (Nav1.6) was validated by performing co-immunostaining and co-immunoprecipitation (co-IP) experiments. RESULTS Our results reveal that PD-1 protein and mRNA levels were upregulated in lesion cores compared with perifocal tissues of surgically resected specimens from patients with intractable epilepsy. Furthermore, we show that anti-PD-1 treatment has anti-seizure effects both in vivo and in vitro. Then, we reveal that PD-1 blockade can alter the electrophysiological properties of sodium channels. Moreover, we reveal that PD-1 acts together with downstream SHP-1 to regulate sodium channel function and hence neuronal excitability. Further investigation suggests that there is a direct interaction between neuronal PD-1 and Nav1.6. CONCLUSION Our study reveals that neuronal PD-1 plays an important role in epilepsy and that anti-PD-1 treatment protects against seizures by suppressing sodium channel function, identifying anti-PD-1 treatment as a novel therapeutic strategy for epilepsy.
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Affiliation(s)
- Yuling Yang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Zhiyun Chen
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jing Zhou
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
- Rehabilitation CenterShenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science CenterShenzhenChina
| | - Shize Jiang
- Department of Neurosurgery, Huashan HospitalFudan UniversityShanghaiChina
| | - Guoxiang Wang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Li Wan
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
- Rehabilitation CenterShenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science CenterShenzhenChina
| | - Jiangning Yu
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Min Jiang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yulong Wang
- Rehabilitation CenterShenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science CenterShenzhenChina
| | - Jie Hu
- Department of Neurosurgery, Huashan HospitalFudan UniversityShanghaiChina
| | - Xu Liu
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yun Wang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan HospitalFudan UniversityShanghaiChina
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166
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Ullah A, Ul Haq M, Iqbal M, Irfan M, Khan S, Muhammad R, Ullah A, Khurram M, Alharbi M, Alasmari AF, Ahmad S. A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach. J Biomol Struct Dyn 2024; 42:2976-2989. [PMID: 37177816 DOI: 10.1080/07391102.2023.2212793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Amin Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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167
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Bouchareb EM, Derbal K, Bedri R, Menas S, Bouchareb R, Dizge N. Enhanced fermentative hydrogen production from potato waste by enzymatic pretreatment. Environ Technol 2024; 45:1801-1809. [PMID: 36449015 DOI: 10.1080/09593330.2022.2154171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Biological pretreatment and enzymatic hydrolysis have a potential role in the economic production of sugars and fuels from starch biomass. In this study, the Inoculum/Substrate (I/S) ratio effect and enzymatic pretreatments of potato peels for biohydrogen production in batch reactors were investigated. Two enzymes, α-Amylase and Cellulase, were tested separately and coexistent. Results showed that enzymatic hydrolysis using α-Amylase in mesophilic conditions enhanced carbohydrate concentration from 24.10 g/L to 53.47 g/L, whereas, the use of Cellulase and equi-volumetric mixture of both tested enzymes resulted in 47.16 and 48.16 g/L, respectively. The maximum biohydrogen cumulative production of 263 mL (equivalent to 430.37 mL H2/gVSadded) was obtained using the optimum I/S ratio of 1/6 gVS/gVS at pH 5.5 and incubation temperature of 55°C after 20 days of dark fermentation of potato waste without enzymatic treatment. Under the same operating conditions of the I/S ratio, pH, temperature and the best enzymatic treatment (3 h of substrate enzymatic hydrolysis by α-Amylase), the maximum yield of biohydrogen was 1088 mL (1780.39 mL H2/gVSadded). The enzymatic hydrolysis method adopted in this study can make overall biohydrogen production an effective process. The modified Gompertz model was found to be an adequate fit for biohydrogen production.
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Affiliation(s)
- Esma Mahfouf Bouchareb
- Department of Environmental Engineering, Process Engineering Faculty, Saleh Boubnider University, Constantine, Algeria
- Department of Engineering, National High School of Biotechnology, Toufik Khaznadar Constantine, Constantine, Algeria
| | - Kerroum Derbal
- Department of Process Engineering, National High School of Polytechnic, Constantine, Algeria
| | - Rayane Bedri
- Department of Engineering, National High School of Biotechnology, Toufik Khaznadar Constantine, Constantine, Algeria
| | - Souha Menas
- Department of Engineering, National High School of Biotechnology, Toufik Khaznadar Constantine, Constantine, Algeria
| | - Raouf Bouchareb
- Department of Environmental Engineering, Process Engineering Faculty, Saleh Boubnider University, Constantine, Algeria
| | - Nadir Dizge
- Department of Environmental Engineering, Mersin University, Mersin, Turkey
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Muczynski V, Nathwani AC. AAV mediated gene therapy for haemophilia B: From the early attempts to modern trials. Thromb Res 2024; 236:242-249. [PMID: 38383218 DOI: 10.1016/j.thromres.2020.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 02/23/2024]
Abstract
Early gene therapy clinical trials for the treatment of Haemophilia B have been instrumental to our global understanding of gene therapy and have significantly contributed to the rapid expansion of the field. The use of adeno-associated viruses (AAVs) as vectors for gene transfer has successfully led to therapeutic expression of coagulation factor IX (FIX) in severe haemophilia B patients. Expression of FIX has remained stable following a single administration of vector for up to 8 years at levels that are clinically relevant to reduce the incidence of spontaneous bleeds and have permitted a significant change in the disease management with reduction or elimination of the need for coagulation factor concentrates. These trials have also shed light on several concerns around AAV-mediated gene transfer such as the high prevalence of pre-existing immunity against the vector capsid as well as the elevation of liver transaminases that is associated with a loss of FIX transgene expression in some patients. However, this field is advancing very rapidly with the development of increasingly more efficient strategies to overcome some of these obstacles and importantly raise the possibility of a functional cure, which has been long sought after. This review overviews the evolution of gene therapy for haemophilia B over the last two decades.
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Affiliation(s)
- Vincent Muczynski
- Department of Haematology, University College London - Cancer Institute, United Kingdom of Great Britain and Northern Ireland
| | - Amit C Nathwani
- Department of Haematology, University College London - Cancer Institute, United Kingdom of Great Britain and Northern Ireland; Katharine Dormandy Haemophilia and Thrombosis Unit, Royal Free London NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland; Freeline Therapeutics Ltd., United Kingdom of Great Britain and Northern Ireland.
