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Peng F, Zou Y, Liu X, Yang Y, Chen J, Nie J, Huang D, Bai Z. The murein endopeptidase MepA regulated by MtrAB and MprAB participate in cell wall homeostasis. Res Microbiol 2024; 175:104188. [PMID: 38286394 DOI: 10.1016/j.resmic.2024.104188] [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: 04/04/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
The complete genome of Corynebacterium glutamicum contain a gene encoding murein endopeptidase MepA which maintain cell wall homeostasis by regulating peptidoglycan biosynthesis. In this study, we investigate the physiological function, localization and regulator of MepA. The result shows that mepA overexpression lead to peptidoglycan degradation and the defects in cell division. MepA-EGFP was shown to localizes exclusively at the cell cell septum. In addition, mepA overexpression increased cell permeability and reduced the resistance of cells to isoniazid, an antibiotic used to treat Mycobacterium tuberculosis infection. Furthermore, transcription analysis showed that mepA affected cell division and membrane transport pathways, and was coordinately regulated by the two-component systems MtrAB and MprAB(CgtS/R2).
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Affiliation(s)
- Feng Peng
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yu Zou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China.
| | - Yankun Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Jianqi Nie
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Danni Huang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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2
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Reddien PW. The purpose and ubiquity of turnover. Cell 2024; 187:2657-2681. [PMID: 38788689 DOI: 10.1016/j.cell.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Turnover-constant component production and destruction-is ubiquitous in biology. Turnover occurs across organisms and scales, including for RNAs, proteins, membranes, macromolecular structures, organelles, cells, hair, feathers, nails, antlers, and teeth. For many systems, turnover might seem wasteful when degraded components are often fully functional. Some components turn over with shockingly high rates and others do not turn over at all, further making this process enigmatic. However, turnover can address fundamental problems by yielding powerful properties, including regeneration, rapid repair onset, clearance of unpredictable damage and errors, maintenance of low constitutive levels of disrepair, prevention of stable hazards, and transitions. I argue that trade-offs between turnover benefits and metabolic costs, combined with constraints on turnover, determine its presence and rates across distinct contexts. I suggest that the limits of turnover help explain aging and that turnover properties and the basis for its levels underlie this fundamental component of life.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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3
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Niu X, Liu Y, Zhao R, Yuan M, Zhao H, Li H, Wang K. Enhancing Electrochemical Signal for Efficient Chiral Recognition by Encapsulating C 60 Fullerene into Chiral Lanthanum-Based MOFs. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17361-17370. [PMID: 38556802 DOI: 10.1021/acsami.4c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Chiral metal-organic frameworks (MOFs) have attracted much attention due to their highly tunable regular microporous structures. However, chiral electrochemical recognition based on chiral MOFs is often limited by poor charge separation and slow charge transfer kinetics. In this case, C60 can be encapsulated into the cavity of [La(BTB)]n by virtue of host-guest interactions through π-π stacking to synthesize the chiral composite C60@[La(BTB)]n and amplify electrochemically controlled enantioselective interactions with the target enantiomers. A large electrostatic potential difference is generated in chiral C60@[La(BTB)]n due to the host-guest interaction and the inhomogeneity of the charge distribution, leading to the generation of a strong built-in electric field and thus an overall enhancement of the conductivity of the chiral material. Their enantioselective detection of tryptophan enantiomers was demonstrated by electrochemical measurement. The results showed that chiral MOF materials can be used for enantiomeric recognition. It is worth noting that this new material derived from the concept of host-guest interaction to enhance charge separation opens up unprecedented possibilities for future enantioselective recognition and separation.
