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Quesada S, Rosso AD, Mascardi F, Soler-Rivero V, Aguilera P, Mascuka SN, Boiro A, Arenielo E, Vijoditz G, Ferreyra-Mufarregue LR, Caputo MF, Cimolai MC, Coluccio Leskow F, Penas-Steinhardt A, Belforte FS. Integrative analysis of systemic lupus erythematosus biomarkers: Role of fecal hsa-mir-223-3p and gut microbiota in transkingdom dynamics. Mol Immunol 2024; 171:77-92. [PMID: 38795687 DOI: 10.1016/j.molimm.2024.05.004] [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: 01/26/2024] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]
Abstract
Systemic lupus erythematosus (SLE) involves a florid set of clinical manifestations whose autoreactive origin is characterized by an overactivation of the immune system and the production of a large number of autoantibodies. Because it is a complex pathology with an inflammatory component, its pathogenesis is not yet fully understood, assuming both genetic and environmental predisposing factors. Currently, it is known that the role of the human microbiome is crucial in maintaining the transkingdom balance between commensal microorganisms and the immune system. In the present work we study the intestinal microbiota of Argentine patients with different stages of SLE receiving or not different treatments. Microbiota composition and fecal miRNAs were assessed by 16 S sequencing and qPCR. hsa-miR-223-3p, a miRNA involved in several inflammation regulation pathways, was found underexpressed in SLE patients without immunosuppressive treatment. In terms of microbiota there were clear differences in population structure (Weighted and Unweighted Unifrac distances, p-value <0.05) and core microbiome between cases and controls. In addition, Collinsella, Bifidobacterium, Streptococcus genera and aromatics degradation metabolisms were overrepresented in the SLE group. Medical treatment was also determinant as several microbial metabolic pathways were influenced by immunosuppressive therapy. Particularly, allantoin degradation metabolism was differentially expressed in the group of patients receiving immunosuppressants. Finally, we performed a logistic regression model (LASSO: least absolute shrinkage and selection operator) considering the expression levels of the fecal hsa-miR223-3p; the core microbiota; the differentially abundant bacterial taxa and the differentially abundant metabolic pathways (p<0.05). The model predicted that SLE patients could be associated with greater relative abundance of the formaldehyde oxidation pathway (RUMP_PWY). On the contrary, the preponderance of the ketodeoxyoctonate (Kdo) biosynthesis and activation route (PWY_1269) and the genera Lachnospiraceae_UCG_004, Lachnospira, Victivallis and UCG_003 (genus belonging to the family Oscillospiraceae of the class Clostridia) were associated with a control phenotype. Overall, the present work could contribute to the development of integral diagnostic tools for the comprehensive phenotyping of patients with SLE. In this sense, studying the commensal microbial profile and possible pathobionts associated with SLE in our population proposes more effective and precise strategies to explore possible treatments based on the microbiota of SLE patients.
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Affiliation(s)
- Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ayelén Daiana Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Valeria Soler-Rivero
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Sebastian Nicolas Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Andrea Boiro
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Evangelina Arenielo
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | - Gustavo Vijoditz
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | | | - Marina Flavia Caputo
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | - María Cecilia Cimolai
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Federico Coluccio Leskow
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fiorella Sabrina Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina.
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Su Z, Chen A, Lipkowski J. Electrochemical and Infrared Studies of a Model Bilayer of the Outer Membrane of Gram-Negative Bacteria and its Interaction with polymyxin─the Last-Resort Antibiotic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8248-8259. [PMID: 38578277 DOI: 10.1021/acs.langmuir.4c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
A model bilayer of the outer membrane (OM) of Gram-negative bacteria, composed of lipid A and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), was assembled on the β-Tg modified gold (111) single crystal surface using a combination of Langmuir-Blodgett and Langmuir-Schaefer transfer. Electrochemical and spectroscopic methods were employed to study the properties of the model bilayer and its interaction with polymyxin. The model bilayer is stable on the gold surface in the transmembrane potential region between 0.0 and -0.7 V. The presence of Mg2+ coordinates with the phosphate and carboxylate groups in the leaflet of lipid A and stabilizes the structure of the model bilayer. Polymyxin causes the model bilayer leakage and damage in the transmembrane potential region between 0.2 and -0.4 V. At transmembrane potentials lower than -0.5 V, polymyxin does not affect the membrane integrity. Polymyxin binds to the phosphate and carboxylate groups in lipid A molecules and causes the increase of the tilt angle of acyl chains and the decrease of the tilt of the C═O bond. The results in this paper indicate that the antimicrobial activity of polymyxin depends on the transmembrane potential at the model bilayer and provides useful information for the development of new antibiotics.
