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Zhang D, Tong D, Wang Z, Wang S, Jia Y, Ning Y. Inactivation mechanism of phenyllactic acid against Bacillus cereus spores and its application in milk beverage. Food Chem 2024; 453:139601. [PMID: 38754350 DOI: 10.1016/j.foodchem.2024.139601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Phenyllactic acid (PLA) as a natural phenolic acid exhibits antibacterial activity against non-spore-forming bacteria, while the inhibitory effect against bacterial spore remained unknown. Herein, this study investigated the inactivation effect of PLA against Bacillus cereus spores. The results revealed that the minimum inhibitory concentration of PLA was 1.25 mg/mL. PLA inhibited the outgrowth of germinated spores into vegetative cells rather than germination of spores. PLA disrupted the spore coat, and damaged the permeability and integrity of inner membrane. Moreover, PLA disturbed the establishment of membrane potential due to the inhibition of oxidative metabolism. SEM observations further visualized the morphological changes and structural disruption caused by PLA. Besides, PLA caused the degradation of DNA of germinated spores. Finally, PLA was applied in milk beverage, and showed promising inhibitory effect against B. cereus spores. This finding could provide scientific basis for the application of PLA against spore-forming bacteria in food industry.
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Affiliation(s)
- Dongchun Zhang
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Danya Tong
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Zhixin Wang
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Shijie Wang
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Yingmin Jia
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Yawei Ning
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China.
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102
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Stovicek V, Lengeler KB, Wendt T, Rasmussen M, Katz M, Förster J. Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast. N Biotechnol 2024; 82:92-106. [PMID: 38788897 DOI: 10.1016/j.nbt.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
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Affiliation(s)
- Vratislav Stovicek
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Klaus B Lengeler
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; Traitomic A/S, J.C. Jacobsens Gade 1, DK-1799 Copenhagen V, Denmark
| | - Magnus Rasmussen
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Jochen Förster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; DTU Biosustain, The Novo Nordisk Foundation Center for Biosustainability, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
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103
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Hemmat-Jou MH, Liu S, Liang Y, Chen G, Fang L, Li F. Microbial arsenic methylation in soil-water systems and its environmental significance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173873. [PMID: 38879035 DOI: 10.1016/j.scitotenv.2024.173873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
In this review, we have summarized the current knowledge about the environmental importance, relevance, and consequences of microbial arsenic (As) methylation in various ecosystems. In this regard, we have presented As biomethylation in terrestrial and aquatic ecosystems particularly in rice paddy soils and wetlands. The functions of As biomethylation by microbial consortia in anaerobic and aerobic conditions are extensively discussed. In addition, we have tried to explain the interconnections between As transformation and carbon (C), such as microbial degradation of organic compounds and methane (CH4) emission. These processes can cause As release because of the reduction of arsenate (As(V)) to the more mobile arsenite (As(III)) as well as As methylation and the formation of toxic trivalent methylated As species in anaerobic conditions. Furthermore, the sulfur (S) transformation can form highly toxic thiolated As species owing to its interference with As biomethylation. Besides, we have focused on many other mutual interlinks that remain elusive between As and C, including As biomethylation, thiolation, and CH4 emission, in the soil-water systems. Recent developments have clarified the significant and complex interactions between the coupled microbial process in anoxic and submerged soils. These processes, performed by little-known/unknown microbial taxa or well-known members of microbial communities with unrecognized metabolic pathways, conducted several concurrent reactions that contributed to global warming on our planet and have unfavorable impacts on water quality and human food resources. Finally, some environmental implications in rice production and arsenic removal from soil-water systems are discussed. Generally, our understanding of the ecological and metabolic evidence for the coupling and synchronous processes of As, C, and S are involved in environmental contamination-caused toxicity in human food, including high As content in rice grain, water resources, and global warming through methanogenesis elucidate combating global rice safety, drinking water, and climate changes.
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Affiliation(s)
- Mohammad Hossein Hemmat-Jou
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Sujie Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yongmei Liang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guanhong Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Liping Fang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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104
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Heydenreich R, Delbrück AI, Peternell C, Trunet C, Mathys A. Characterization of high-pressure-treated Bacillus subtilis spore populations using flow cytometry - Shedding light on spore superdormancy at 550 MPa. Int J Food Microbiol 2024; 422:110812. [PMID: 38970996 DOI: 10.1016/j.ijfoodmicro.2024.110812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/04/2024] [Accepted: 06/23/2024] [Indexed: 07/08/2024]
Abstract
Mild spore inactivation can be challenging in industry because of the remarkable resistance of bacterial spores. High pressure (HP) can trigger spore germination, which reduces the spore's resistance, and thereby allows mild spore inactivation. However, spore germination is heterogenous. Some slowly germinating or non-germinating spores called superdormant spores remain resistant and can survive. Therefore, superdormant spores need to be characterized to understand the causes of their germination deficiency. Bacillus subtilis spores were pressurized for 50 s - 6 min at a very high pressure (vHP) level of 550 MPa and 60 °C in buffer to trigger germination. For a rapid quantification of the remaining ungerminated superdormant spores, flow cytometry (FCM) analysis was validated using single cell sorting and growth analysis. FCM based on propidium iodide (PI) and SYTO16 can be used for 550 MPa-superdormant spores after short vHP treatments of ≤1 min and post-HP incubation at 37 °C or 60 °C. The need for a post-HP incubation is particular for vHP treatments. The incubation was successful to separate FCM signals from superdormant and germinated spores, thus allowing superdormant spore quantification. The SYTO16 and PI fluorescence levels did not necessarily indicate superdormancy or apparent viability. This highlights the general need for FCM validation for different HP treatment conditions. The ∼7 % of ungerminated, i.e., superdormant, spores were isolated after a vHP treatment (550 MPa, 60 °C, 43-52 s). This allowed the characterization of vHP superdormant spores for the first time. The superdormant spores had a similar dipicolinic acid content as spores of the initial dormant population. Descendants of superdormant spores had a normal vHP germination capacity. The causes of vHP superdormancy were thus unlikely linked to the dipicolinic acid content or a permanent genetic change. Isolated superdormant spores germinated better in a second vHP treatment compared to the initial spore population. This has not been observed for other germination stimuli so far. In addition, the germination capacity of the initial spore population was time-dependent. A vHP germination deficiency can therefore be lost over time and seems to be caused by transient factors. Permanent cellular properties played a minor role as causes of superdormancy under chosen HP treatment conditions. The study gained new fundamental insights in vHP superdormancy which are of applied interest. Understanding superdormancy helps to efficiently develop a strategy to avoid superdormant spores and hence to inactivate all spores. The development of a mild HP spore germination-inactivation process aims at better preserving the food quality.
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Affiliation(s)
- Rosa Heydenreich
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition, and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Alessia I Delbrück
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition, and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Christina Peternell
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition, and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Clément Trunet
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Quimper, France.
| | - Alexander Mathys
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition, and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland.
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105
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Wang L, Lee E, Barlaz MA, de Los Reyes FL. Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 186:77-85. [PMID: 38865907 DOI: 10.1016/j.wasman.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/18/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.
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Affiliation(s)
- Ling Wang
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695
| | - Eunyoung Lee
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695
| | - Morton A Barlaz
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695
| | - Francis L de Los Reyes
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695.
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106
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Xia L, Cheng L, Xi W, Zhang X, Shi X. Distinct influence of model electron shuttles on anaerobic mononitrophenols reduction in aquatic environments by Shewanella oneidensis MR-1. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135348. [PMID: 39079298 DOI: 10.1016/j.jhazmat.2024.135348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
The environmental fate and risks of mononitrophenols (mono-NPs), the simplest nitrophenols (NPs) often found in aquatic environments, are profoundly influenced by anaerobic bioreduction and co-existing electron shuttles (ESs), but little is known about the underlying mechanisms. Here, we elucidate the pathways of anaerobic mono-NPs bioreduction by Shewanella oneidensis MR-1 and assess the effect of model ESs on these processes. We found that all three mono-NPs isomers could be readily reduced to their corresponding aminophenols by S. oneidensis MR-1 under anaerobic conditions. CymA, a core component of the Mtr respiratory pathway, performs a dynamic role in these bioreduction, which is highly dependent on the bioreduction kinetics. The exogenous addition of quinones was found to accelerate the mono-NPs bioreduction through interactions with key outer-membrane proteins (e.g., OmcA and MtrC), and all these processes matched well to linear free energy relationships (LFERs). Surprisingly, adding riboflavin did not influence the bioreduction of all three mono-NPs isomers, which may be due to the contribution of OmcA and MtrC to these bioreduction processes and their downregulated expression. This study enhances our understanding of the environmental fate of mono-NPs and their bioconversion processes, providing valuable insights for the bioremediation of nitrophenol-contaminated sites.
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Affiliation(s)
- Lisong Xia
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Lei Cheng
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China.
| | - Wenni Xi
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Xiliang Zhang
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Xianyang Shi
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China.