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Affiliation(s)
- Xiaohui Niu
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Yongqi Liu
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Rui Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Mei Yuan
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Hongfang Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Hongxia Li
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
| | - Kunjie Wang
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou 730050, P. R. China
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4
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Kwan JMC, Liang Y, Ng EWL, Sviriaeva E, Li C, Zhao Y, Zhang XL, Liu XW, Wong SH, Qiao Y. In silico MS/MS prediction for peptidoglycan profiling uncovers novel anti-inflammatory peptidoglycan fragments of the gut microbiota. Chem Sci 2024; 15:1846-1859. [PMID: 38303944 PMCID: PMC10829024 DOI: 10.1039/d3sc05819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Peptidoglycan is an essential exoskeletal polymer across all bacteria. Gut microbiota-derived peptidoglycan fragments (PGNs) are increasingly recognized as key effector molecules that impact host biology. However, the current peptidoglycan analysis workflow relies on laborious manual identification from tandem mass spectrometry (MS/MS) data, impeding the discovery of novel bioactive PGNs in the gut microbiota. In this work, we built a computational tool PGN_MS2 that reliably simulates MS/MS spectra of PGNs and integrated it into the user-defined MS library of in silico PGN search space, facilitating automated PGN identification. Empowered by PGN_MS2, we comprehensively profiled gut bacterial peptidoglycan composition. Strikingly, the probiotic Bifidobacterium spp. manifests an abundant amount of the 1,6-anhydro-MurNAc moiety that is distinct from Gram-positive bacteria. In addition to biochemical characterization of three putative lytic transglycosylases (LTs) that are responsible for anhydro-PGN production in Bifidobacterium, we established that these 1,6-anhydro-PGNs exhibit potent anti-inflammatory activity in vitro, offering novel insights into Bifidobacterium-derived PGNs as molecular signals in gut microbiota-host crosstalk.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Yaquan Liang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Evan Wei Long Ng
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Ekaterina Sviriaeva
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Chenyu Li
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Yilin Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Xiao-Lin Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Xue-Wei Liu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University 11 Mandalay Road 308232 Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University 21 Nanyang Link 637371 Singapore
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Abstract
ConspectusElastomers have been extensively used in diverse industrial sectors such as footwear, seals, tires, and cable jacketing and have attracted more and more attention in emerging fields such as regenerative medicine, soft robotics, and stretchable electronics. Global consumption of natural and synthetic elastomers amounted to nearly 27 million metric tons in 2020. In addition, to further enhance the common properties of elastomers, it is highly desired to endow elastomers with functionalities such as reprocessability, biomimetic mechanical properties, self-healing ability, bioactivity, and electrical conductivity, which will significantly broaden their applications. The covalent or noncovalent cross-linked structure is the essential factor for the elasticity of elastomers. Traditional elastomers usually comprise a single type of cross-linked molecular network, for which it is difficult to modulate the properties and introduce functionalities. Inspired by the simultaneous existence of multiple cross-linked structures in proteins, researchers have employed a hybrid cross-linking strategy to construct elastomers. Various noncovalent interactions (e.g., hydrogen bonds, metal-ligand coordination, ionic interactions, and chain folding) and dynamic covalent bonds (e.g., disulfide bonds, oxime-urethane bonds, and urea bonds) have been integrated in elastomers. Accordingly, the properties and functionalities of elastomers can be tuned by regulating the types, ratios, and distributions of cross-links. The hybrid cross-linking strategy provides a versatile and effective way to construct diverse functional elastomers for broad applications in various important fields.In this Account, we present our recent progress on functional elastomers constructed by a hybrid cross-linking strategy, including their design, preparation, properties, and diverse applications. First, we provide a brief introduction of the basic concept of functional elastomers and outline general strategies and mechanics for functional elastomers constructed by hybrid cross-linking. Then, we classify hybrid cross-linked elastomers by their design strategies, including multiple cross-linking, topological design, chemical coupling, and multiple networks. The relationships between the functionalities and hybrid cross-linked structures are summarized. At the same time, we also introduce diverse applications of these hybrid cross-linked elastomers in biomedicine, flexible electronics, soft robotics, 3D printing, and so on. Finally, we discuss our perspective on open challenges and future development trends of this rapidly evolving field. This Account highlighting the diverse hybrid cross-linked elastomers not only provides insights into strategies for elastomer functionalization but also provides new ideas for material design and inspires a variety of new applications.