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169
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Abe R, Ram-Mohan N, Yang S. Re-visiting humoral constitutive antibacterial heterogeneity in bloodstream infections. Lancet Infect Dis 2024; 24:e245-e251. [PMID: 37944543 DOI: 10.1016/s1473-3099(23)00494-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 11/12/2023]
Abstract
Although cellular immunity has garnered much attention in the era of single-cell technologies, humoral innate immunity has receded in priority due to its presumed limited roles. Hence, despite the long-recognised bactericidal activity of serum-a functional characteristic of constitutive humoral immunity-much remains unclear regarding mechanisms underlying its inter-individual heterogeneity and clinical implications in bloodstream infections. Recent work suggests that the immediate antimicrobial effect of humoral innate immunity contributes to suppression of the excessive inflammatory responses to infection by reducing the amount of pathogen-associated molecular patterns. In this Personal View, we propose the need to re-explore factors underlying the inter-individual heterogeneity in serum antibacterial competence as a new approach to better understand humoral innate immunity and revisit the clinical use of measuring serum antibacterial activity in the management of bacterial bloodstream infections. Given the current emphasis on subtyping sepsis, a serum bactericidal assay might prove useful in defining a distinct sepsis endotype, to enable more personalised management.
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Affiliation(s)
- Ryuichiro Abe
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.
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170
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Li Z, Shen Q, Usher ET, Anderson AP, Iburg M, Lin R, Zimmer B, Meyer MD, Holehouse AS, You L, Chilkoti A, Dai Y, Lu GJ. Phase transition of GvpU regulates gas vesicle clustering in bacteria. Nat Microbiol 2024; 9:1021-1035. [PMID: 38553608 DOI: 10.1038/s41564-024-01648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.
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Affiliation(s)
- Zongru Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Qionghua Shen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emery T Usher
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | | | - Manuel Iburg
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Richard Lin
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Brandon Zimmer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative BioDesign, Duke University, Durham, NC, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, USA.
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171
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Groß R, Reßin H, von Maltitz P, Albers D, Schneider L, Bley H, Hoffmann M, Cortese M, Gupta D, Deniz M, Choi JY, Jansen J, Preußer C, Seehafer K, Pöhlmann S, Voelker DR, Goffinet C, Pogge-von Strandmann E, Bunz U, Bartenschlager R, El Andaloussi S, Sparrer KMJ, Herker E, Becker S, Kirchhoff F, Münch J, Müller JA. Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defence against apoptotic mimicry viral pathogens. Nat Microbiol 2024; 9:905-921. [PMID: 38528146 PMCID: PMC10994849 DOI: 10.1038/s41564-024-01637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024]
Abstract
Some viruses are rarely transmitted orally or sexually despite their presence in saliva, breast milk, or semen. We previously identified that extracellular vesicles (EVs) in semen and saliva inhibit Zika virus infection. However, the antiviral spectrum and underlying mechanism remained unclear. Here we applied lipidomics and flow cytometry to show that these EVs expose phosphatidylserine (PS). By blocking PS receptors, targeted by Zika virus in the process of apoptotic mimicry, they interfere with viral attachment and entry. Consequently, physiological concentrations of EVs applied in vitro efficiently inhibited infection by apoptotic mimicry dengue, West Nile, Chikungunya, Ebola and vesicular stomatitis viruses, but not severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus 1, hepatitis C virus and herpesviruses that use other entry receptors. Our results identify the role of PS-rich EVs in body fluids in innate defence against infection via viral apoptotic mimicries, explaining why these viruses are primarily transmitted via PS-EV-deficient blood or blood-ingesting arthropods rather than direct human-to-human contact.
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Affiliation(s)
- Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Hanna Reßin
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dan Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Laura Schneider
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Hanna Bley
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Georg-August University Göttingen, Göttingen, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Dhanu Gupta
- Biomolecular Medicine, Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Miriam Deniz
- Clinic for Gynecology and Obstetrics, Ulm University Medical Center, Ulm, Germany
| | - Jae-Yeon Choi
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Jenny Jansen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Preußer
- Core Facility Extracellular Vesicles, Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, Marburg, Germany
| | - Kai Seehafer
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Georg-August University Göttingen, Göttingen, Germany
| | | | - Christine Goffinet
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elke Pogge-von Strandmann
- Core Facility Extracellular Vesicles, Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, Marburg, Germany
| | - Uwe Bunz
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Samir El Andaloussi
- Biomolecular Medicine, Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Eva Herker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.
- Institute of Virology, Philipps University Marburg, Marburg, Germany.
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172
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Cho A, Lax G, Livingston SJ, Masukagami Y, Naumova M, Millar O, Husnik F, Keeling PJ. Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses. PLoS Genet 2024; 20:e1011218. [PMID: 38557755 PMCID: PMC11008856 DOI: 10.1371/journal.pgen.1011218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel J. Livingston
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mariia Naumova
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Olivia Millar
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Filip Husnik
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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173
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Grün P, Pfaffeneder-Mantai F, Schneider B, Meier M, Bytyqi D, Bandura P, Turhani D. Can jaw bone healed from chronic sclerosing osteomyelitis be considered healthy when planning dental implants? Case report with 20-year follow-up. Ann Med Surg (Lond) 2024; 86:2266-2276. [PMID: 38576989 PMCID: PMC10990345 DOI: 10.1097/ms9.0000000000001826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/02/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction and importance Extraction of mandibular third molars can lead to complications such as chronic sclerosing osteomyelitis (CSO), an inflammatory bone marrow disease that tends to progress. CSO involves the cortical plates and often the periosteal tissues and is caused by a variety of microorganisms, including Corynebacterium spp. The treatment of chronic osteomyelitis (CO) and CSO remains challenging, as there is no universal treatment protocol. This case report investigated whether jaw bone that has healed from chronic sclerosing osteomyelitis can be considered healthy bone when planning dental implants. Case presentation A 21-year-old Caucasian woman developed CO and CSO after third molar surgery. Clinical discussion A combination of alveolar ridge bone resection, extraction of teeth 47-32, and long-term specific antibiotic therapy against Corynebacterium spp. was administered. An attempt at preprosthetic alveolar ridge reconstruction with an anterior superior iliac crest bone graft resulted in graft failure and the patient refused further harvesting procedures. Implantation in the intraforaminal zone also resulted in the loss of two implants after loading. Finally, inferior alveolar nerve transposition resulted in the successful reimplantation of two implants, which were fully functional almost 11 years later. Conclusion This case report presents the treatment history of this patient. With a longitudinal observation period of greater than 20 years, the results of this case demonstrate the successful treatment of bone with CO, CSO, and Corynebacterium spp. infection. Following the removal of infected bone, radical debridement, and long-term antibiotic therapy, bone health was restored.