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107
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Papale M, Fazi S, Severini M, Scarinci R, Dell'Acqua O, Azzaro M, Venuti V, Fazio B, Fazio E, Crupi V, Irrera A, Rizzo C, Giudice AL, Caruso G. Structural properties and microbial diversity of the biofilm colonizing plastic substrates in Terra Nova Bay (Antarctica). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173773. [PMID: 38844237 DOI: 10.1016/j.scitotenv.2024.173773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization on plastic polymers has been extensively explored, however the temporal dynamics of biofilm community in Antarctic environments are almost unknown. As a contribute to fill this knowledge gap, the structural characteristics and microbial diversity of the biofilm associated with polyvinyl chloride (PVC) and polyethylene (PE) panels submerged at 5 m of depth and collected after 3, 9 and 12 months were investigated in four coastal sites of the Ross Sea. Additional panels placed at 5 and 20 m were retrieved after 12 months. Chemical characterization was performed by FTIR-ATR and Raman (through Surface-Enhanced Raman Scattering, SERS) spectroscopy. Bacterial community composition was quantified at a single cell level by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and Confocal Laser Scanning Microscopy (CLSM); microbial diversity was assessed by 16S rRNA gene sequencing. This multidisciplinary approach has provided new insights into microbial community dynamics during biofouling process, shedding light on the biofilm diversity and temporal succession on plastic substrates in the Ross Sea. Significant differences between free-living and microbial biofilm communities were found, with a more consolidated and structured community composition on PVC compared to PE. Spectral features ascribable to tyrosine, polysaccharides, nucleic acids and lipids characterized the PVC-associated biofilms. Pseudomonadota (among Gamma-proteobacteria) and Alpha-proteobacteria dominated the microbial biofilm community. Interestingly, in Road Bay, close to the Italian "Mario Zucchelli" research station, the biofilm growth - already observed during summer season, after 3 months of submersion - continued afterwards leading to a massive microbial abundance at the end of winter (after 12 months). After 3 months, higher percentages of Gamma-proteobacteria in Road Bay than in the not-impacted site were found. These observations lead us to hypothesize that in this site microbial fouling developed during the first 3 months could serve as a starter pioneering community stimulating the successive growth during winter.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Stefano Fazi
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy; National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Maila Severini
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy
| | - Roberta Scarinci
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy
| | - Ombretta Dell'Acqua
- DISTAV, Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa, 26, 16132 Genoa, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Valentina Venuti
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Barbara Fazio
- URT "LabSens of Beyond Nano" of the Department of Physical Sciences and Technologies of Matter, National Research Council (CNR- DSFTM-ME), Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy; Institute for Chemical and Physical Processes, National Research Council (CNR-IPCF), Viale Ferdinando Stagno d'Alcontres, 37, 98158 Messina, Messina, Italy
| | - Enza Fazio
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Vincenza Crupi
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Alessia Irrera
- URT "LabSens of Beyond Nano" of the Department of Physical Sciences and Technologies of Matter, National Research Council (CNR- DSFTM-ME), Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy.
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy; Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy; National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy.
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108
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Müller S, Corbera-Rubio F, Schoonenberg Kegel F, Laureni M, van Loosdrecht MCM, van Halem D. Shifting to biology promotes highly efficient iron removal in groundwater filters. WATER RESEARCH 2024; 262:122135. [PMID: 39067270 DOI: 10.1016/j.watres.2024.122135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Rapid sand filters are established and widely applied technologies for groundwater treatment. In these filters, main groundwater contaminants such as iron, manganese, and ammonium are oxidized and removed. Conventionally, intensive aeration is employed to provide oxygen for these redox reactions. While effective, intensive aeration promotes flocculent iron removal, which results in iron oxide flocs that rapidly clog the filter. In this study, we operated two parallel full-scale sand filters at different aeration intensities to resolve the relative contribution of homogeneous, heterogeneous and biological iron removal pathways, and identify their operational controls. Our results show that mild aeration in the LOW filter (5 mg/L O2, pH 6.9) promoted biological iron removal and enabled iron oxidation at twice the rate compared to the intensively aerated HIGH filter (>10 mg/L O2, pH 7.4). Microscopy images showed distinctive twisted stalk-like iron solids, the biosignatures of Gallionella ferruginea, both in the LOW filter sand coatings as well as in its backwash solids. In accordance, 10 times higher DNA copy numbers of G. ferruginea were found in the LOW filter effluent. Clogging by biogenic iron solids was slower than by chemical iron flocs, resulting in lower backwash frequencies and yielding four times more water per run. Ultimately, our results reveal that biological iron oxidation can be actively controlled and favoured over competing physico-chemical routes. The production of more compact and practically valuable iron oxide solids is of outmost interest. We conclude that, although counterintuitive, slowing down iron oxidation in the water before filtration enables rapid iron removal in the biofilter.
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Affiliation(s)
- Simon Müller
- Delft University of Technology, the Netherlands.
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109
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Shi YZ, Wang ZJ, Shi N, Bai LY, Jiang YM, Jiang L, Liu T, Wei MZ, Qin ML, Luo XD. Anti-MRSA mechanism of spirostane saponin in Rohdea pachynema F.T.Wang & tang. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118327. [PMID: 38750987 DOI: 10.1016/j.jep.2024.118327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
ETHNOPHARMACOLOGY RELEVANCE Rohdea pachynema F.T.Wang & Tang (R. pachynema), is a traditional folk medicine used for the treatment of stomach pain, stomach ulcers, bruises, and skin infections in China. Some of the diseases may relate to microbial infections in traditional applications. However few reports on its antimicrobial properties and bioactive components. AIM OF THE STUDY To identify its bioactive constituents against methicillin-resistant Staphylococcus aureus (MRSA) in vitro and in vivo, and its mechanism. MATERIALS AND METHODS The anti-MRSA ingredient 6α-O-[β-D-xylopyranosyl-(1 → 3)-β-D-quinovopyranosyl]-(25S)-5α-spirostan-3β-ol (XQS) was obtained from R. pachynema by phytochemical isolation. Subsequently, XQS underwent screening using the broth microdilution method and growth inhibition curves to assess its antibacterial activity. The mechanism of XQS was evaluated by multigeneration induction, biofilm resistance assay, scanning electron microscopy, transmission electron microscopy, and metabolomics. Additionally, a mouse skin infection model was established in vivo. RESULTS 26 compounds were identified from the R. pachynema, in which anti-MRSA spirostane saponin (XQS) was reported for the first time with a minimum inhibitory concentration (MIC) of 8 μg/mL. XQS might bind to peptidoglycan (PGN) of the cell wall, phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) of the cell membrane, then destroying the cell wall and the cell membrane, resulting in reduced membrane fluidity and membrane depolarization. Furthermore, XQS affected MRSA lipid metabolism, amino acid metabolism, and ABC transporters by metabolomics analysis, which targeted cell walls and membranes causing less susceptibility to drug resistance. Furthermore, XQS (8 mg/kg) recovered skin wounds in mice infected by MRSA effectively, superior to vancomycin (8 mg/kg). CONCLUSIONS XQS showed anti-MRSA bioactivity in vitro and in vivo, and its mechanism association with cell walls and membranes was reported for the first, which supported the traditional uses of R. pachynema and explained its sensitivity to MRSA.
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Affiliation(s)
- Yang-Zhu Shi
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Zhao-Jie Wang
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Nian Shi
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Li-Yu Bai
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yue-Ming Jiang
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ling Jiang
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Tie Liu
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Mei-Zheng Wei
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ma-Long Qin
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xiao-Dong Luo
- Yunnan Characteristic Plant Extraction Laboratory, Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China.
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110
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Wei N, Hu C, Dittmann E, Song L, Gan N. The biological functions of microcystins. WATER RESEARCH 2024; 262:122119. [PMID: 39059200 DOI: 10.1016/j.watres.2024.122119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
Microcystins are potent hepatotoxins predominantly produced by bloom-forming freshwater cyanobacteria (e.g., Microcystis, Planktothrix, Dolichospermum). Microcystin biosynthesis involves large multienzyme complexes and tailoring enzymes encoded by the mcy gene cluster. Mutation, recombination, and deletion events have shaped the mcy gene cluster in the course of evolution, resulting in a large diversity of microcystin congeners and the natural coexistence of toxic and non-toxic strains. The biological functions of microcystins and their association with algal bloom formation have been extensively investigated over the past decades. This review synthesizes recent advances in decoding the biological role of microcystins in carbon/nitrogen metabolism, antioxidation, colony formation, and cell-to-cell communication. Microcystins appear to adopt multifunctional roles in cyanobacteria that reflect the adaptive plasticity of toxic cyanobacteria to changing environments.
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Affiliation(s)
- Nian Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chenlin Hu
- College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Elke Dittmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Lirong Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Nanqin Gan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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111
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Markus V. Gut bacterial quorum sensing molecules and their association with inflammatory bowel disease: Advances and future perspectives. Biochem Biophys Res Commun 2024; 724:150243. [PMID: 38857558 DOI: 10.1016/j.bbrc.2024.150243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/15/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
Inflammatory Bowel Disease (IBD) is an enduring inflammatory disease of the gastrointestinal tract (GIT). The complexity of IBD, its profound impact on patient's quality of life, and its burden on healthcare systems necessitate continuing studies to elucidate its etiology, refine care strategies, improve treatment outcomes, and identify potential targets for novel therapeutic interventions. The discovery of a connection between IBD and gut bacterial quorum sensing (QS) molecules has opened exciting opportunities for research into IBD pathophysiology. QS molecules are small chemical messengers synthesized and released by bacteria based on population density. These chemicals are sensed not only by the microbial species but also by host cells and are essential in gut homeostasis. QS molecules are now known to interact with inflammatory pathways, therefore rendering them potential therapeutic targets for IBD management. Given these intriguing developments, the most recent research findings in this area are herein reviewed. First, the global burden of IBD and the disruptions of the gut microbiota and intestinal barrier associated with the disease are assessed. Next, the general QS mechanism and signaling molecules in the gut are discussed. Then, the roles of QS molecules and their connection with IBD are elucidated. Lastly, the review proposes potential QS-based therapeutic targets for IBD, offering insights into the future research trajectory in this field.
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Affiliation(s)
- Victor Markus
- Near East University, Faculty of Medicine, Department of Medical Biochemistry, Nicosia, TRNC Mersin 10, Turkey.
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112
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Jiang H, Okoye CO, Chen X, Zhang F, Jiang J. High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173775. [PMID: 38844238 DOI: 10.1016/j.scitotenv.2024.173775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3- accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.