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Affiliation(s)
- Luzhi Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Institute of Functional Materials, College of Materials Science and Engineering, Research Base of Textile Materials for Flexible Electronics and Biomedical Applications (China Textile Engineering Society), Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, Donghua University, 201620 Shanghai, China
| | - Shuo Chen
- College of Biological Science and Medical Engineering, Donghua University, 201620 Shanghai, China
| | - Zhengwei You
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Institute of Functional Materials, College of Materials Science and Engineering, Research Base of Textile Materials for Flexible Electronics and Biomedical Applications (China Textile Engineering Society), Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, Donghua University, 201620 Shanghai, China
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Pismennõi D, Kattel A, Belouah I, Nahku R, Vilu R, Kobrin EG. The Quantitative Measurement of Peptidoglycan Components Obtained from Acidic Hydrolysis in Gram-Positive and Gram-Negative Bacteria via Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry. Microorganisms 2023; 11:2134. [PMID: 37763978 PMCID: PMC10534856 DOI: 10.3390/microorganisms11092134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
The high throughput in genome sequencing and metabolic model (MM) reconstruction has democratised bioinformatics approaches such as flux balance analysis. Fluxes' prediction accuracy greatly relates to the deepness of the MM curation for a specific organism starting from the cell composition. One component is the cell wall, which is a functional barrier (cell shape, exchanges) with the environment. The bacterial cell wall (BCW), including its thickness, structure, and composition, has been extensively studied in Escherichia coli but poorly described for other organisms. The peptidoglycan (PG) layer composing the BCW is usually thinner in Gram- bacteria than in Gram+ bacteria. In both bacteria groups, PG is a polymeric mesh-like structure of amino acids and sugars, including N-acetylglucosamine, N-acetylmuramic acid, and amino acids. In this study, we propose a high-throughput method to characterise and quantify PG in Gram-positive and Gram-negative bacteria using acidic hydrolysis and hydrophilic interaction liquid chromatography coupled with mass spectrometry (HILIC-MS). The method showed a relatively short time frame (11 min analytical run), low inter- and intraday variability (3.2% and 4%, respectively), and high sensitivity and selectivity (limits of quantification in the sub mg/L range). The method was successfully applied on two Gram-negative bacteria (Escherichia coli K12 MG1655, Bacteroides thetaiotaomicron DSM 2079) and one Gram-positive bacterium (Streptococcus salivarius ssp. thermophilus DSM20259). The PG concentration ranged from 1.6% w/w to 14% w/w of the dry cell weight. The results were in good correlation with previously published results. With further development, the PG concentration provided by this newly developed method could reinforce the curation of MM.
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Affiliation(s)
- Dmitri Pismennõi
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia Tee 15, 12618 Tallinn, Estonia
| | - Anna Kattel
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia Tee 15, 12618 Tallinn, Estonia
| | - Isma Belouah
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
| | - Ranno Nahku
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
| | - Raivo Vilu
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
| | - Eeva-Gerda Kobrin
- Center of Food and Fermentation Technologies (TFTAK), Mäealuse 2/4, 12618 Tallinn, Estonia; (D.P.); (A.K.); (I.B.); (R.N.); (R.V.)