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Affiliation(s)
- Pascal Grün
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
| | - Florian Pfaffeneder-Mantai
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
- Division for Chemistry and Physics of Materials, Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University, Krems, Austria
| | | | - Marius Meier
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
| | - Ditjon Bytyqi
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
| | - Patrick Bandura
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
| | - Dritan Turhani
- Center for Oral and Maxillofacial Surgery, Department of Dentistry
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174
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Shaukat A, Khaliq N, Riaz R, Munsab R, Ashraf T, Raufi N, Shah H. Noninvasive diagnostic biomarkers, genomic profiling, and advanced microscopic imaging in the early detection and characterization of Naegleria fowleri infections leading to primary amebic meningoencephalitis (PAM). Ann Med Surg (Lond) 2024; 86:2032-2048. [PMID: 38576920 PMCID: PMC10990330 DOI: 10.1097/ms9.0000000000001843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/08/2024] [Indexed: 04/06/2024] Open
Abstract
This review delves into the strategies for early detection and characterization of Naegleria fowleri infections leading to primary amoebic meningoencephalitis (PAM). The study provides an in-depth analysis of current diagnostic approaches, including cerebrospinal fluid analysis, brain tissue examination, immunostaining techniques, and culture methods, elucidating their strengths and limitations. It explores the geographical distribution of N. fowleri, with a focus on regions near the equator, and environmental factors contributing to its prevalence. The review emphasizes the crucial role of early detection in PAM management, discussing the benefits of timely identification in treatment, personalized care, and prevention strategies. Genomic profiling techniques, such as conventional PCR, nested PCR, multiplex PCR, and real-time PCR, are thoroughly examined as essential tools for accurate and prompt diagnosis. Additionally, the study explores advanced microscopic imaging techniques to characterize N. fowleri's morphology and behavior at different infection stages, enhancing our understanding of its life cycle and pathogenic mechanisms. In conclusion, this review underscores the potential of these strategies to improve our ability to detect, understand, and combat N. fowleri infections, ultimately leading to better patient outcomes and enhanced public health protection.
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Affiliation(s)
| | - Nawal Khaliq
- Dow University of Health Sciences, Karachi, Pakistan
| | - Rumaisa Riaz
- Dow University of Health Sciences, Karachi, Pakistan
| | - Rabbia Munsab
- Dow University of Health Sciences, Karachi, Pakistan
| | | | - Nahid Raufi
- Department of Medicine, Kabul Medical University, Kabul, Afghanistan
| | - Hafsa Shah
- Dow University of Health Sciences, Karachi, Pakistan
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175
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Su B, Lai P, Deng MR, Zhu H. Global rewiring of lipid metabolism to produce carotenoid by deleting the transcription factor genes ino2/ino4 in Saccharomyces cerevisiae. Int J Biol Macromol 2024; 264:130400. [PMID: 38412934 DOI: 10.1016/j.ijbiomac.2024.130400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/03/2024] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
The transcription factor complex INO2 and INO4 in Saccharomyces cerevisiae plays a vital role in lipid biosynthesis by activating multiple genes in the biosynthetic pathways of phospholipid, fatty acid, and sterol. Previous studies have reported conflicting results regarding the effects of ino2 and ino4 gene expression levels on target chemicals. Therefore, this study aimed to examine the influence of different ino2 and ino4 expression levels on carotenoid production (e.g., lycopene), which shares a common precursor, acetyl-CoA, with lipid metabolism. Surprisingly, 2.6- and 1.8-fold increase in lycopene yield in the ino2 and ino4 deletion strains were found, respectively. In contrast, ino2 overexpression did not promote lycopene accumulation. Additionally, there was a decrease in intracellular free fatty acids in the ino2 deletion strain. Comparative transcriptome analysis revealed a significant downregulation of genes related to lipid biosynthesis in the ino2 deletion strain. To our knowledge, this is the first report showing that deletion of transcription factor genes ino2 and ino4 can facilitate lycopene accumulation. These findings hold significant implications for the development of metabolically engineered S. cerevisiae with enhanced carotenoid production.
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Affiliation(s)
- Buli Su
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China
| | - Peixuan Lai
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China
| | - Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China.
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China.
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176
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Hassan A, Hamid FS, Pariatamby A, Ossai IC, Ahmed A, Barasarathi J, Auta HS. Influence of bioaugmented fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora Sw. DC in heavy metal-polluted landfill soil. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-33018-1. [PMID: 38561536 DOI: 10.1007/s11356-024-33018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
The research aimed to determine the influence of endophytic fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora in heavy metal-polluted landfill soil. A consortium of 13 fungal isolates as well as Prosopis juliflora Sw. DC was used to decontaminate heavy metal-polluted landfill soil. Enhanced plant growth (biomass and root and shoot lengths) and production of carotenoids, chlorophyll and amino acids L-phenylalanine and L-leucine that are known to enhance growth were found in the treated P. juliflora. Better accumulations of heavy metals were observed in fungi-treated P. juliflora over the untreated one. An upregulated activity of peroxidase, catalase and ascorbate peroxidase was recorded in fungi-treated P. juliflora. Additionally, other metabolites, such as glutathione, 3,5,7,2',5'-pentahydroxyflavone, 5,2'-dihydroxyflavone and 5,7,2',3'-tetrahydroxyflavone, and small peptides, which include Lys Gln Ile, Ser Arg Ala, Asp Arg Gly, Arg Ser Ser, His His Arg, Arg Thr Glu, Thr Arg Asp and Ser Pro Arg, were also detected. These provide defence supports to P. juliflora against toxic metals. Inoculating the plant with the fungi improved its growth, metal accumulation as well as tolerance against heavy metal toxicity. Such a combination can be used as an effective strategy for the bioremediation of metal-polluted soil.
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Affiliation(s)
- Auwalu Hassan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Biological Sciences, Faculty of Science, Federal University of Kashere, Kashere, Gombe State, Nigeria.
| | - Fauziah Shahul Hamid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Agamuthu Pariatamby
- Jeffrey Sachs Center On Sustainable Development, Sunway University, Sunway, Malaysia
| | - Innocent Chukwunonso Ossai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Aziz Ahmed
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Center for Research in Waste Management, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Balochistan, Pakistan
| | - Jayanthi Barasarathi
- Faculty of Health and Life Sciences (FHLS), INTI International University, Pesiaran Perdana BBN, Nilai, Negeri Sambilan, Malaysia
| | - Helen Shnada Auta
- Department of Microbiology, Federal University of Technology, Minna, Niger State, Nigeria
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177
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Kinet R, Richelle A, Colle M, Demaegd D, von Stosch M, Sanders M, Sehrt H, Delvigne F, Goffin P. Giving the cells what they need when they need it: Biosensor-based feeding control. Biotechnol Bioeng 2024; 121:1271-1283. [PMID: 38258490 DOI: 10.1002/bit.28657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
"Giving the cells exactly what they need, when they need it" is the core idea behind the proposed bioprocess control strategy: operating bioprocess based on the physiological behavior of the microbial population rather than exclusive monitoring of environmental parameters. We are envisioning to achieve this through the use of genetically encoded biosensors combined with online flow cytometry (FCM) to obtain a time-dependent "physiological fingerprint" of the population. We developed a biosensor based on the glnA promoter (glnAp) and applied it for monitoring the nitrogen-related nutritional state of Escherichia coli. The functionality of the biosensor was demonstrated through multiple cultivation runs performed at various scales-from microplate to 20 L bioreactor. We also developed a fully automated bioreactor-FCM interface for on-line monitoring of the microbial population. Finally, we validated the proposed strategy by performing a fed-batch experiment where the biosensor signal is used as the actuator for a nitrogen feeding feedback control. This new generation of process control, -based on the specific needs of the cells, -opens the possibility of improving process development on a short timescale and therewith, the robustness and performance of fermentation processes.