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Affiliation(s)
- Huifang Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Xunfeng Chen
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fusheng Zhang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Kafle S, Montoya B, Tang L, Tam YK, Muramatsu H, Pardi N, Sigal LJ. The roles of CD4 + T cell help, sex, and dose in the induction of protective CD8 + T cells against a lethal poxvirus by mRNA-LNP vaccines. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102279. [PMID: 39188304 PMCID: PMC11345529 DOI: 10.1016/j.omtn.2024.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 07/16/2024] [Indexed: 08/28/2024]
Abstract
The role of CD4+ T cells in the induction of protective CD8+ T cells by mRNA lipid nanoparticle (LNP) vaccines is unknown. We used B6 or Tlr9 -/- mice depleted or not of CD4+ T cells and LNP vaccines loaded with mRNAs encoding the ectromelia virus (ECTV) MHC class I H-2 Kb-restricted immunodominant CD8+ T cell epitope TSYKFESV (TSYKFESV mRNA-LNPs) or the ECTV EVM158 protein, which contains TSYKFESV (EVM-158 mRNA-LNPs). Following prime and boost with 10 μg of either vaccine, Kb-TSYKFESV-specific CD8+ T cells fully protected male and female mice from ECTV at 29 (both mRNA-LNPs) or 90 days (EVM158 mRNA-LNPs) post boost (dpb) independently of CD4+ T cells. However, at 29 dpb with 1 μg mRNA-LNPs, males had lower frequencies of Kb-TSYKFESV-specific CD8+ T cells and were much less well protected than females from ECTV, also independently of CD4+ T cells. At 90 dpb with 1 μg EVM158 mRNA-LNPs, the frequencies of Kb-TSYKFESV-specific CD8+ T cells in males and females were similar, and both were similarly partially protected from ECTV, independently of CD4+ T cells. Therefore, at optimal or suboptimal doses of mRNA-LNP vaccines, CD4+ T cell help is unnecessary to induce protective anti-poxvirus CD8+ T cells specific to a dominant epitope. At suboptimal doses, protection of males requires more time to develop.
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Affiliation(s)
- Samita Kafle
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Brian Montoya
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lingjuan Tang
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ying K. Tam
- Acuitas Therapeutics, Vancouver, BC V6T 1Z3, Canada
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis J. Sigal
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
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114
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Nef C, Pierella Karlusich JJ, Bowler C. From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230172. [PMID: 39034691 PMCID: PMC11293860 DOI: 10.1098/rstb.2023.0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/26/2024] [Accepted: 03/21/2024] [Indexed: 07/23/2024] Open
Abstract
Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris75005, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris75016, France
| | | | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris75005, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris75016, France
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115
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Bronstein JL, Sridhar H. Connecting and integrating cooperation within and between species. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230203. [PMID: 39034697 PMCID: PMC11293865 DOI: 10.1098/rstb.2023.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 07/23/2024] Open
Abstract
There has long been a fundamental divide in the study of cooperation: researchers focus either on cooperation within species, including but not limited to sociality, or else on cooperation between species, commonly termed mutualism. Here, we explore the ecologically and evolutionarily significant ways in which within- and between-species cooperation interact. We highlight two primary cross-linkages. First, cooperation of one type can change the context in which cooperation of the other type functions, and thus potentially its outcome. We delineate three possibilities: (i) within-species cooperation modulates benefits for a heterospecific partner; (ii) between-species cooperation affects the dynamics of within-species cooperation; and (iii) both processes take place interactively. The second type of cross-linkage emerges when resources or services that cooperation makes available are obtainable either from members of the same species or from different species. This brings cooperation at the two levels into direct interaction, to some extent obscuring the distinction between them. We expand on these intersections between within- and between-species cooperation in a diversity of taxa and interaction types. These interactions have the potential to weave together social networks and trophic dynamics, contributing to the structure and functioning of ecological communities in ways that are just beginning to be explored. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.
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Affiliation(s)
- Judith L. Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ85721, USA
| | - Hari Sridhar
- Konrad Lorenz Institute for Evolution and Cognition Research, KlosterneuburgA-3400, Austria
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116
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Ni JB, Ding CJ, Zhang JS, Fang XM, Xiao HW. Insight into the surface discharge cold plasma efficient inactivation of Pseudomonas fluorescens in water based on exogenous reactive oxygen and nitrogen species: Synergistic mechanism and energy benefits. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134984. [PMID: 38943891 DOI: 10.1016/j.jhazmat.2024.134984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
As well known, surface discharge cold plasma has efficient inactivation ability and a variety of RONS are main active particles for inactivation, but their synergistic mechanism is still not clear. Therefore, surface discharge cold plasma system was applied to treat Pseudomonas fluorescens to study bacterial inactivation mechanism and energy benefit. Results showed that energy efficiency was directly proportional to applied voltage and inversely proportional to initial concentration. Cold plasma treatment for 20 min was inactivated by approximately > 4-log10Pseudomonas fluorescens and application of •OH and 1O2 scavengers significantly improved survival rate. In addition, •OH and 1O2 destroyed cell membrane structure and membrane permeability, which promoted diffusion of RONS into cells and affecting energy metabolism and antioxidant capacity, leading to bacterial inactivation. Furthermore, accumulation of intracellular NO and ONOOH was related to infiltration of exogenous RNS, while accumulation of •OH, H2O2, 1O2, O2- was the result of joint action of endogenous and exogenous ROS. Transcriptome analysis revealed that different RONS of cold plasma were responsible for Pseudomonas fluorescens inactivation and related to activation of intracellular antioxidant defense system and regulation of genes expression related to amino acid metabolism and energy metabolism, which promoting cellular process, catalytic activity and other biochemical pathways.
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Affiliation(s)
- Jia-Bao Ni
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China; State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 1 Xiangshan Beigou, Beijing 100093, China
| | - Chang-Jiang Ding
- College of Science, Inner Mongolia University of Technology, Hohhot, China
| | - Jing-Shou Zhang
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China
| | - Xiao-Ming Fang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 1 Xiangshan Beigou, Beijing 100093, China.
| | - Hong-Wei Xiao
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China.
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117
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Hu CJ, Lv YQ, Xian WD, Jiao JY, Lian ZH, Tan S, Li MM, Luo ZH, Liu ZT, Lv AP, Liu L, Ali M, Liu WQ, Li WJ. Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135017. [PMID: 38936185 DOI: 10.1016/j.jhazmat.2024.135017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 06/22/2024] [Indexed: 06/29/2024]
Abstract
Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066T and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066T carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066T might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".
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Affiliation(s)
- Chao-Jian Hu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yi-Qing Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen-Dong Xian
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Mukhtiar Ali
- Advanced Water Technology Laboratory, National University of Singapore (Suzhou) Research Institute, Suzhou, Jiangsu 215123, China.
| | - Wei-Qiu Liu
- School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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Xu H, Zou Z, Jin Y, Kuzyakov Y, Huang X, Wu X, Zhu F. Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135135. [PMID: 38986409 DOI: 10.1016/j.jhazmat.2024.135135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.
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Affiliation(s)
- Hongyang Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Ziying Zou
- School of Geographical Sciences, Hunan Normal University, Changsha 410081, China
| | - Yuke Jin
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37077, Germany; Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Xinhao Huang
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China
| | - Xiaohong Wu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Fan Zhu
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China.
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Rai SN, Dutta T. Role of Yrn2 under oxidative stress in Deinococcus radiodurans. Biochem Biophys Res Commun 2024; 723:150169. [PMID: 38815487 DOI: 10.1016/j.bbrc.2024.150169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Among the two Y RNAs in Deinococcus radiodurans, the functional properties of Yrn2 are still not known. Yrn2 although consists of a long stem-loop for Rsr binding, differs from Yrn1 in the effector binding site. An initial study on Yrn2 delineated it to be a UV-induced noncoding RNA. Apart from that Yrn2 has scarcely been investigated. In the current study, we identified Yrn2 as an γ-radiation induced Y RNA, which is also induced upon H2O2 and mitomycin treatment. Ectopically expressed Yrn2 appeared to be nontoxic to the cell growth. An overabundance of Yrn2 was found to ameliorate cell survival under oxidative stress through the detoxification of intracellular reactive oxygen species with a subsequent decrease in total protein carbonylation. A significant accumulation of intracellular Mn(II) with unaltered Fe(II) and Zn(II) with detected while Yrn2 is overabundant in the cells. This study identified the role of a novel Yrn2 under oxidative stress in D. radiodurans.
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Affiliation(s)
- Shiv Narayan Rai
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Hesse E, Luján AM, O'Brien S, Newbury A, McAvoy T, Soria Pascual J, Bayer F, Hodgson DJ, Buckling A. Parallel ecological and evolutionary responses to selection in a natural bacterial community. Proc Natl Acad Sci U S A 2024; 121:e2403577121. [PMID: 39190353 DOI: 10.1073/pnas.2403577121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024] Open
Abstract
Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.
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Affiliation(s)
- Elze Hesse
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Adela M Luján
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas, Consejo Nacional de Investigaciones Científicas y Técnicas/Universidad Católica de Córdoba, Córdoba X5016DHK, Argentina
- Facultad de Ciencias de la Salud, Universidad Católica de Córdoba (UCC), Córdoba X5004ASK, Argentina
| | - Siobhan O'Brien
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Arthur Newbury
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Terence McAvoy
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Jesica Soria Pascual
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Florian Bayer
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - David J Hodgson
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Centre for Ecology and Conservation & Environment and Sustainability Institute, Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, United Kingdom
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121
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Rodriguez A, Diehl JD, Wright GS, Bonar CD, Lundgren TJ, Moss MJ, Li J, Milenkovic T, Huber PW, Champion MM, Emrich SJ, Clark PL. Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production. Proc Natl Acad Sci U S A 2024; 121:e2405510121. [PMID: 39190361 DOI: 10.1073/pnas.2405510121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications.