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Pérez-Lorente AI, Molina-Santiago C, de Vicente A, Romero D. Sporulation Activated via σ W Protects Bacillus from a Tse1 Peptidoglycan Hydrolase Type VI Secretion System Effector. Microbiol Spectr 2023; 11:e0504522. [PMID: 36916921 PMCID: PMC10100999 DOI: 10.1128/spectrum.05045-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Within bacterial communities, community members engage in interactions employing diverse offensive and defensive tools to reach coexistence. Extracellular-matrix production and sporulation are defensive mechanisms used by Bacillus subtilis cells when they interact with Pseudomonas chlororaphis strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas chlororaphis T6SS that triggers sporulation in Bacillus subtilis. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor σW and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response permits bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector. IMPORTANCE The study of bacterial interactions is helping to define species-specific strategies used to modulate the competition dynamics underlying the development of community compositions. In this study, we deciphered the role of Pseudomonas T6SS when competing with Bacillus and the mechanism by which a T6SS-toxin modifies Bacillus physiology. We found that Pseudomonas triggers Bacillus sporulation by injecting through T6SS a toxin that we called Tse1. We found that Tse1 is a hydrolase that degrades Bacillus peptidoglycan and indirectly damages Bacillus membrane functionality. In addition, we demonstrated the mechanism by which Bacillus cells increase the sporulation rate upon recognition of the presence of Tse1. Interestingly, asporogenic Bacillus cells are more sensitive to T6SS activity, which led us to propose sporulation as a last resort of bacilli to overcome this family of toxins.
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Affiliation(s)
- Alicia I. Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
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8
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Makvandi P, Song H, Yiu CKY, Sartorius R, Zare EN, Rabiee N, Wu WX, Paiva-Santos AC, Wang XD, Yu CZ, Tay FR. Bioengineered materials with selective antimicrobial toxicity in biomedicine. Mil Med Res 2023; 10:8. [PMID: 36829246 PMCID: PMC9951506 DOI: 10.1186/s40779-023-00443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/31/2023] [Indexed: 02/26/2023] Open
Abstract
Fungi and bacteria afflict humans with innumerous pathogen-related infections and ailments. Most of the commonly employed microbicidal agents target commensal and pathogenic microorganisms without discrimination. To distinguish and fight the pathogenic species out of the microflora, novel antimicrobials have been developed that selectively target specific bacteria and fungi. The cell wall features and antimicrobial mechanisms that these microorganisms involved in are highlighted in the present review. This is followed by reviewing the design of antimicrobials that selectively combat a specific community of microbes including Gram-positive and Gram-negative bacterial strains as well as fungi. Finally, recent advances in the antimicrobial immunomodulation strategy that enables treating microorganism infections with high specificity are reviewed. These basic tenets will enable the avid reader to design novel approaches and compounds for antibacterial and antifungal applications.
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Affiliation(s)
- Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Materials Interfaces, Pontedera, 56025, Italy. .,The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
| | - Hao Song
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cynthia K Y Yiu
- Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong SAR, China
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | | | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia
| | - Wei-Xi Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal.,REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Xiang-Dong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Cheng-Zhong Yu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA, 30912, USA.
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9
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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10
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Wang C, Wang J, Xue K, Xiao M, Wu K, Lv S, Hao B, Zhu C. Polarity-Sensitive Fluorescent Probe for Reflecting the Packing Degree of Bacterial Membrane Lipids. Anal Chem 2022; 94:3303-3312. [PMID: 35133812 DOI: 10.1021/acs.analchem.1c05268] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The maintenance of an intact membrane structure is of great importance for bacteria to execute various biological functions. However, chemical probes for monitoring the dynamic changes of bacterial membranes are barely reported. Herein, we, for the first time, report a novel polarity-sensitive probe for reflecting the packing degree of bacterial membrane lipids. Specifically, we synthesize a membrane-targeting fluorescent probe (TICT-lipid) that possesses both twist intramolecular charge transfer and aggregation-induced emission properties. TICT-lipid exhibits sensitive responses to the minute difference in the packing degree of membrane lipids, facilitating rapid differentiation of Gram-negative and Gram-positive bacteria. Interestingly, in the presence of membrane-disrupting antibiotics, the localization of TICT-lipid shifts from the outer membrane to the cell membrane by outputting blue-shifted and enhanced emission, making the mechanism of action of antibiotics clearly visible. TICT-lipid is a polarity-sensitive fluorescent probe, holding great promise in the study of membrane-related bacterial processes and antibiotic screening.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaxin Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ke Xue