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Affiliation(s)
| | | | | | | | | | | | - Hannah Sehrt
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Philippe Goffin
- Molecular and Cellular Biology, University of Brussels, Brussels, Belgium
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178
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Yang J, Xu X, Wu J, Champer J, Xie M. Involvement of miR-8510a-3p in response to Cry1Ac protoxin by regulating PxABCG3 in Plutella xylostella. Int J Biol Macromol 2024; 263:130271. [PMID: 38373570 DOI: 10.1016/j.ijbiomac.2024.130271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
Overuse of insecticides has accelerated the evolution of insecticide resistance and created serious environmental concerns worldwide, thus incentivizing development of alternative methods. Bacillus thuringiensis (Bt) is an insecticidal bacterium that has been developed as a biopesticide to successfully control multiple species of pests. It operates by secreting several insect toxins such as Cry1Ac. However, metabolic resistance based on ATP-binding cassette (ABC) transporters may play a crucial role in the development of metabolic resistance to Bt. Here, we characterized an ABCG gene from the agricultural pest Plutella xylostella (PxABCG3) and found that it was highly expressed in a Cry1Ac-resistant strain, up-regulated after Cry1Ac protoxin treatment. Binding miR-8510a-3p to the coding sequence (CDS) of PxABCG3 was then confirmed by a luciferase reporter assay and RNA immunoprecipitation. miR-8510a-3p agomir delivery markedly reduced PxABCG3 expression in vivo and consequently decreased the tolerance of P. xylostella to Cry1Ac, while reduction of miR-8510a-3p significantly increased PxABCG3 expression, accompanied by an increased tolerance to Cry1Ac. Our results suggest that miR-8510a-3p could potentially be used as a novel molecular target against P. xylostella or other lepidopterans, providing novel insights into developing effective and environmentally friendly pesticides.
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Affiliation(s)
- Jie Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuejiao Xu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiaqi Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jackson Champer
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Miao Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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179
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Zhang WL, Lai MC, Lin S, Chen WC, Deng YC, Lai SJ, Wu SY, Hung CC, Ding JY, Chen SC. Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634834 DOI: 10.1099/ijsem.0.006322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).
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Affiliation(s)
- Wei-Ling Zhang
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Chieh Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chen Deng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, ROC
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chuan-Chuan Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, PR China
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180
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Fiedler SM, Graumann PL. Dynamics of cell wall-binding proteins at a single molecule level: B. subtilis autolysins show different kinds of motion. Mol Biol Cell 2024; 35:ar55. [PMID: 38381561 DOI: 10.1091/mbc.e23-10-0387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Abstract
The bacterial cell wall is a meshwork of crosslinked peptidoglycan strands, with a thickness of up to 50 nm in Firmicutes. Little is known about how proteins move through the cell wall to find sites of enzymatic activity. Cell wall synthesis for cell elongation involves the integration of new peptidoglycan strands by integral membrane proteins, as well as the degradation of existing strands by so-called autolysins, soluble proteins that are secreted through the cell membrane. Autolysins comprise different classes of proteases and glucanases and mostly contain cell-wall binding domains in addition to their catalytic domain. We have studied dynamics of Bacillus subtilis autolysins LytC, a major endopeptidase required for lateral cell wall growth, and LytF, a peptidase acting at the newly formed division site in order to achieve separation of daughter cells. We show that both proteins, fused to moxVenus are present as three distinct populations of different diffusion constants. The fastest population is compatible with free diffusion in a crowded liquid environment, that is similar to that of cytosolic enzymes, likely reflecting autolysins diffusing through the periplasm. The medium mobile fraction can be explained by constrained motion through a polymeric substance, indicating mobility of autolysins through the wall similar to that of DNA-binding proteins within the nucleoid. The slow-mobile fraction are most likely autolysins bound to their specific substrate sites. We show that LytF is more static during exponential phase, while LytC appears to be more active during the transition to stationary phase. Both autolysins became more static in backgrounds lacking redundant other autolysins, suggesting stochastic competition for binding sites. On the other hand, lack of inhibitor IseA or autolysin CwlS lead to an altered preference for polar localization of LytF within the cell wall, revealing that inhibitors and autolysins also affect each other's pattern of localization, in addition to their activity.
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Affiliation(s)
- Svenja M Fiedler
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Strasse 4, 35043 Marburg, Germany
| | - Peter L Graumann
- Fachbereich Chemie und Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein Strasse 4, 35043 Marburg, Germany
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181
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Etesami H, Glick BR. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience. Microbiol Res 2024; 281:127602. [PMID: 38228017 DOI: 10.1016/j.micres.2024.127602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.
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Affiliation(s)
- Hassan Etesami
- Soil Science Department, University of Tehran, Tehran, Iran.
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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182
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Ait-Itto FZ, Behan JA, Martinez M, Barrière F. Development of bioanodes rich in exoelectrogenic bacteria using iron-rich palaeomarine sediment inoculum. Bioelectrochemistry 2024; 156:108618. [PMID: 37988978 DOI: 10.1016/j.bioelechem.2023.108618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
Microbial Fuel Cells (MFC) convert energy stored in chemicals into electrical energy thanks to exoelectrogenic microorganisms who also play a crucial role in geochemical cycles in their natural environment, including that of iron. In this study, we investigated paleomarine sediments as inoculum for bioanode development in MFCs. These sediments were formed under anoxic conditions ca. 113 million years ago and are rich in clay minerals, organic matter, and iron. The marlstone inoculum was incubated in the anolyte of an MFC using acetate as the added electron donor and ferricyanide as the electron acceptor in the catholyte. After seven weeks of incubation, the current density increased to 0.15 mA.cm-2 and a stable + 700 mV open circuit potential was reached. Community analysis revealed the presence of two exoelectrogenic bacterial genera, Geovibrio and Geobacter. Development of electroactive biofilms was correlated to bulk chemical transformations of the sediment inoculum with an increase in the Fe(II) to Fetotal ratio. Comparisons to sediments sterilized prior to inoculation confirmed that bioanode development derives from the native microbiota of these paleomarine sediments. This study illustrates the feasibility of developing exoelectrogenic biofilms from iron-rich marlstone and has implications for the role of such bacteria in broader paleoenvironmental phenomena.
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Affiliation(s)
- Fatima-Zahra Ait-Itto
- Université de Rennes, CNRS, Institut des Sciences Chimiques de Rennes, UMR 6226, Rennes, France; Université de Rennes, CNRS, Géosciences de Rennes - UMR 6118, Rennes, France
| | - James A Behan
- Université de Rennes, CNRS, Institut des Sciences Chimiques de Rennes, UMR 6226, Rennes, France
| | - Mathieu Martinez
- Université de Rennes, CNRS, Géosciences de Rennes - UMR 6118, Rennes, France
| | - Frédéric Barrière
- Université de Rennes, CNRS, Institut des Sciences Chimiques de Rennes, UMR 6226, Rennes, France.