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Affiliation(s)
- Anabel Rodriguez
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jacob D Diehl
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Gabriel S Wright
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Christopher D Bonar
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Taylor J Lundgren
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - McKenze J Moss
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556
| | - Tijana Milenkovic
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W Huber
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew M Champion
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37996
| | - Patricia L Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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122
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Ali DH, Gaji RY. TKL family kinases in human apicomplexan pathogens. Mol Biochem Parasitol 2024; 259:111628. [PMID: 38719028 PMCID: PMC11182715 DOI: 10.1016/j.molbiopara.2024.111628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Apicomplexan parasites are the primary causative agents of many human diseases, including malaria, toxoplasmosis, and cryptosporidiosis. These opportunistic pathogens undergo complex life cycles with multiple developmental stages, wherein many key steps are regulated by phosphorylation mechanisms. The genomes of apicomplexan pathogens contain protein kinases from different groups including tyrosine kinase-like (TKL) family proteins. Although information on the role of TKL kinases in apicomplexans is quite limited, recent studies have revealed the important role of this family of proteins in apicomplexan biology. TKL kinases in these protozoan pathogens show unique organization with many novel domains thus making them attractive candidates for drug development. In this mini review, we summarize the current understanding of the role of TKL kinases in human apicomplexan pathogens' (Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium parvum) biology and pathogenesis.
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Affiliation(s)
- Dima Hajj Ali
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Rajshekhar Y Gaji
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA.
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123
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Zhong S, Feng JC, Chen X, Huang YJ, Wu XN, Zhang S. Exploring optimal incubation conditions and characteristics of methane oxidizing organisms in deep-sea environments. BIORESOURCE TECHNOLOGY 2024; 407:131084. [PMID: 39025372 DOI: 10.1016/j.biortech.2024.131084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
Anaerobic methanotrophic archaea (ANME) play key roles in buffering the methane budget in the deep-sea environment. This study aimed to explore the optimal environmental conditions for ANME enrichment. The result showed that the sample at 10.5 MPa contained the largest copy numbers of methyl-coenzyme M reductase alpha subunit (mcrA) gene (1.1 × 106 copies/g) compared to any other pressures and the sample at 4 °C contained higher mcrA gene (1.6 × 106 copies/g) than other temperatures. The optimal enrichment pressure for ANME-2c is 10.5 MPa at 4 °C, with an optimal subsequent incubation for ANME-2c less than 211days. Moreover, the beta nearest taxon index was significantly correlated with the incubation time (P<0.05). Total inorganic carbon and sulfate ion were key environmental factors driving community construction. This study offers insights into how ANME-2c was enriched and how species coexist in shared habitats during enrichment.
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Affiliation(s)
- Song Zhong
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Jing-Chun Feng
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangzhou 511458, China.
| | - Xiao Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Yong-Ji Huang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Xiao-Nan Wu
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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124
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Atsbeha G, Kebede M, Samuel B, Baraki H, Tadesse H, Sbhatu DB. Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes. J Genet Eng Biotechnol 2024; 22:100397. [PMID: 39179324 PMCID: PMC11231716 DOI: 10.1016/j.jgeb.2024.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/08/2024] [Accepted: 06/12/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Rhizobium giardinii has been demonstrated to colonize the roots of a variety of legume species, including common beans, and to increase nitrogen fixation. This suggests that Rhizobium giardinii might be a beneficial tool for sustainable agriculture by lowering dependency on synthetic nitrogen fertilizers and enhancing soil fertility. Understanding the regulatory components in the R. giardinii A3AY_RS01 genes might also lead to the creation of innovative ways for increasing the effectiveness of nitrogen fixation in other agriculturally important bacteria. Therefore, this study was aimed to predict regulatory element of R. giardinii DNA-binding response regulator A3AY_RS01 genes. RESULTS The locations for 19 % of the Transcriptional start site (TSSs) were within -300 bp relative to the start codon and ten candidate motifs were identified that are shared by at least 50 % of the R. giardinii A3AY_RS01 promoter input sequences from both strands. Motif 1 was revealed as the common promoter motif for all of R. giardinii A3AY_RS01 genes that serves as binding sites for TFs involved in the expression regulation of these genes. Hence, it was revealed that Motif 1 may serve as the binding site chiefly for Ferric uptake regulator (Fur) transcription factor family to regulate expression of A3AY_RS01 genes. High CpG density in the promoter than body regions were observed for most of the genes except for A3AY_RS0102950, A3AY_RS0120195 and A3AY_RS0131150 genes. Nonetheless, promoter areas were richer than body regions in both techniques. CONCLUSIONS MV1 motif can serve as a binding site for the Fur transcription factor gene family in R. giardinii to regulate the expression of R. giardinii A3AY_RS01 genes. R. giardinii A3AY_RS01 genes are rich in CpG Islands, and play an important role in the regulation of the gene expression of nitrogen fixing in this bacterium.
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Affiliation(s)
- Genet Atsbeha
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia.
| | - Mulugeta Kebede
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Behailu Samuel
- Department of Animal Science, College of Agriculture and Natural Resource, Salale University, Fitche, Ethiopia.
| | - Haftom Baraki
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
| | - Hailekiros Tadesse
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
| | - Desta Berhe Sbhatu
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
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125
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Tran DM, Huynh TU, Do TO. Novel domain-structure-containing chitinases A and B of Bacillus velezensis produced by recombinant Escherichia coli cells: Synergism on chitin degradation and their potential in suppressing Candida albicans cell germination. J Genet Eng Biotechnol 2024; 22:100402. [PMID: 39179322 PMCID: PMC11318559 DOI: 10.1016/j.jgeb.2024.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/12/2024] [Accepted: 07/10/2024] [Indexed: 08/26/2024]
Abstract
Bacillus velezensis RB.IBE29 harbors two chitinases belonging to the glycoside hydrolase family 18 and exhibiting a novel domain structure. The roles of these chitinases in crop production have been reported; nevertheless, their contribution to controlling human pathogens is unknown. In this initial work, the chitinases A (BvChiA) and B (BvChiB) of strain RB.IBE29 were produced in recombinant Escherichia coli BL21-CodonPlus (DE3)-RIPL cells and subsequently purified using HisTrap FF column. The purified BvChiA and BvChiB exhibited the highest chitinase and binding activities against colloidal chitin. Combining both chitinases for the hydrolysis of powdered chitin increased the reducing sugar content by 88.7 %. Moreover, the purified chitinases remarkably suppressed the germination of Candida albicans VTCC 20568 (=JCM 2070) cells. These results indicated that the novel domain-structure-containing chitinases of strain RB.IBE29 have great potential and can be further developed as a novel therapeutic agent against human pathogenic C. albicans.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam.
| | - To Uyen Huynh
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
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126
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Hariri Akbari F, Song Z, Turk M, Gunde-Cimerman N, Gostinčar C. Experimental evolution of extremotolerant and extremophilic fungi under osmotic stress. IUBMB Life 2024; 76:617-631. [PMID: 38647201 DOI: 10.1002/iub.2825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
Experimental evolution was carried out to investigate the adaptive responses of extremotolerant fungi to a stressful environment. For 12 cultivation cycles, the halotolerant black yeasts Aureobasidium pullulans and Aureobasidium subglaciale were grown at high NaCl or glycerol concentrations, and the halophilic basidiomycete Wallemia ichthyophaga was grown close to its lower NaCl growth limit. All evolved Aureobasidium spp. accelerated their growth at low water activity. Whole genomes of the evolved strains were sequenced. No aneuploidies were detected in any of the genomes, contrary to previous studies on experimental evolution at high salinity with other species. However, several hundred single-nucleotide polymorphisms were identified compared with the genomes of the progenitor strains. Two functional groups of genes were overrepresented among the genes presumably affected by single-nucleotide polymorphisms: voltage-gated potassium channels in A. pullulans at high NaCl concentration, and hydrophobins in W. ichthyophaga at low NaCl concentration. Both groups of genes were previously associated with adaptation to high salinity. Finally, most evolved Aureobasidium spp. strains were found to have increased intracellular and decreased extracellular glycerol concentrations at high salinity, suggesting that the strains have optimised their management of glycerol, their most important compatible solute. Experimental evolution therefore not only confirmed the role of potassium transport, glycerol management, and cell wall in survival at low water activity, but also demonstrated that fungi from extreme environments can further improve their growth rates under constant extreme conditions in a relatively short time and without large scale genomic rearrangements.
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Affiliation(s)
- Farhad Hariri Akbari
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Martina Turk
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Cene Gostinčar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
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127
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Nikoloudaki O, Aheto F, Di Cagno R, Gobbetti M. Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes. Food Res Int 2024; 192:114780. [PMID: 39147468 DOI: 10.1016/j.foodres.2024.114780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/25/2024] [Accepted: 07/14/2024] [Indexed: 08/17/2024]
Abstract
This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.
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Affiliation(s)
- Olga Nikoloudaki
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Francis Aheto
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Marco Gobbetti
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
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128
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Wu Q, Li W, Kwok LY, Lv H, Sun J, Sun Z. Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut. Food Res Int 2024; 192:114840. [PMID: 39147525 DOI: 10.1016/j.foodres.2024.114840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Huimin Lv
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Jiaqi Sun
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, PR China; Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, PR China.