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Minghui Xiao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kaiyu Wu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shuyi Lv
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Boyi Hao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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11
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Zhang L, Liang J, Jiang C, Liu Z, Sun L, Chen S, Xuan H, Lei D, Guan Q, Ye X, You Z. Peptidoglycan-inspired autonomous ultrafast self-healing bio-friendly elastomers for bio-integrated electronics. Natl Sci Rev 2021; 8:nwaa154. [PMID: 34691631 PMCID: PMC8288426 DOI: 10.1093/nsr/nwaa154] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/31/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022] Open
Abstract
Elastomers are essential for stretchable electronics, which have become more and more important in bio-integrated devices. To ensure high compliance with the application environment, elastomers are expected to resist, and even self-repair, mechanical damage, while being friendly to the human body. Herein, inspired by peptidoglycan, we designed the first room-temperature autonomous self-healing biodegradable and biocompatible elastomers, poly(sebacoyl 1,6-hexamethylenedicarbamate diglyceride) (PSeHCD) elastomers. The unique structure including alternating ester-urethane moieties and bionic hybrid crosslinking endowed PSeHCD elastomers superior properties including ultrafast self-healing, tunable biomimetic mechanical properties, facile reprocessability, as well as good biocompatibility and biodegradability. The potential of the PSeHCD elastomers was demonstrated as a super-fast self-healing stretchable conductor (21 s) and motion sensor (2 min). This work provides a new design and synthetic principle of elastomers for applications in bio-integrated electronics.
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Affiliation(s)
- Luzhi Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Jiahui Liang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Chenyu Jiang
- Department of Cardiac Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zenghe Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Lijie Sun
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Shuo Chen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Huixia Xuan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Dong Lei
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Qingbao Guan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaofeng Ye
- Department of Cardiac Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhengwei You
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Belt and Road Joint Laboratory of Advanced Fiber and Low-dimension Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
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12
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New approaches and techniques for bacterial cell wall analysis. Curr Opin Microbiol 2021; 60:88-95. [PMID: 33631455 DOI: 10.1016/j.mib.2021.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
Peptidoglycan (PG) has remained for decades in the spotlight of the never-ending battle against pathogenic bacteria as this essential bacterial structure is one of the most successful targets for antibiotics. Most of our current understanding about the composition, architecture, and dynamics of the PG relies on techniques which have experienced great technological and methodological improvements in the past years. Here we summarize recent advances in these methods with the intention to furnish a valuable resource for both PG experts and newcomers.
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13
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Grishin AV, Karyagina AS, Vasina DV, Vasina IV, Gushchin VA, Lunin VG. Resistance to peptidoglycan-degrading enzymes. Crit Rev Microbiol 2020; 46:703-726. [PMID: 32985279 DOI: 10.1080/1040841x.2020.1825333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The spread of bacterial strains resistant to commonly used antibiotics urges the development of novel antibacterial compounds. Ideally, these novel antimicrobials should be less prone to the development of resistance. Peptidoglycan-degrading enzymes are a promising class of compounds with a fundamentally different mode of action compared to traditionally used antibiotics. The difference in the mechanism of action implies differences both in the mechanisms of resistance and the chances of its emergence. To critically assess the potential of resistance development to peptidoglycan-degrading enzymes, we review the available evidence for the development of resistance to these enzymes in vitro, along with the known mechanisms of resistance to lysozyme, bacteriocins, autolysins, and phage endolysins. We conclude that genetic determinants of resistance to peptidoglycan-degrading enzymes are unlikely to readily emerge de novo. However, resistance to these enzymes would probably spread by the horizontal transfer between intrinsically resistant and susceptible species. Finally, we speculate that the higher cost of the therapeutics based on peptidoglycan degrading enzymes compared to classical antibiotics might result in less misuse, which in turn would lead to lower selective pressure, making these antibacterials less prone to resistance development.