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183
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Ko Y, Yang Y, Kim D, Lee YH, Ghatge S, Hur HG. Fungal biodegradation of poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based commercial bio-plastic film at ambient conditions. Chemosphere 2024; 353:141554. [PMID: 38430940 DOI: 10.1016/j.chemosphere.2024.141554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Microbial biodegradation of commercially available poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based bio-plastic has been pursued at high temperatures exceeding 55 °C. Herein, we first reported three newly isolated fungal strains from farmland soil samples of Republic of Korea namely, Pyrenochaetopsis sp. strain K2, Staphylotrichum sp. S2-1, and Humicola sp. strain S2-3 were capable of degrading a commercial bio-plastic film with degradation rates of 9.5, 8.6, and 12.2%, respectively after 3 months incubation at ambient conditions. Scanning electron microscopy (SEM) analyses showed that bio-plastic film was extensively fragmented with severe cracking on the surface structure after incubation with isolated fungal strains. X-ray diffraction (XRD) analysis also revealed that high crystallinity of the commercial bio-plastic film was significantly decreased after degradation by fungal strains. Liquid chromatography-mass spectrometry (LC-MS) analyses of the fungal culture supernatants containing the bio-plastic film showed the peaks for adipic acid, terephthalic acid (TPA), and terephthalate-butylene (TB) as major metabolites, suggesting cleavage of ester bonds and accumulation of TPA. Furthermore, a consortium of fungal strain K2 with TPA degrading bacterium Pigmentiphaga sp. strain P3-2 isolated from the same sampling site exhibited faster degradation rate of the bio-plastic film within 1 month of incubation with achieving complete biodegradation of accumulated TPA. We assume that the extracellular lipase activity presented in the fungal cultures could hydrolyze the ester bonds of PBAT component of bio-plastic film. Taken together, the fungal and bacterial consortium investigated herein could be beneficial for efficient biodegradation of the commercial bio-plastic film at ambient conditions.
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Affiliation(s)
- Yongseok Ko
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Youri Yang
- Department of Biological Environment, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon State, 24341, Republic of Korea
| | - Dockyu Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yong Hwan Lee
- GREEN-BIO Co., Ltd, 201, Venture Support Center, 333, Gwangju 61005, Republic of Korea
| | - Sunil Ghatge
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea; GREEN-BIO Co., Ltd, 201, Venture Support Center, 333, Gwangju 61005, Republic of Korea.
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
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184
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Horiguchi Y. Current understanding of Bordetella-induced cough. Microbiol Immunol 2024; 68:123-129. [PMID: 38318657 DOI: 10.1111/1348-0421.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Typical pathogenic bacteria of the genus Bordetella cause respiratory diseases, many of which are characterized by severe coughing in host animals. In human infections with these bacteria, such as whooping cough, coughing imposes a heavy burden on patients. The pathophysiology of this severe coughing had long been uncharacterized because convenient animal models that reproduce Bordetella-induced cough have not been available. However, rat and mouse models were recently shown as useful for understanding, at least partially, the causative factors and the mechanism of Bordetella-induced cough. Many types of coughs are induced under various physiological conditions, and the neurophysiological pathways of coughing are considered to vary among animal species, including humans. However, the neurophysiological mechanisms of the coughs in different animal species have not been entirely understood, and, accordingly, the current understanding of Bordetella-induced cough is still incomplete. Nevertheless, recent research findings may open the way for the development of prophylaxis and therapeutic measures against Bordetella-induced cough.
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Affiliation(s)
- Yasuhiko Horiguchi
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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185
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Potok P, Zawada M, Potocki S. Determination of the role of specific amino acids in the binding of Zn(II), Ni(II), and Cu(II) to the active site of the M10 family metallopeptidase. J Inorg Biochem 2024; 253:112500. [PMID: 38301386 DOI: 10.1016/j.jinorgbio.2024.112500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 → Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel β-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).
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Affiliation(s)
- Paulina Potok
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Martyna Zawada
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland.
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186
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Hurt RC, Jin Z, Soufi M, Wong KK, Sawyer DP, Shen HK, Dutka P, Deshpande R, Zhang R, Mittelstein DR, Shapiro MG. Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening. bioRxiv 2024:2024.03.30.587094. [PMID: 38617214 PMCID: PMC11014471 DOI: 10.1101/2024.03.30.587094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm. 1 Within the past decade, reporter genes for US have been introduced 2,3 and engineered 4,5 to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). 6 Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semi-automated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologs of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.
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187
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Ueda H, Tomioka A, Higashiyama M, Kimoto Y, Oguro T, Okazaki S, Ayaki K, Yoshidome Y, Tahara H, Nishimura H, Ito S, Tanemoto R, Takajo T, Narimatsu K, Komoto S, Tomita K, Matsukuma S, Hokari R. Fulminant necrotizing fasciitis by Edwardsiella tarda in a patient with alcoholic liver cirrhosis: A case report. J Infect Chemother 2024; 30:343-347. [PMID: 37866623 DOI: 10.1016/j.jiac.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/15/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
We herein present a unique and extremely rare fulminant case of Edwardsiella tarda infection-related necrotizing fasciitis. The patient had alcoholic cirrhosis and preferred to consume raw fish. He experienced painful swelling of the right forearm one day after he got a minor injury when falling from the ladder, and visited our hospital. His accompanied symptoms were diarrhea and general fatigue. His consciousness got deteriorated after the admission. The lesion of the right forearm had spread and the color had deteriorated with epidermolysis in a few hours. Necrotizing soft-tissue infection was suspected, and emergency debridement of the swollen forearm was performed 4 hours after the admission. However, unfortunately, he died of sepsis approximately 5 hours later. Histological examination of the biopsy specimen revealed features consistent with those of necrotizing fasciitis. The bacterial cultures of blood and the wound identified E. tarda. Since this microorganism is usually isolated from aquatic environments and can cause intestinal infection, sometimes followed by bacteremia especially in immunocompromised hosts, two possible infection routes were suspected. One route was from the skin injury, leading to bacteremia. Another possible route was per oral: orally taken E. tarda invaded deeper tissues from the intestine and reach the bloodstream, leading to extraintestinal infections, although direct evidence remains elusive. Raw fish eaten 1 week prior is considered to be the most possible contaminated food. Overall mortality rate of E. tarda bacteremia is very high and the clinician should pay attention on characteristic clinical findings of E. tarda infection on cirrhotic patients.