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129
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Liu X, Cai X, Yin N, Huang X, Wang P, Basheer MZ, Fan C, Chang X, Hu Z, Sun G, Cui Y. The pH-dependent role of different manganese oxides in the fate of arsenic during microbial reduction of arsenate-bearing goethite. WATER RESEARCH 2024; 261:121988. [PMID: 38986281 DOI: 10.1016/j.watres.2024.121988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/08/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Manganese oxides reduce arsenic (As) toxicity by promoting aqueous-phase As(III) oxidation and immobilization in natural aquatic ecosystems. In anaerobic water-sediment systems, arsenic exists both in a free state in the liquid phase and in an adsorbed state on iron (Fe) minerals. However, the influence of different manganese oxides on the fate of As in this system remains unclear. Therefore, in this study, we constructed an anaerobic microbial As(V) reduction environment and investigated the effects of three different manganese oxides on the fate of both aqueous-phase and goethite-adsorbed As under different pH conditions. The results showed that δ-MnO2 had a superior As(III) oxidation ability in both aqueous and solid phase due not only to the higher SSA, but also to its wrinkled crystalline morphology, less favorable structure for bacterial reduction, structure conducive to ion exchange, and less interference caused by the formation of secondary Fe-minerals compared to α-MnO2 and γ-MnO2. Regarding aqueous-phase As, δ-MnO2, α-MnO2, and γ-MnO2 required an alkaline condition (pH 9) to exhibit their strongest As(III) oxidation and immobilization capability. For goethite-adsorbed As, under microbial-reducing conditions, all manganese oxides had the highest As immobilization effect in neutral pH environments and the strongest As oxidation effect in alkaline environments. This was because at pH 7, Fe(II) and Mn(II) formed hydrated complexes, which was more favorable for As adsorption. At pH 9, the negatively charged state of goethite hindered As adsorption but promoted the adsorption and oxidation of As by the manganese oxides. Our research offers new insights for optimizing As removal from water using various manganese oxides and for controlling the mobilization of As in water-sediment system under different pH conditions.
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Affiliation(s)
- Xiaotong Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xiaolin Cai
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
| | - Naiyi Yin
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xuhan Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Pengfei Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Muhammad Zeeshan Basheer
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Chuanfang Fan
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xuhui Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Zhengyi Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China
| | - Guoxin Sun
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
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130
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Sarma M, Borkotoky S, Dubey VK. Structure-based drug designing against Leishmania donovani using docking and molecular dynamics simulation studies: exploring glutathione synthetase as a drug target. J Biomol Struct Dyn 2024; 42:7628-7636. [PMID: 37491862 DOI: 10.1080/07391102.2023.2240429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database against Leishmania donovani glutathione synthetase. The three-dimensional structure of Leishmania donovani glutathione synthetase was constructed by homology modeling, using the crystallographic structure of Trypanosoma brucei glutathione synthetase as a template. Subsequently, molecular docking studies were carried out for a large number of compounds using AutoDock Vina. Among the screened compounds, we selected the top five with strong binding affinity to Leishmania donovani glutathione synthetase but having a very low affinity to its human homolog. Further investigations on protein-ligand complexes were done by conducting molecular dynamics (MD) simulation and MM/PBSA analysis. The results revealed that Olysio (Simeprevir) exhibited the lowest binding energy (-89.21 kcal/mol), followed by Telithromycin (-45.34 kcal/mol). These findings showed that these compounds have the potential to act as inhibitors of glutathione synthetase. Hence, our study provides valuable insights for the development of a novel therapeutic strategy against Leishmania donovani by targeting the glutathione synthetase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manash Sarma
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Subhomoi Borkotoky
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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131
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Panda B, Tripathy A, Patra S, Kullu B, Tabrez S, Jena M. Imperative connotation of SODs in cancer: Emerging targets and multifactorial role of action. IUBMB Life 2024; 76:592-613. [PMID: 38600696 DOI: 10.1002/iub.2821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Superoxide dismutase (SOD) is a crucial enzyme responsible for the redox homeostasis inside the cell. As a part of the antioxidant defense system, it plays a pivotal role in the dismutation of the superoxide radicals (O 2 - ) generated mainly by the oxidative phosphorylation, which would otherwise bring out the redox dysregulation, leading to higher reactive oxygen species (ROS) generation and, ultimately, cell transformation, and malignancy. Several studies have shown the involvement of ROS in a wide range of human cancers. As SOD is the key enzyme in regulating ROS, any change, such as a transcriptional change, epigenetic remodeling, functional alteration, and so forth, either activates the proto-oncogenes or aberrant signaling cascades, which results in cancer. Interestingly, in some cases, SODs act as tumor promoters instead of suppressors. Furthermore, SODs have also been known to switch their role during tumor progression. In this review, we have tried to give a comprehensive account of SODs multifactorial role in various human cancers so that SODs-based therapeutic strategies could be made to thwart cancers.
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Affiliation(s)
- Biswajit Panda
- Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Ankita Tripathy
- Post Graduate Department of Botany, Utkal University, Bhubaneswar, India
| | - Srimanta Patra
- Post Graduate Department of Botany, Berhampur University, Berhampur, India
| | - Bandana Kullu
- Post Graduate Department of Botany, Utkal University, Bhubaneswar, India
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mrutyunjay Jena
- Post Graduate Department of Botany, Berhampur University, Berhampur, India
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132
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Ye L, Huang Y, Yang X, Zhang B, Li X, Zhang X, Tan W, Song C, Ao Z, Shen C, Li X. Metabolic profiles and biomarkers of Auricularia cornea based on de-oiled camphor leaf substrate. Food Res Int 2024; 191:114704. [PMID: 39059912 DOI: 10.1016/j.foodres.2024.114704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
This study investigates the metabolic responses of Auricularia cornea when cultured on de-oiled leaves of Cinnamomum longepaniculatum (DeCL), an underutilized waste product. The metabolic profiles of A. cornea cultured with four different quality ratios of DeCL substrate (0 %, 14 %, 28 % and 42 %) were analyzed by UHPLC-MS/MS-based metabolomics. A total of 516 metabolites were identified and classified into 78 categories, with phenols, alkaloids and flavonoids accounting for 26.7 % of the total. In addition, 32 metabolite biomarkers associated with eight major metabolic pathways were identified. This pioneering research provides valuable insights into the utilization of DeCL, and expands our knowledge of the metabolic dynamics underlying the growth of A. cornea on alternative substrates.
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Affiliation(s)
- Lei Ye
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; College of Resources, Sichuan Agricultural University, Chengdu 611134, China
| | - Yu Huang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xuezhen Yang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Bo Zhang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xin Li
- College of Resources, Sichuan Agricultural University, Chengdu 611134, China
| | - Xiaoping Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611134, China
| | - Wei Tan
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Chuan Song
- Luzhou Laojiao Co. Ltd., Luzhou 646000, China
| | - Zonghua Ao
- Luzhou Laojiao Co. Ltd., Luzhou 646000, China
| | | | - Xiaolin Li
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co. Ltd., Luzhou 646000, China.
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133
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Zhu H, Zhu D, Wu K, He W, Li L, Li T, Liu L, Liu Z, Song X, Cheng W, Mo J, Yao Y, Li J. Establishment and evaluation of a qPCR method for the detection of pfmdr1 mutations in Plasmodium falciparum, the causal agent of fatal malaria. Diagn Microbiol Infect Dis 2024; 110:116400. [PMID: 38909426 DOI: 10.1016/j.diagmicrobio.2024.116400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
Drug resistance surveillance is a major integral part of malaria control programs. Molecular methods play a pivotal role in drug resistance detection and related molecular research. This study aimed to develop a rapid and accurate detection method for drug resistance of Plasmodium falciparum (P. falciparum). A quantitative real-time PCR (qPCR) assay has been developed that identifies the mutation at locus A256T in the P.falciparum multi-drug resistance(pfmdr1) gene producing amino acid change at position 86. The results of 198 samples detected by qPCR were consistent with nested PCR and sequencing, giving an accuracy of 94.3%. The sensitivity, specificity, positive and negative predictive value of qPCR were 85.7%, 97.6%, 90.0% and 96.4%, respectively. The results of qPCR are basically consistent with the nested PCR, which is expected to replace the nested PCR as a new molecular biological method for drug resistance detection, providing reliable technical support for global malaria prevention and control.
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Affiliation(s)
- Huiyin Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China; Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Daiqian Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Kai Wu
- Wuhan Centers for Disease Prevention and Control, Wuhan 430024, PR China
| | - Wei He
- Jiangnan University, Wuxi 442000, PR China
| | - Liugen Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Tongfei Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Long Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Zhixin Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Xiaonan Song
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Weijia Cheng
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Jinyu Mo
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Yi Yao
- Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Jian Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China.
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134
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Hayes EK, Gagnon GA. From capture to detection: A critical review of passive sampling techniques for pathogen surveillance in water and wastewater. WATER RESEARCH 2024; 261:122024. [PMID: 38986282 DOI: 10.1016/j.watres.2024.122024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/05/2024] [Accepted: 06/29/2024] [Indexed: 07/12/2024]
Abstract
Water quality, critical for human survival and well-being, necessitates rigorous control to mitigate contamination risks, particularly from pathogens amid expanding urbanization. Consequently, the necessity to maintain the microbiological safety of water supplies demands effective surveillance strategies, reliant on the collection of representative samples and precise measurement of contaminants. This review critically examines the advancements of passive sampling techniques for monitoring pathogens in various water systems, including wastewater, freshwater, and seawater. We explore the evolution from conventional materials to innovative adsorbents for pathogen capture and the shift from culture-based to molecular detection methods, underscoring the adaptation of this field to global health challenges. The comparison highlights passive sampling's efficacy over conventional techniques like grab sampling and its potential to overcome existing sampling challenges through the use of innovative materials such as granular activated carbon, thermoplastics, and polymer membranes. By critically evaluating the literature, this work identifies standardization gaps and proposes future research directions to augment passive sampling's efficiency, specificity, and utility in environmental and public health surveillance.