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Affiliation(s)
- Alexander V Grishin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna S Karyagina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Daria V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir A Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir G Lunin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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14
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Narayanan J, Hernández JG, Aguilar CAH, Rodríguez MM, Cerda SDG. Glutamine chelation governs the selective inhibition of Staphylococcus aureus and Salmonella typhi growth by cis-dichloro-bis(8-quinolinolato)zirconium(IV): Theory and experiment. Eur J Pharm Sci 2020; 151:105427. [PMID: 32544422 DOI: 10.1016/j.ejps.2020.105427] [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: 03/31/2020] [Revised: 05/25/2020] [Accepted: 06/11/2020] [Indexed: 10/24/2022]
Abstract
Quinolone-based Schiff base zirconium(IV) complex was studied as potential bacterial inhibitor against Gram-positive Staphylococcus aureus and Gram-negative Salmonella typhi growth, showing that the interaction of the complex with L-glutamine which presents in the membrane of wall leads cell death, and the mode of bacterial interaction was analyzed theoretically by DFT. Furthermore, the interaction of different amino acid residues L-alanine, D-alanine, L-lysine and D-glutamine with the metal complex through UV-vis docking studies was conducted observing that D-glutamine interacts efficiently among other amino acid residues. This observation is consistent with the interaction of the metal complex that was effective when participating in an insight of the peptidoglycan cell wall since the binding nature of glutamine potentially inhibits these microorganisms.
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Affiliation(s)
- Jayanthi Narayanan
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan, Estado de México, CP 54910, México.
| | - José Guadalupe Hernández
- Centro Tecnológico, Facultad de Estudios Superiores (FES-Aragón), Universidad Nacional Autónoma de México (UNAM), Estado de México, CP 57130, México
| | - Carlos Alberto Huerta Aguilar
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan, Estado de México, CP 54910, México
| | - Miguel Morales Rodríguez
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan, Estado de México, CP 54910, México
| | - Susana Dianey Gallegos Cerda
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de México, Av. Mexiquense s/n esquina Av. Universidad Politécnica, Tultitlan, Estado de México, CP 54910, México
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15
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Samiee S, Bahmaie M, Motamedi H, Shiralinia A, Gable RW. Synthesis, crystallographic studies, antibacterial and antifungal activities of mononuclear mercury(II) complexes derived from [PPh2(CH2)nPPh2CH2C(O)C6H4Cl)]Br ligands. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Evaluation of Feasibility of Using the Bacteriophage T4 Lysozyme to Improve the Hydrolysis and Biochemical Methane Potential of Secondary Sludge. ENERGIES 2019. [DOI: 10.3390/en12193644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Anaerobic digestion (AD) of secondary sludge is a rate-limiting step due to the bacterial cell wall. In this study, experiments were performed to characterize secondary sludges from three wastewater treatment plants (WWTPs), and to investigate the feasibility of using bacteriophage lysozymes to speed up AD by accelerating the degradation of bacterial cell walls. Protein was the main organic material (67.7% of volatile solids in the sludge). The bacteriophage T4 lysozyme (T4L) was tested for hydrolysis and biochemical methane potential. Variations in the volatile suspended solid (VSS) concentration and biogas production were monitored. The VSS reduction efficiencies by hydrolysis using T4L for 72 h increased and ranged from 17.8% to 26.4%. Biogas production using T4L treated sludges increased and biogas production was increased by as much as 82.4%. Biogas production rate also increased, and the average reaction rate coefficient of first-order kinetics was 0.56 ± 0.02/d, which was up to 47.5% higher compared to the untreated samples at the maximum. Alphaproteobacteria, Betaproteobacteria, Flavobacteriia, Gammaproteobacteria, and Sphingobacteriia were major microbial classes in all sludges. The interpretation of the microbial community structure indicated that T4L treatment is likely to increase the rate of cell wall digestion.
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