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Affiliation(s)
- Hiroki Ueda
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Akira Tomioka
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Masaaki Higashiyama
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan.
| | - Yuya Kimoto
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Takuma Oguro
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Soya Okazaki
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Kana Ayaki
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Yuta Yoshidome
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Hiroyuki Tahara
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Hiroyuki Nishimura
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Suguru Ito
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Rina Tanemoto
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Takeshi Takajo
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Kazuyuki Narimatsu
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Shunsuke Komoto
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Kengo Tomita
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Susumu Matsukuma
- Department of Pathology and Laboratory Medicine, National Defense Medical College, Saitama, Japan
| | - Ryota Hokari
- Department of Internal Medicine, National Defense Medical College, Saitama, Japan
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188
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Hernández-Sarmiento LJ, Tamayo-Molina YS, Valdés-López JF, Urcuqui-Inchima S. Mayaro virus infection elicits a robust pro-inflammatory and antiviral response in human macrophages. Acta Trop 2024; 252:107146. [PMID: 38342287 DOI: 10.1016/j.actatropica.2024.107146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Mayaro virus (MAYV), the etiological agent of Mayaro fever (MAYF), is an emergent arbovirus pathogen belonging to Togaviridae family. MAYF is characterized by high inflammatory component that can cause long-lasting arthralgia that persists for months. Macrophages are viral targets and reservoirs, key components of innate immunity and host response. Given the importance of this pathogen, our aim was to determine the inflammatory and antiviral response of human monocyte-derived macrophages (MDMs) infected with MAYV. First, we established the replication kinetics of the virus. Thereafter, we determined the expression of pattern recognition receptors, NF-ĸB complex, interferons (IFNs), two interleukin 27 (IL27) subunits, IFN-stimulated genes (ISGs), and the production of cytokines/chemokines. We found that human MDMs are susceptible to MAYV infection in vitro, with a peak of viral particles released between 24- and 48-hours post-infection (h.p.i) at MOI 0.5, and between 12 and 24 h.p.i at MOI 1. Interestingly, we observed a significant decline in the production of infectious viral particles at 72 h.p.i that was associated with the induction of antiviral response and high cytotoxic effect of MAYV infection in MDMs. We observed modulation of several genes after MAYV infection, as well, we noted the activation of antiviral detection and response pathways (Toll-like receptors, RIG-I/MDA5, and PKR) at 48 h.p.i but not at 6 h.p.i. Furthermore, MAYV-infected macrophages express high levels of the three types of IFNs and the two IL27 subunits at 48 h.p.i. Moreover, we found higher production of IL6, IL1β, CXCL8/IL8, CCL2, and CCL5 at 48 h.p.i as compared to 6 h.p.i. A robust antiviral response (ISG15, APOBEC3A, IFITM1, and MX2) was observed at 48 but not at 6 h.p.i. The innate and antiviral responses of MAYV-infected MDMs differ at 6 and 48 h.p.i. We conclude that MAYV infection induces robust pro-inflammatory and antiviral responses in human primary macrophages.
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Affiliation(s)
| | - Y S Tamayo-Molina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan Felipe Valdés-López
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Silvio Urcuqui-Inchima
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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189
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Yang X, Shao J, Zhang Y, Wang T, Ge S, Li J. Microenvironment-Driven Fenton Nanoreactor Enabled by Metal-Phenolic Encapsulation of Calcium Peroxide for Effective Control of Dental Caries. Adv Healthc Mater 2024; 13:e2303466. [PMID: 37985941 DOI: 10.1002/adhm.202303466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/12/2023] [Indexed: 11/22/2023]
Abstract
Caries are one of the most common oral diseases caused by pathogenic bacterial infections, which are widespread and persistently harmful to human health. Using nanoparticles to invade biofilms and produce reactive oxygen species (ROS) in situ is a promising strategy for killing bacteria and disrupting the structure of biofilms. In this work, a biofilm-targeting Fenton nanoreactor is reported that can generate ROS responsive to the cariogenic microenvironment. The nanoreactor is constructed by metal-phenolic encapsulation of calcium peroxide (CaO2) followed by modification with a biofilm targeting ligand dextran. Within the cariogenic biofilm, the Fenton nanoreactor is activated by an acidic microenvironment to be decomposed into H2O2 and iron ions, triggering a Fenton-like reaction to generate ROS that can eliminate the biofilm by breaking down extracellular polymeric substances (EPS) and killing cariogenic bacteria. Meanwhile, the depletion of excess protons in biofilm leads to a reversal of the cariogenic microenvironment. The Fenton nanoreactor can effectively inhibit the biofilm formation of Streptococcus mutans on ex vivo human teeth and is effective in preventing caries meanwhile maintaining the oral microbial diversity in rat caries infection model. This work provides a novel and efficient modality for acid microenvironment-driven ROS therapy.
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Affiliation(s)
- Xiaoru Yang
- Department of Biomaterials, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Jinlong Shao
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Yandi Zhang
- Department of Biomaterials, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Ting Wang
- Department of General Debtistry, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Shaohua Ge
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Jianhua Li
- Department of Biomaterials, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
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190
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Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. J Phycol 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
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Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
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191
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Leelapornpisid W, Wanwatanakul P, Mahatnirunkul T. Efficacy of calcium hydroxide-loaded poly(lactic-co-glycolic acid) biodegradable nanoparticles as an intracanal medicament against endodontopathogenic microorganisms in a multi-species biofilm model. AUST ENDOD J 2024; 50:89-96. [PMID: 37947038 DOI: 10.1111/aej.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 09/29/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
This study aimed to evaluate the antimicrobial activity of calcium hydroxide-loaded poly(lactic-co-glycolic acid) nanoparticles (CH-loaded PLGA NPs) on multi-species biofilms. Human root blocks were prepared (n = 40), and multi-species suspensions of Candida albicans, Enterococcus faecalis and Streptococcus gordonii were incubated within the root canals for 21 days. Canals (n = 10/group) were then medicated with saline solution (negative control), chlorhexidine (positive control), calcium hydroxide and CH-loaded PLGA NPs for 7 days. Samples taken from the 0.1 mm root canal dentin were collected, and cell growth was detected by culture on BHI agar. The viable cell count of the Ca(OH)2, chlorhexidine gel and CH-loaded PLGA NPs group was significantly lower than the normal saline group (p < 0.001). CH-loaded PLGA NPs demonstrated a significant lower viable cell than Ca(OH)2 (p < 0.001); it has potential as a medicament for endodontic therapy.
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Affiliation(s)
- Warat Leelapornpisid
- Department of Restorative Dentistry and Periodontology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | | | - Thanisorn Mahatnirunkul
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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192
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Merra G, Dominici F, Gualtieri P, Capacci A, Cenname G, Esposito E, Dri M, Di Renzo L, Marchetti M. Role of vitamin K2 in bone-vascular crosstalk. INT J VITAM NUTR RES 2024; 94:143-152. [PMID: 36039403 DOI: 10.1024/0300-9831/a000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vitamin K (VK) is a fat-soluble vitamin that is indispensable for the activation of vitamin K-dependent proteins (VKDPs). It has been shown to play an important role in the proper calcium deposit at the bone level, hindering that on the vascular walls. The deficiency of this vitamin in European populations is frequent and unknown. It is related to several factors, poor dietary intake, altered intestinal absorption or altered production by bacteria, indicating possible dysbiosis. For Vitamin K2 (VK2), there is currently no official reference daily intake (RDI). However, the effects of VK2 on the improvement of health in cardiovascular diseases, on bone metabolism, on chronic kidney diseases have been the subject of research in recent decades. The microbiota in the gastrointestinal tract plays an important role: Bacteroides are primarily capable of synthetizing very long chain forms of menaquinones and, in addition to the bacteria present in the intestinal flora, VK2 is also produced by bacteria used in food fermentation processes. This review provides an update on the current literature regarding the origin of VK2 and its implications in what is called the "calcium paradox", namely the lack of calcium in the bone and its storage in the wall of the vessel.