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Affiliation(s)
- Emalie K Hayes
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Graham A Gagnon
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
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135
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Viksna J, Cerans K, Lace L, Melkus G. Characterizing behavioural differentiation in gene regulatory networks with representation graphs. NAR Genom Bioinform 2024; 6:lqae102. [PMID: 39131820 PMCID: PMC11310862 DOI: 10.1093/nargab/lqae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/20/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024] Open
Abstract
We introduce the formal notion of representation graphs, encapsulating the state space structure of gene regulatory network models in a compact and concise form that highlights the most significant features of stable states and differentiation processes leading to distinct stability regions. The concept has been developed in the context of a hybrid system-based gene network modelling framework; however, we anticipate that it can also be adapted to other approaches of modelling gene networks in discrete terms. We describe a practical algorithm for representation graph computation as well as two case studies demonstrating their real-world application and utility. The first case study presents models for three phage viruses. It shows that the process of differentiation into lytic and lysogenic behavioural states for all these models is described by the same representation graph despite the distinctive underlying mechanisms for differentiation. The second case study shows the advantages of our approach for modelling the process of myeloid cell differentiation from a common progenitor into different cell types. Both case studies also demonstrate the potential of the representation graph approach for deriving and validating hypotheses about regulatory interactions that must be satisfied for biologically viable behaviours.
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Affiliation(s)
- Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Raina bulvaris 29, Riga LV1459, Latvia
| | - Karlis Cerans
- Institute of Mathematics and Computer Science, University of Latvia, Raina bulvaris 29, Riga LV1459, Latvia
| | - Lelde Lace
- Institute of Mathematics and Computer Science, University of Latvia, Raina bulvaris 29, Riga LV1459, Latvia
| | - Gatis Melkus
- Institute of Mathematics and Computer Science, University of Latvia, Raina bulvaris 29, Riga LV1459, Latvia
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136
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Gómez-Gaviria M, Mora-Montes HM. Exploring the potential of chitin and chitosan in nanobiocomposites for fungal immunological detection and antifungal action. Carbohydr Res 2024; 543:109220. [PMID: 39038396 DOI: 10.1016/j.carres.2024.109220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Chitin is a polymer of N-acetylglucosamine and an essential component of the fungal cell wall. Chitosan is the deacetylated form of chitin and is also important for maintaining the integrity of this structure. Both polysaccharides are widely distributed in nature and have been shown to have a variety of applications in biomedicine, including their potential in immune sensing and as potential antifungal agents. In addition, chitin has been reported to play an important role in the pathogen-host interaction, involving innate and adaptive immune responses. This paper will explore the role of chitin and chitosan when incorporated into nanobiocomposites to improve their efficacy in detecting fungi of medical interest and inhibiting their growth. Potential applications in diagnostic and therapeutic medicine will be discussed, highlighting their promise in the development of more sensitive and effective tools for the early diagnosis of fungal infections. This review aims to highlight the importance of the convergence of nanotechnology and biology in addressing public health challenges.
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Affiliation(s)
- Manuela Gómez-Gaviria
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Gto, Mexico
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Gto, Mexico.
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137
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Ma K, Xian W, Liu H, Shu R, Ge J, Luo ZQ, Liu X, Qiu J. Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy. Autophagy 2024; 20:1968-1983. [PMID: 38818749 PMCID: PMC11346569 DOI: 10.1080/15548627.2024.2353492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/21/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network to evade clearance by the innate immune system. Here, we report that OTUB1, one of the most abundant deubiquitinases (DUBs) in mammalian cells, is subjected to both canonical and noncanonical ubiquitination during Legionella pneumophila infection. The effectors SidC and SdcA catalyze OTUB1 ubiquitination at multiple lysine residues, resulting in its association with a Legionella-containing vacuole. Lysine ubiquitination by SidC and SdcA promotes interactions between OTUB1 and DEPTOR, an inhibitor of the MTORC1 pathway, thus suppressing MTORC1 signaling. The inhibition of MTORC1 leads to suppression of host protein synthesis and promotion of host macroautophagy/autophagy during L. pneumophila infection. In addition, members of the SidE family effectors (SidEs) induce phosphoribosyl (PR)-linked ubiquitination of OTUB1 at Ser16 and Ser18 and block its DUB activity. The levels of the lysine and serine ubiquitination of OTUB1 are further regulated by effectors that function to antagonize the activities of SidC, SdcA and SidEs, including Lem27, DupA, DupB, SidJ and SdjA. Our study reveals an effectors-mediated complicated mechanism in regulating the activity of a host DUB.Abbreviations: BafA1: bafilomycin A1; BMDMs: bone marrow-derived macrophages; DUB: deubiquitinase; Dot/Icm: defective for organelle trafficking/intracellular multiplication; DEPTOR: DEP domain containing MTOR interacting protein; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; L. pneumophila: Legionella pneumophila; LCV: Legionella-containing vacuole; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTORC1: mechanistic target of rapamycin kinase complex 1; OTUB1: OTU deubiquitinase, ubiquitin aldehyde binding 1; PR-Ub: phosphoribosyl (PR)-linked ubiquitin; PTM: posttranslational modification; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SidEs: SidE family effectors; Ub: ubiquitin.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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138
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Yan A, Tian J, Ye J, Gao C, Ye L, Zhang D, Song Q. Construction of Toxoplasma gondii SRS29C nucleic acid vaccine and comparative immunoprotective study of an SRS29C and SAG1 combination. Mol Biochem Parasitol 2024; 259:111630. [PMID: 38795969 DOI: 10.1016/j.molbiopara.2024.111630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/29/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Toxoplasma gondii is an intracellular protozoan parasite that infects all nucleated cells except the red blood cells. Currently, nucleic acid vaccines are being widely investigated in Toxoplasma gondii control, and several nucleic acid vaccine candidate antigens have shown good protection in various studies. The aim of this study was to construct a nucleic acid vaccine with Toxoplasma gondii SRS29C as the target gene. We explored the nucleic acid vaccine with Toxoplasma surface protein SRS29C and the combined gene of SRS29C and SAG1 and evaluated its immunoprotective effect against Toxoplasma gondii. To amplify the gene fragment and clone it to the expression vector, the recombinant plasmid pEGFP-SRS29C was constructed by PCR. Eukaryotic cells were transfected with the plasmid, and the expression of the target protein was assessed using the Western blot method. The level of serum IgG was determined via ELISA, and the splenic lymphocyte proliferation ability was detected using the CCK-8 method. The percentages of CD4+ and CD8+ T cells were measured by flow cytometry. Mice were immunised three times with single-gene nucleic acid vaccine and combination vaccine. Splenic lymphocytokine expression was determined using ELISA kits. The mice's survival time was monitored and recorded during an in vivo insect assault experiment, and the vaccine's protective power was assessed. The outcomes showed that PCR-amplification of an SRS29C gene fragment was successful. The 4,733-bp vector fragment and the 1,119-bp target segment were both recognised by double digestion. Additionally, after transfection of the recombinant plasmid pEGFP-SRS29C, Western blot examination of the extracted protein revealed the presence of a target protein strip at 66 kDa. The test results demonstrated that the IgG content in the serum of the pEGFP-SRS29C group and the co-immunization group was significantly higher than that of the PBS group and the empty vector group. The IgG potency induced by the co-immunization group was higher than that of the pEGFP-SRS29C group and the pEGFP-SAG1 group, the number of splenic lymphocyte proliferation number was higher than that of the PBS group and the empty vector group. The CD4+/CD8+ T ratio was higher than that of the PBS group and the empty vector group. The expression of IFN-γ and TNF-α in the splenocytes of the pEGFP-SRS29C group and the combined immunisation group was significantly higher following antigen stimulation. In the worm attack experiments, mice in the PBS and empty vector groups perished within 9 days of the worm attack, whereas mice in the pEGFP-SRS29C group survived for 18 days, mice in the pEGFP-SAG1 group survived for 21 days, and mice in the co-immunization group survived for 24 days. This demonstrates that the constructed Toxoplasma gondii nucleic acid vaccine pEGFP-SRS29C and the combined gene vaccine can induce mice to develop certain humoral and cellular immune responses, and enhance their ability to resist Toxoplasma gondii infection.
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MESH Headings
- Animals
- Toxoplasma/immunology
- Toxoplasma/genetics
- Vaccines, DNA/immunology
- Vaccines, DNA/genetics
- Vaccines, DNA/administration & dosage
- Protozoan Proteins/immunology
- Protozoan Proteins/genetics
- Protozoan Vaccines/immunology
- Protozoan Vaccines/genetics
- Mice
- Antibodies, Protozoan/blood
- Antibodies, Protozoan/immunology
- Antigens, Protozoan/immunology
- Antigens, Protozoan/genetics
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Female
- Toxoplasmosis, Animal/prevention & control
- Toxoplasmosis, Animal/immunology
- Mice, Inbred BALB C
- CD8-Positive T-Lymphocytes/immunology
- Spleen/immunology
- Spleen/parasitology
- Cell Proliferation
- Plasmids/genetics
- Plasmids/immunology
- Cytokines/metabolism
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Affiliation(s)
- An Yan
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Jing Tian
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Jianjun Ye
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Chuanliang Gao
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Liying Ye
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Dongchao Zhang
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China
| | - Qiqi Song
- Agricultural Animal Breeding and Healthy Breeding Main Laboratory in Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, China.