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Affiliation(s)
- ZhangFei Su
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Aicheng Chen
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacek Lipkowski
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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Yang M, Zhang X, Ma S, Zhang Q, Peng C, Fan H, Dai L, Li J, Cheng L. Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis. Antonie Van Leeuwenhoek 2023; 116:1359-1374. [PMID: 37843737 DOI: 10.1007/s10482-023-01878-1] [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: 10/13/2022] [Accepted: 09/03/2023] [Indexed: 10/17/2023]
Abstract
A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0 µm in length and 0.4-0.6 µm in diameter. The strain Y-P2T grew optimally at 25 °C (range from 15 to 30 °C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826 T = JCM 34766 T).
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Affiliation(s)
- Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China
| | - Qiumei Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Chenghui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, Sichuan Province, People's Republic of China.
- Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, 610041, People's Republic of China.
- National Agricultural Experimental Station for Microorganisms, Shuangliu, Chengdu, 610213, Sichuan Province, People's Republic of China.
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5
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Liang L, Zhong LL, Wang L, Zhou D, Li Y, Li J, Chen Y, Liang W, Wei W, Zhang C, Zhao H, Lyu L, Stoesser N, Doi Y, Bai F, Feng S, Tian GB. A new variant of the colistin resistance gene MCR-1 with co-resistance to β-lactam antibiotics reveals a potential novel antimicrobial peptide. PLoS Biol 2023; 21:e3002433. [PMID: 38091366 PMCID: PMC10786390 DOI: 10.1371/journal.pbio.3002433] [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: 04/03/2023] [Revised: 01/12/2024] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
The emerging and global spread of a novel plasmid-mediated colistin resistance gene, mcr-1, threatens human health. Expression of the MCR-1 protein affects bacterial fitness and this cost correlates with lipid A perturbation. However, the exact molecular mechanism remains unclear. Here, we identified the MCR-1 M6 variant carrying two-point mutations that conferred co-resistance to β-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe disturbance in lipid A, resulting in up-regulation of L, D-transpeptidases (LDTs) pathway, which explains co-resistance to β-lactams. Moreover, we show that a lipid A loading pocket is localized at the linker domain of MCR-1 where these 2 mutations are located. This pocket governs colistin resistance and bacterial membrane permeability, and the mutated pocket in M6 enhances the binding affinity towards lipid A. Based on this new information, we also designed synthetic peptides derived from M6 that exhibit broad-spectrum antimicrobial activity, exposing a potential vulnerability that could be exploited for future antimicrobial drug design.
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Affiliation(s)
- Lujie Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lan-Lan Zhong
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Dianrong Zhou
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yaxin Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiachen Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yong Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Wanfei Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Wenjing Wei
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Hui Zhao
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lingxuan Lyu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Yohei Doi
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Siyuan Feng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Guo-Bao Tian
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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Wang Z, Zhao A, Qiao J, Yu J, He F, Bi Y, Yu L, Wang X. Engineering Escherichia coli MG1655 to Efficiently Produce 3-Deacyl-4'-monophosphoryl Lipid A. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13376-13390. [PMID: 37656614 DOI: 10.1021/acs.jafc.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Monophosphoryl lipid A, derived from Salmonella minnesota R595, has been used in various adjuvant formulations. Escherichia coli can produce lipid A, but its structure is different. In this study, E. coli MG1655 has been engineered to efficiently produce the monophosphoryl lipid A. First, 126 genes relevant to the biosynthesis of the fimbriae, flagella, and ECA were deleted in MG1655, resulting in WQM027. Second, the genes pldA, mlaA, and mlaC related to the phospholipid transport system, the gene ptsG related to the carbohydrate phosphotransferase system, and the gene eptA encoding phosphoethanolamine transferase for lipid A modification were further deleted from WQM027, resulting in MW020. Third, lpxE from Francisella novicida and pagP and pagL from Salmonella were overexpressed in pFT24, resulting in pTEPL. pTEPL was transformed into MW020, resulting in MW020/pTEPL. Finally, fabI encoding an enoyl-ACP reductase was deleted from the genome of MW020/pTEPL, resulting in MW021/pTEPL. MW021/pTEPL could produce 85.31 mg/L of lipid A species after 26 h of fed-batch fermentation. Mainly two monophosphoryl lipid A species were produced in MW021/pTEPL, one is 3-deacyl-2-acyloxyacyl-4'-monophosphoryl lipid A and the other is 3-deacyl-4'-monophosphoryl lipid A. E. coli MW021/pTEPL constructed in this study could be an ideal host for the industrial production of monophosphoryl lipid A.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Aizhen Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jing Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fenfang He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yibing Bi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Letong Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Castelletto V, Seitsonen J, Hamley IW. Effect of Glycosylation on Self-Assembly of Lipid A Lipopolysaccharides in Aqueous Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37289534 DOI: 10.1021/acs.langmuir.3c00828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipopolysaccharides (LPSs) based on lipid A produced by bacteria are of interest due to their bioactivity in stimulating immune responses, as are simpler synthetic components or analogues. Here, the self-assembly in water of two monodisperse lipid A derivatives based on simplified bacterial LPS structures is examined and compared to that of a native Escherichia coli LPS using small-angle X-ray scattering and cryogenic transmission electron microscopy. The critical aggregation concentration is obtained from fluorescence probe experiments, and conformation is probed using circular dichroism spectroscopy. The E. coli LPS is found to form wormlike micelles, whereas the synthetic analogues bearing six lipid chains and with four or two saccharide head groups (Kdo2-lipid A and monophosphoryl lipid A) self-assemble into nanosheets or vesicles, respectively. These observations are rationalized by considering the surfactant packing parameter.