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Affiliation(s)
- Giuseppe Merra
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Dominici
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Paola Gualtieri
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Annunziata Capacci
- Department of Medical and Surgical Sciences, Agostino Gemelli General Hospital Foundation-IRCCS, Rome, Italy
| | - Giuseppe Cenname
- Comando Generale Arma Carabinieri, Direzione di Sanità, Rome, Italy
| | - Ernesto Esposito
- General Directorate, Department of Human Policies of Basilicata Region, Potenza, Italy
| | - Maria Dri
- Department of Surgical Sciences, School of Applied Medical-Surgical Sciences, University of Rome Tor Vergata, Rome, Italy
| | - Laura Di Renzo
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marco Marchetti
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
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193
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Stefan A, Mucchi A, Hochkoeppler A. The catalytic action of human d-lactate dehydrogenase is severely inhibited by oxalate and is impaired by mutations triggering d-lactate acidosis. Arch Biochem Biophys 2024; 754:109932. [PMID: 38373542 DOI: 10.1016/j.abb.2024.109932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
d-lactate dehydrogenases are known to be expressed by prokaryotes and by eukaryotic invertebrates, and over the years the functional and structural features of some bacterial representatives of this enzyme ensemble have been investigated quite in detail. Remarkably, a human gene coding for a putative d-lactate dehydrogenase (DLDH) was identified and characterized, disclosing the occurrence of alternative splicing of its primary transcript. This translates into the expression of two human DLDH (hDLDH) isoforms, the molecular mass of which is expected to differ by 2.7 kDa. However, no information on these two hDLDH isoforms is available at the protein level. Here we report on the catalytic action of these enzymes, along with a first analysis of their structural features. In particular, we show that hDLDH is strictly stereospecific, with the larger isoform (hDLDH-1) featuring higher activity at the expense of d-lactate when compared to its smaller counterpart (hDLDH-2). Furthermore, we found that hDLDH is strongly inhibited by oxalate, as indicated by a Ki equal to 1.2 μM for this dicarboxylic acid. Structurally speaking, hDLDH-1 and hDLDH-2 were determined, by means of gel filtration and dynamic light scattering experiments, to be a hexamer and a tetramer, respectively. Moreover, in agreement with previous studies performed with human mitochondria, we identified FAD as the cofactor of hDLDH, and we report here a model of FAD binding by the human d-lactate dehydrogenase. Interestingly, the mutations W323C and T412 M negatively affect the activity of hDLDH, most likely by impairing the enzyme electron-acceptor site.
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Affiliation(s)
- Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Alberto Mucchi
- Department of Industrial Chemistry "Toso Montanari", Viale Risorgimento 4, 40136, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
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194
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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024. [PMID: 38555564 DOI: 10.1111/febs.17125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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195
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Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mixed Wolbachia infections resolve rapidly during in vitro evolution. bioRxiv 2024:2024.03.27.586911. [PMID: 38585949 PMCID: PMC10996604 DOI: 10.1101/2024.03.27.586911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species, tissues, and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.
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Affiliation(s)
- Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Pingting Wang
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Maximilian Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, USA
| | - William T Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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196
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Caron-Godon CA, Collington E, Wolf JL, Coletta G, Glerum DM. More than Just Bread and Wine: Using Yeast to Understand Inherited Cytochrome Oxidase Deficiencies in Humans. Int J Mol Sci 2024; 25:3814. [PMID: 38612624 PMCID: PMC11011759 DOI: 10.3390/ijms25073814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Inherited defects in cytochrome c oxidase (COX) are associated with a substantial subset of diseases adversely affecting the structure and function of the mitochondrial respiratory chain. This multi-subunit enzyme consists of 14 subunits and numerous cofactors, and it requires the function of some 30 proteins to assemble. COX assembly was first shown to be the primary defect in the majority of COX deficiencies 36 years ago. Over the last three decades, most COX assembly genes have been identified in the yeast Saccharomyces cerevisiae, and studies in yeast have proven instrumental in testing the impact of mutations identified in patients with a specific COX deficiency. The advent of accessible genome-wide sequencing capabilities has led to more patient mutations being identified, with the subsequent identification of several new COX assembly factors. However, the lack of genotype-phenotype correlations and the large number of genes involved in generating a functional COX mean that functional studies must be undertaken to assign a genetic variant as being causal. In this review, we provide a brief overview of the use of yeast as a model system and briefly compare the COX assembly process in yeast and humans. We focus primarily on the studies in yeast that have allowed us to both identify new COX assembly factors and to demonstrate the pathogenicity of a subset of the mutations that have been identified in patients with inherited defects in COX. We conclude with an overview of the areas in which studies in yeast are likely to continue to contribute to progress in understanding disease arising from inherited COX deficiencies.
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Affiliation(s)
- Chenelle A. Caron-Godon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Emma Collington
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Jessica L. Wolf
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Genna Coletta
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - D. Moira Glerum
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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197
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Misra HS, Rajpurohit YS. DNA damage response and cell cycle regulation in bacteria: a twist around the paradigm. Front Microbiol 2024; 15:1389074. [PMID: 38605710 PMCID: PMC11007091 DOI: 10.3389/fmicb.2024.1389074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
The co-protease activity in the RecA-ssDNA complex cleaves the autorepressor LexA, resulting in the derepression of a large number of genes under LexA control. This process is called the SOS response, and genes that are expressed in response to DNA damage are called SOS genes. The proteins encoded by the SOS genes are involved in both DNA repair and maintaining the functions of crucial cell division proteins (e.g., FtsZ) under check until the damaged DNA is presumably repaired. This mechanism of SOS response is the only known mechanism of DNA damage response and cell cycle regulation in bacteria. However, there are bacteria that do not obey this rule of DNA damage response and cell cycle regulation, yet they respond to DNA damage, repair it, and survive. That means such bacteria would have some alternate mechanism(s) of DNA damage response and cell cycle regulation beyond the canonical pathway of the SOS response. In this study, we present the perspectives that bacteria may have other mechanisms of DNA damage response and cell cycle regulation mediated by bacterial eukaryotic type Ser/Thr protein kinases as an alternate to the canonical SOS response and herewith elaborate on them with a well-studied example in the radioresistant bacterium Deinococcus radiodurans.