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139
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Afandizada Y, Abeywansha T, Guerineau V, Zhang Y, Sargueil B, Ponchon L, Iannazzo L, Etheve-Quelquejeu M. Copper catalyzed cycloaddition for the synthesis of non isomerisable 2' and 3'-regioisomers of arg-tRNA arg. Methods 2024; 229:94-107. [PMID: 38834165 DOI: 10.1016/j.ymeth.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
In this report, non-isomerisable analogs of arginine tRNA (Arg-triazole-tRNA) have been synthesized as tools to study tRNA-dependent aminoacyl-transferases. The synthesis involves the incorporation of 1,4 substituted-1,2,3 triazole ring to mimic the ester bond that connects the amino acid to the terminal adenosine in the natural substrate. The synthetic procedure includes (i) a coupling between 2'- or 3'-azido-adenosine derivatives and a cytidine phosphoramidite to access dinucleotide molecules, (ii) Cu-catalyzed cycloaddition reactions between 2'- or 3'-azido dinucleotide in the presence of an alkyne molecule mimicking the arginine, providing the corresponding Arg-triazole-dinucleotides, (iii) enzymatic phosphorylation of the 5'-end extremity of the Arg-triazole-dinucleotides with a polynucleotide kinase, and (iv) enzymatic ligation of the 5'-phosphorylated dinucleotides with a 23-nt RNA micro helix that mimics the acceptor arm of arg-tRNA or with a full tRNAarg. Characterization of nucleoside and nucleotide compounds involved MS spectrometry, 1H, 13C and 31P NMR analysis. This strategy allows to obtain the pair of the two stable regioisomers of arg-tRNA analogs (2' and 3') which are instrumental to explore the regiospecificity of arginyl transferases enzyme. In our study, a first binding assay of the arg-tRNA micro helix with the Arginyl-tRNA-protein transferase 1 (ATE1) was performed by gel shift assays.
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Affiliation(s)
- Yusif Afandizada
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006 Paris, France
| | - Thilini Abeywansha
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vincent Guerineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bruno Sargueil
- Université Paris Cité, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France
| | - Luc Ponchon
- Université Paris Cité, CNRS, UMR 8038/CiTCoM, F-75006 Paris, France.
| | - Laura Iannazzo
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006 Paris, France.
| | - Mélanie Etheve-Quelquejeu
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006 Paris, France.
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140
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He L, Zhu G. Regulation and application of quorum sensing on anaerobic digestion system. CHEMOSPHERE 2024; 363:142983. [PMID: 39089336 DOI: 10.1016/j.chemosphere.2024.142983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
Quorum sensing (QS) plays an important role in the social behavior of microbial communities. Anaerobic digestion (AD) is a biological process using anaerobic microorganisms to degrade organic macromolecules into small molecules for biogas and biofertilizer production. In AD, the QS signaling molecule N-acyl homoserine lactones (AHLs) induces bacterial metabolism, improving AD process efficiency. However, there are fewer systematic reports about QS regulation of microbial behavior in AD. In this report, the effects of signaling molecules on extracellular polymer secretion, biofilm formation, granulation of granular sludge and bacterial metabolism in AD were investigated in detail. At present, the regulation behavior of QS on AD is a group phenomenon, and there are few in-depth studies on the regulation pathway. Therefore, we conducted an in-depth analysis of the pure culture system, granular sludge and reactor in the AD. Then we pointed out that the future application potential of QS in the AD may be combined with quorum quenching (QQ) and omics technology, which is of great significance for the future application of AD.
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Affiliation(s)
- Liyan He
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, PR China
| | - Gefu Zhu
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, PR China.
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141
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Prakash P, Verma S, Gupta S. Influence of microbiome in intraprostatic inflammation and prostate cancer. Prostate 2024; 84:1179-1188. [PMID: 38899408 DOI: 10.1002/pros.24756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/22/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Chronic infection and inflammation have been linked to the development of prostate cancer. Dysbiosis of the oral and gut microbiomes and subsequent microbial translocation can lead to pathogenic prostate infections. Microbial-produced metabolites have also been associated with signaling pathways that promote prostate cancer development. A comprehensive discussion on the mechanisms of microbiome infection and the prostate microenvironment is essential to understand prostate carcinogenesis. METHODS Published studies were used from the National Center for Biotechnology Information (NCBI) database to conduct a narrative review. No restrictions were applied in the selection of articles. RESULTS Microbiome-derived short-chain fatty acids (SCFAs) have been found to upregulate multiple signaling pathways, including MAPK and PI3K, through IGF-1 signaling and M2 macrophage polarization. SCFAs can also upregulate Toll-like receptors, leading to chronic inflammation and the creation of a pro-prostate cancer environment. Dysbiosis of oral microbiota has been correlated with prostate infection and inflammation. Additionally, pathogenic microbiomes associated with urinary tract infections have shown a link to prostate cancer, with vesicoureteral reflux potentially contributing to prostate infection. CONCLUSIONS This review offers a comprehensive understanding of the impact of microbial infections linked to intraprostatic inflammation as a causative factor for prostate cancer. Further studies involving the manipulation of the microbiome and its produced metabolites may provide a more complete understanding of the microenvironmental mechanisms that promote prostate carcinogenesis.
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Affiliation(s)
- Pranav Prakash
- College of Arts and Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shiv Verma
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Sanjay Gupta
- Department of Urology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, USA
- Division of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, Ohio, USA
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142
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He Y, Bright R, Vasilev K, Zilm P. Development of "Intelligent particles" for the treatment of dental caries. Eur J Pharm Biopharm 2024; 202:114374. [PMID: 38942176 DOI: 10.1016/j.ejpb.2024.114374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Dental caries is one of the most prevalent non-communicable diseases worldwide, mediated by a multispecies biofilm that consists of high levels of acidogenic bacteria which ferment sugar to acid and cause teeth demineralization. Current treatment practice remains insufficient in addressing 1) rapid clearance of therapeutic agents from the oral environment 2) destroying bacteria that contribute to the healthy oral microbiome. In addition, increasing concerns over antibiotic resistance calls for innovative alternatives. In this study, we developed a pH responsive nano-carrier for delivery of polycationic silver nanoparticles. Branched-PEI capped silver nanoparticles (BPEI-AgNPs) were encapsulated in a tannic acid - Fe (III) complex-modified poly(D,L-lactic-co-glycolic acid) (PLGA) particle (Fe(III)-TA/PLGA@BPEI-AgNPs) to enhance binding to the plaque biofilm and demonstrate "intelligence" by releasing BPEI-AgNPs under acidic conditions that promote dental caries The constructed Fe(III)-TA/PLGA@BPEI-AgNPs (intelligent particles - IPs) exhibited significant binding to an axenic S. mutans biofilm grown on hydroxyapatite. Ag+ ions were released faster from the IPs at pH 4.0 (cariogenic pH) compared to pH 7.4. The antibiofilm results indicated that IPs can significantly reduce S. mutans biofilm volume and viability under acidic conditions. Cytotoxicity on differentiated Caco-2 cells and human gingival fibroblasts indicated that IPs were not cytotoxic. These findings demonstrate great potential of IPs in the treatment of dental caries.
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Affiliation(s)
- Yanping He
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Richard Bright
- College of Medicine and Public Health, Flinders University, Bedford Park SA 5042, Australia
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Bedford Park SA 5042, Australia
| | - Peter Zilm
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia.
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143
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024; 22:572-586. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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144
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Han K, Yue J, Li J, Zhang J, Lin J, Zhuang Q, Li N, Li S, Rong C, Hua M, Liu Y, Yang D, Gu C, Chen L, Zeng H, Chen C. Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105636. [PMID: 38972619 DOI: 10.1016/j.meegid.2024.105636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 Shewanella strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.
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Affiliation(s)
- Kai Han
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jinglin Yue
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiarui Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiuming Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinghui Zhuang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Na Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Sha Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chengbo Rong
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yuwei Liu
- Emergency Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Duo Yang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chaoyang Gu
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liang Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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145
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Fries-Craft K, Schmitz-Esser S, Bobeck EA. Broiler chicken distal jejunum microbial communities are more responsive to coccidiosis or necrotic enteritis challenge than dietary anti-interleukin-10 in a model using Salmonella Typhimurium- Eimeria maxima- Clostridium perfringens coinfection. Poult Sci 2024; 103:104000. [PMID: 39002369 DOI: 10.1016/j.psj.2024.104000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024] Open
Abstract
Dietary anti-interleukin (IL)-10 antibodies may protect broiler performance during coccidiosis by inhibiting Eimeria host-evasion pathways; however, anti-IL-10's effects on microbial communities during coccidiosis and secondary Clostridium perfringens (necrotic enteritis) challenge is unknown. The study objectives were to assess the jejunal microbiota of broilers fed anti-IL-10 during E. maxima ± C. perfringens challenge. Two replicate studies using Ross 308 chicks placed in wire-floor cages (32 cages/ replicate study; 20 chicks/ cage) were conducted, with chicks assigned to diets ± 0.03% anti-IL-10 for 25 d. In both replicate studies, challenge-designated chicks were inoculated with 1 × 108Salmonella Typhimurium colony forming units (CFU) at placement. On d14, S. Typhimurium-inoculated chicks were gavaged with 15,000 sporulated Eimeria maxima M6 oocysts and half the E. maxima-challenged chicks received 1×108C. perfringens CFUs on d 18 and 19. Six chicks/ treatment were euthanized for distal jejunum content collection at baseline (d 14), 7 d post-inoculation (pi) with E. maxima/ 3 dpi with C. perfringens (peak) or 11 dpi with E. maxima/ 7 dpi with C. perfringens (post-peak) for 16S rRNA gene amplicon sequencing. Sequences were quality screened (Mothur V.1.43.0) and clustered into de novo operation taxonomical units (OTU; 99% similarity) using the SILVA reference database (v138). Alpha diversity and log-transformed relative abundance data were analyzed in SAS 9.4 with replicate study, diet, challenge, and timepoint main effects plus associated interactions (P ≤ 0.05). Few baseline changes were observed, but E. maxima ± C. perfringens challenge reduced Romboutsia and Staphylococcus relative abundance 4- to 800-fold in both replicate studies (P ≤ 0.008). At peak challenge with secondary C. perfringens, feeding anti-IL-10 instead of the control diet reduced Clostridium sensu stricto 1 relative abundance 13- and 1,848-fold in both replicate studies (P < 0.0001); however, OTUs identified as C. perfringens were not affected by dietary anti-IL-10. These results indicate that anti-IL-10 does not affect the jejunal microbiota of unchallenged broilers, while coccidiosis or necrotic enteritis challenge generally contributed to greater microbiota alterations than diet.