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Affiliation(s)
- Valeria Castelletto
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K
| | - Jani Seitsonen
- Nanomicroscopy Center, Aalto University, Puumiehenkuja 2, Espoo FIN-02150, Finland
| | - Ian W Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [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: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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9
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Wang Z, Zhao A, Wang C, Huang D, Yu J, Yu L, Wu Y, Wang X. Metabolic engineering of Escherichia coli to efficiently produce monophosphoryl lipid A. Biotechnol Appl Biochem 2023. [PMID: 36659840 DOI: 10.1002/bab.2443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/08/2023] [Indexed: 01/21/2023]
Abstract
Monophosphoryl lipid A (MPL), mainly isolated from Salmonella minnesota R595, has been used as adjuvant in several vaccines. In this study, an Escherichia coli strain that can efficiently produce the MPL has been constructed. The gene clusters related to the biosynthesis of O-antigen, core oligosaccharide, enterobacterial common antigen, and colanic acid were sequentially removed to save the carbon source and to increase the activity of PagP in E. coli MG1655. Then, the genes pldA, mlaA, and mlaC related to the phospholipid transport system were further deleted, resulting in the strain MW012. Finally, the genes lpxE from Francisella novicida and pagP and pagL from Salmonella were overexpressed in MW012 to modify the structure of lipid A, resulting in the strain MW012/pWEPL. Lipid A species were isolated from MW012/pWEPL and analyzed by thin-layer chromatography and liquid chromatography-mass spectrometry. The results showed that mainly two MPL species were produced in E. coli MW012/pWEPL, one is hexa-acylated, and the other is penta-acylated. More importantly, the proportion of the hexa-acylated MPL, which is the most effective component of lipid A vaccine adjuvant, reached 75%. E. coli MW012/pWEPL constructed in this study provided a good alternative for the production of lipid A vaccine adjuvant MPL.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Aizhen Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Chenhui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Danyang Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jing Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Letong Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yuanming Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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10
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Heine H, Zamyatina A. Therapeutic Targeting of TLR4 for Inflammation, Infection, and Cancer: A Perspective for Disaccharide Lipid A Mimetics. Pharmaceuticals (Basel) 2022; 16:23. [PMID: 36678520 PMCID: PMC9864529 DOI: 10.3390/ph16010023] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
The Toll-like receptor 4 (TLR4) signaling pathway plays a central role in the prompt defense against infectious challenge and provides immediate response to Gram-negative bacterial infection. The TLR4/MD-2 complex can sense and respond to various pathogen-associated molecular patterns (PAMPs) with bacterial lipopolysaccharide (LPS) being the most potent and the most frequently occurring activator of the TLR4-mediated inflammation. TLR4 is believed to be both a friend and foe since improperly regulated TLR4 signaling can result in the overactivation of immune responses leading to sepsis, acute lung injury, or pathologic chronic inflammation involved in cancer and autoimmune disease. TLR4 is also considered a legitimate target for vaccine adjuvant development since its activation can boost the adaptive immune responses. The dual action of the TLR4 complex justifies the efforts in the development of both TLR4 antagonists as antisepsis drug candidates or remedies for chronic inflammatory diseases and TLR4 agonists as vaccine adjuvants or immunotherapeutics. In this review, we provide a brief overview of the biochemical evidences for possible pharmacologic applications of TLR4 ligands as therapeutics and report our systematic studies on the design, synthesis, and immunobiological evaluation of carbohydrate-based TLR4 antagonists with nanomolar affinity for MD-2 as well as disaccharide-based TLR4 agonists with picomolar affinity for the TLR4/MD-2 complex.