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Affiliation(s)
- Hari Sharan Misra
- School of Sciences, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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Dellaqua JVT, Rigueiro ALN, Silvestre AM, Pereira MCS, Felizari LD, Demartini BL, Dias EFF, Silva LAF, Casali DM, Souza KLR, Souza JM, Millen DD. Impact of combined management strategies of monensin and virginiamycin in high energy diets on ruminal fermentation and nutrients utilization. Front Vet Sci 2024; 11:1325198. [PMID: 38605925 PMCID: PMC11008231 DOI: 10.3389/fvets.2024.1325198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Feed additives such as monensin (MON) and virginiamycin (VM) are commonly utilized in feedlot diets to enhance rumen fermentation. Nevertheless, the precise effects of combining MON and VM during specific feedlot periods and the advantages of this combination remain unclear. This study was designed to investigate the effects of withdrawal of MON when associated with VM during the adaptation and finishing periods on ruminal metabolism, feeding behavior, and nutrient digestibility in Nellore cattle. The experimental design was a 5 × 5 Latin square, where each period lasted 28 days. Five rumen-cannulated Nellore yearling bulls were used (414,86 ± 21,71 kg of body weight), which were assigned to five treatments: (1) MON during the entire feeding period; (2) VM during the entire feeding period; (3) MON + VM during the adaptation period and only VM during the finishing period 1 and 2; (4) MON + VM during the entire feeding period; (5) MON + VM during the adaptation and finishing period 1 and only VM during the finishing period 2. For the finishing period 1, animals fed T3 had improved potential degradability of dry matter (p = 0.02). Cattle fed T3 and T5 had the highest crude protein degradability when compared to animals receiving T2 (p = 0.01). Animals fed T2 and T3 had reduced the time (p < 0.01) and area under pH 6.2 (p = 0.02). Moreover, animals fed T4 had greater population of protozoa from the genus Diplodinium (p = 0.04) when compared to those from animals fed T2, T3 and T5. For the finishing period 2, animals fed T3 had greater starch degradability when compared to animals receiving T4 and T5 (p = 0.04). Animals fed T3, T4 and T5 had increased the duration of time in which pH was below 5.6 (p = 0.03). The area under the curve for ruminal pH 5.2 and pH 5.6 was higher for the animals fed T3 (p = 0.01), and the area under pH 6.2 was higher for the animals fed T3 and T5 (p < 0.01) when compared to animals receiving T2. There is no substantial improvement on the rumen fermentation parameters by the concurrent utilization of MON and VM molecules, where the higher starch and protein degradability did not improve the rumen fermentation.
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Affiliation(s)
- João V. T. Dellaqua
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - André L. N. Rigueiro
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Antonio M. Silvestre
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Murilo C. S. Pereira
- Department of Animal Production, School of Agricultural and Technological Sciences, São Paulo State University (UNESP), Dracena, Brazil
| | - Luana D. Felizari
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Breno L. Demartini
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Evandro F. F. Dias
- Department of Animal Production, School of Agricultural and Technological Sciences, São Paulo State University (UNESP), Dracena, Brazil
| | - Leandro A. F. Silva
- Department of Animal Science, School of Agricultural and Veterinary Studies, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Daniel M. Casali
- Department of Animal Science, School of Agricultural and Veterinary Studies, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Katia L. R. Souza
- Department of Breeding and Animal Nutrition, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Johnny M. Souza
- Department of Animal Science, School of Agricultural and Veterinary Studies, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Danilo D. Millen
- Department of Animal Science, School of Agricultural and Veterinary Studies, São Paulo State University (UNESP), Jaboticabal, Brazil
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199
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Lax C, Nicolás FE, Navarro E, Garre V. Molecular mechanisms that govern infection and antifungal resistance in Mucorales. Microbiol Mol Biol Rev 2024; 88:e0018822. [PMID: 38445820 DOI: 10.1128/mmbr.00188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
SUMMARYThe World Health Organization has established a fungal priority pathogens list that includes species critical or highly important to human health. Among them is the order Mucorales, a fungal group comprising at least 39 species responsible for the life-threatening infection known as mucormycosis. Despite the continuous rise in cases and the poor prognosis due to innate resistance to most antifungal drugs used in the clinic, Mucorales has received limited attention, partly because of the difficulties in performing genetic manipulations. The COVID-19 pandemic has further escalated cases, with some patients experiencing the COVID-19-associated mucormycosis, highlighting the urgent need to increase knowledge about these fungi. This review addresses significant challenges in treating the disease, including delayed and poor diagnosis, the lack of accurate global incidence estimation, and the limited treatment options. Furthermore, it focuses on the most recent discoveries regarding the mechanisms and genes involved in the development of the disease, antifungal resistance, and the host defense response. Substantial advancements have been made in identifying key fungal genes responsible for invasion and tissue damage, host receptors exploited by the fungus to invade tissues, and mechanisms of antifungal resistance. This knowledge is expected to pave the way for the development of new antifungals to combat mucormycosis. In addition, we anticipate significant progress in characterizing Mucorales biology, particularly the mechanisms involved in pathogenesis and antifungal resistance, with the possibilities offered by CRISPR-Cas9 technology for genetic manipulation of the previously intractable Mucorales species.
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Affiliation(s)
- Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco E Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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200
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Yang JE, Jeon HS, Kim S, Kim YY, Kim JC, Kim HM, Hwang IM, Park HW. Valorization of Cabbage Waste as a Feedstock for Microbial Polyhydroxyalkanoate Production: Optimizing Hydrolysis Conditions and Polyhydroxyalkanoate Production. J Agric Food Chem 2024; 72:6110-6117. [PMID: 38372212 DOI: 10.1021/acs.jafc.3c07057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Establishing a platform for the bioconversion of waste resources into value-added compounds is critical for achieving a sustainable and eco-friendly economy. Herein, we produced polyhydroxyalkanoate via microbial fermentation using cabbage waste as a feedstock and metabolically engineered Escherichia coli. For this, the hydrolysis conditions of cabbage waste were optimized by focusing on parameters such as substrate and enzyme concentrations to enhance the saccharification efficiency. The phaABC operon, which encodes key enzymes responsible for polyhydroxyalkanoate biosynthesis in Ralstonia eutropha H16, was overexpressed in E. coli. Using cabbage hydrolysate as the feedstock, this engineered E. coli strain could produce poly(3-hydroxybutyrate) with a polymer content of 26.0 wt % of dry cell weight. Moreover, malic acid in cabbage hydrolysate significantly enhanced poly(3-hydroxybutyrate) production; the addition of 0.5 g/L malic acid markedly increased poly(3-hydroxybutyrate) content by 59.9%. This study demonstrates the potential of cabbage waste as a promising raw material for the microbial production of polyhydroxyalkanoate.
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Affiliation(s)
- Jung Eun Yang
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Hye Sung Jeon
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Seulbi Kim
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
- Division of Applied Bioscience & Biotechnology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Yeong Yeol Kim
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Jong-Cheol Kim
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Ho Myeong Kim
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - In Min Hwang
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
| | - Hae Woong Park
- Technology Innovation Research Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju 61755, Republic of Korea
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