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Affiliation(s)
- K Fries-Craft
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; Interdepartmental Graduate Microbiology Program, Iowa State University, Ames, IA 50011, USA
| | - E A Bobeck
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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146
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Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
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Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
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147
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Yang X, Yang J, Huang H, Yan X, Li X, Lin Z. Achieving robust synthetic tolerance in industrial E. coli through negative auto-regulation of a DsrA-Hfq module. Synth Syst Biotechnol 2024; 9:462-469. [PMID: 38634002 PMCID: PMC11021974 DOI: 10.1016/j.synbio.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/29/2024] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
In industrial fermentation processes, microorganisms often encounter acid stress, which significantly impact their productivity. This study focused on the acid-resistant module composed of small RNA (sRNA) DsrA and the sRNA chaperone Hfq. Our previous study had shown that this module improved the cell growth of Escherichia coli MG1655 at low pH, but failed to obtain this desired phenotype in industrial strains. Here, we performed a quantitative analysis of DsrA-Hfq module to determine the optimal expression mode. We then assessed the potential of the CymR-based negative auto-regulation (NAR) circuit for industrial application, under different media, strains and pH levels. Growth assay at pH 4.5 revealed that NAR-05D04H circuit was the best acid-resistant circuit to improve the cell growth of E. coli MG1655. This circuit was robust and worked well in the industrial lysine-producing strain E. coli SCEcL3 at a starting pH of 6.8 and without pH control, resulting in a 250 % increase in lysine titer and comparable biomass in shaking flask fermentation compared to the parent strain. This study showed the practical application of NAR circuit in regulating DsrA-Hfq module, effectively and robustly improving the acid tolerance of industrial strains, which provides a new approach for breeding industrial strains with tolerance phenotype.
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Affiliation(s)
- Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jingduan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Haozheng Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofang Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- School of Biomedicine, Guangdong University of Technology, Guangzhou 510006, China
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148
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Zhang X, Zheng Y, Zhou C, Cao J, Pan D, Cai Z, Wu Z, Xia Q. Comparative physiological and transcriptomic analysis of sono-biochemical control over post-acidification of Lactobacillus delbrueckii subsp. bulgaricus. Food Microbiol 2024; 122:104563. [PMID: 38839237 DOI: 10.1016/j.fm.2024.104563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/27/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Thermosonication (UT) prestress treatments combining with varied fermentation patterns has been revealed as an effective method to regulate post-acidification as exerted by Lactobacillus delbrueckii subsp. bulgaricus (L. delbrueckii), but sono-biochemical controlling mechanisms remain elusive. This study employed physiological and transcriptomic analysis to explore the response mechanism of L. delbrueckii to UT-induced microstress (600 W, 33 kHz, 10 min). UT stress-induced inhibition of acidification of L. delbrueckii during (post)-fermentation was first confirmed, relying on the UT process parameters such as stress exposure duration and UT power. The significantly enhanced membrane permeability in cells treated by 600 W for 10 min than the microbes stressed by 420 W for 20 min suggested the higher dependence of UT-derived stresses on the treatment durations, relative to the ultrasonic powers. In addition, ultrasonication treatment-induced changes in cell membrane integrity enhanced and/or disrupted permeability of L. delbrueckii, resulting in an imbalance in intracellular conditions associated with corresponding alterations in metabolic behaviors and fermentation efficiencies. UT-prestressed inoculum exhibited a 21.46% decrease in the membrane potential during the lag phase compared to untreated samples, with an intracellular pH of 5.68 ± 0.12, attributed to the lower activities of H+-ATPase and lactate dehydrogenase due to UT stress pretreatments. Comparative transcriptomic analysis revealed that UT prestress influenced the genes related to glycolysis, pyruvate metabolism, fatty acid synthesis, and ABC transport. The genes encoding 3-oxoacyl-[acyl-carrier-protein] reductases I, II, and III, CoA carboxylase, lactate dehydrogenase, pyruvate oxidase, glucose-6-phosphate isomerase, and glycerol-3-phosphate dehydrogenase were downregulated, thus identifying the relevance of the UT microstresses-downregulated absorption and utilization of carbohydrates with the attenuated fatty acid production and energy metabolisms. These findings could contribute to provide a better understanding of the inactivated effects on the post-acidification of L. delbrueckii by ultrasonic pretreatments, thus providing theoretical basis for the targeted optimization of acidification inhibition efficiencies for yogurt products during chilled preservation processes.
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Affiliation(s)
- Xiaohui Zhang
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Yuanrong Zheng
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, 200436, China
| | - Changyu Zhou
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Jinxuan Cao
- School of Food and Health, China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, 11 Fucheng Road, Beijing, 100048, China
| | - Daodong Pan
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhendong Cai
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhen Wu
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
| | - Qiang Xia
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
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149
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Alymanesh MR, Solhjoo A, Pishgar E, Akhlaghi M. Falcaria vulgaris extract: A mixture of quorum sensing inhibitors for controlling Pectobacterium carotovorum subsp. carotovorum. Food Microbiol 2024; 122:104535. [PMID: 38839215 DOI: 10.1016/j.fm.2024.104535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/09/2024] [Accepted: 04/05/2024] [Indexed: 06/07/2024]
Abstract
A promising strategy to control bacterial diseases involves using Quorum Sensing Inhibitor (QSI) compounds. This study aimed to evaluate the potential of Falcaria vulgaris plant extract to combat the phytopathogenic Pectobacterium carotovorum subsp. carotovorum (Pcc) via its QSI activity. Using biosensors and Minimum Inhibitory Concentration (MIC) assays, the QSI and antimicrobial aspects of the extract were assessed. Furthermore, the effect of the extract on the reduction of tuber maceration in potatoes was examined. Subsequently, homology modeling based on LasR was conducted to analyze interactions between ligand 3-oxo-C8-AHL, and ExpR2 protein. Docking studies were performed on all extract compounds identified via Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The extract effectively reduced maceration at sub-MIC concentrations across various pathogenic strains. Furthermore, Cyclopentadecanone, 2-hydroxy, showed more negative docking energy than the native ligand. Z,E-2,13-Octadecadien-1-ol showed energy equivalence to the native ligand. Additionally, this plant included certain compounds or their analogs that had previously been discovered as QSI compounds. These compounds included oleic acid, n-Hexadecanoic acid, cytidine, and linoleic acid, and they had energies that were comparable to that of the native ligand. In conclusion, the remarkable QSI property showed by this plant is likely attributed to a combination of compounds possessing this characteristic.
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Affiliation(s)
- Mohammad Reza Alymanesh
- Assistant Professor, Department of Plant Protection, Faculty of Agriculture, Ilam University, Ilam, Iran.
| | - Aida Solhjoo
- Department of Quality Control of Drug Products, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elham Pishgar
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
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150
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Xu G, Peng G, Yang J, Wu M, Li W, Wang J, Zhu L, Zhang W, Ge F, Song P. Molybdenum disulfide nanosheets based non-oxygen-dependent and heat-initiated free radical nanogenerator with antimicrobial peptides for antimicrobial, biofilm ablation and wound healing. BIOMATERIALS ADVANCES 2024; 162:213920. [PMID: 38901063 DOI: 10.1016/j.bioadv.2024.213920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024]
Abstract
Chronic refractory wounds caused by multidrug-resistant (MDR) bacterial and biofilm infections are a substantial threat to human health, which presents a persistent challenge in managing clinical wound care. We here synthesized a composite nanosheet AIPH/AMP/MoS2, which can potentially be used for combined therapy because of the photothermal effect induced by MoS2, its ability to deliver antimicrobial peptides, and its ability to generate alkyl free radicals independent of oxygen. The synthesized nanosheets exhibited 61 % near-infrared (NIR) photothermal conversion efficiency, marked photothermal stability and free radical generating ability. The minimal inhibitory concentrations (MICs) of the composite nanosheets against MDR Escherichia coli (MDR E. coli) and MDR Staphylococcus aureus (MDR S. aureus) were approximately 38 μg/mL and 30 μg/mL, respectively. The composite nanosheets (150 μg/mL) effectively ablated >85 % of the bacterial biofilm under 808-nm NIR irradiation for 6 min. In the wound model experiment, approximately 90 % of the wound healed after the 4-day treatment with the composite nanosheets. The hemolysis experiment, mouse embryonic fibroblast (MEFs) cytotoxicity experiment, and mouse wound healing experiment all unveiled the excellent biocompatibility of the composite nanosheets. According to the transcriptome analysis, the composite nanosheets primarily exerted a synergistic therapeutic effect by disrupting the cellular membrane function of S. aureus and inhibiting quorum sensing mediated by the two-component system. Thus, the synthesized composite nanosheets exhibit remarkable antibacterial and biofilm ablation properties and therefore can be used to improve wound healing in chronic biofilm infections.
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Affiliation(s)
- Guanglin Xu
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China
| | - Guanglan Peng
- The first Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241002, Anhui, China
| | - Jianping Yang
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China
| | - Mingcai Wu
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, 241002, Anhui, China
| | - Wanzhen Li
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China
| | - Jun Wang
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China
| | - Longbao Zhu
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China
| | - Weiwei Zhang
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China.
| | - Fei Ge
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China.
| | - Ping Song
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, Anhui, China.
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