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Affiliation(s)
- Holger Heine
- Research Group Innate Immunity, Research Center Borstel—Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 22, 23845 Borstel, Germany
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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11
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Brace N, Megson IL, Rossi AG, Doherty MK, Whitfield PD. SILAC-based quantitative proteomics to investigate the eicosanoid associated inflammatory response in activated macrophages. J Inflamm (Lond) 2022; 19:12. [PMID: 36050729 PMCID: PMC9438320 DOI: 10.1186/s12950-022-00309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Macrophages play a central role in inflammation by phagocytosing invading pathogens, apoptotic cells and debris, as well as mediating repair of tissues damaged by trauma. In order to do this, these dynamic cells generate a variety of inflammatory mediators including eicosanoids such as prostaglandins, leukotrienes and hydroxyeicosatraenoic acids (HETEs) that are formed through the cyclooxygenase, lipoxygenase and cytochrome P450 pathways. The ability to examine the effects of eicosanoid production at the protein level is therefore critical to understanding the mechanisms associated with macrophage activation. RESULTS This study presents a stable isotope labelling with amino acids in cell culture (SILAC) -based proteomics strategy to quantify the changes in macrophage protein abundance following inflammatory stimulation with Kdo2-lipid A and ATP, with a focus on eicosanoid metabolism and regulation. Detailed gene ontology analysis, at the protein level, revealed several key pathways with a decrease in expression in response to macrophage activation, which included a promotion of macrophage polarisation and dynamic changes to energy requirements, transcription and translation. These findings suggest that, whilst there is evidence for the induction of a pro-inflammatory response in the form of prostaglandin secretion, there is also metabolic reprogramming along with a change in cell polarisation towards a reduced pro-inflammatory phenotype. CONCLUSIONS Advanced quantitative proteomics in conjunction with functional pathway network analysis is a useful tool to investigate the molecular pathways involved in inflammation.
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Affiliation(s)
- Nicole Brace
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Ian L Megson
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Adriano G Rossi
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mary K Doherty
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK
| | - Phillip D Whitfield
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Science, Old Perth Road, Inverness, IV2 3JH, UK.
- Present Address: Glasgow Polyomics, Garscube Campus, University of Glasgow, Glasgow, G61 1BD, UK.
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12
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Yan L, Dong H, Li H, Liu X, Deng Z, Dong C, Zhang Z. Uncovering lipopolysaccharide regulation in bacteria via the critical lipid binding tunnel of YciS/YciM. iScience 2022; 25:104988. [PMID: 36093049 PMCID: PMC9460159 DOI: 10.1016/j.isci.2022.104988] [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: 03/31/2022] [Revised: 06/04/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Gram-negative bacteria contain an asymmetric outer membrane, in which the outer leaflet is composed of lipopolysaccharide (LPS). LPS, a drug target of polymyxin, plays an essential role in drug resistance, biofilm formation, and pathogenesis. An important inner membrane protein, YciM, may be responsible for the regulation of LPS biosynthesis and transport. Here, we report the crystal structure of YciM from Salmonella typhimurium in a complex with a non-specifically bond molecule, an ethylene glycol, which identified a tunnel that could bind lipids. Our in vitro assays showed that YciM could bind lipid molecules with affinity in the micromolar range, while mutagenic and functional studies confirmed that lipid-binding residues are critical for the function of YciM. Additionally, our data also showed that YciM accurately regulates LPS biosynthesis and transport with YciS, which could help to better understand the regulation mechanism of LPS. Identifying a critical lipid binding tunnel of YciS/YciM The lipid binding tunnel could bind lipid molecules Mutants of lipid binding tunnel inhibit cell growth severely
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13
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Dey S, Shahrear S, Afroj Zinnia M, Tajwar A, Islam ABMMK. Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity. Bioinform Biol Insights 2022; 16:11779322221115535. [PMID: 35958299 PMCID: PMC9358594 DOI: 10.1177/11779322221115535] [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: 04/01/2022] [Accepted: 06/11/2022] [Indexed: 11/25/2022] Open
Abstract
Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.
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Affiliation(s)
- Supantha Dey
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Ahnaf Tajwar
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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14
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Minias P, Vinkler M. Selection balancing at innate immune genes: adaptive polymorphism maintenance in Toll-like receptors. Mol Biol Evol 2022; 39:6586215. [PMID: 35574644 PMCID: PMC9132207 DOI: 10.1093/molbev/msac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Balancing selection is a classic mechanism for maintaining variability in immune genes involved in host–pathogen interactions. However, it remains unclear how widespread the mechanism is across immune genes other than the major histocompatibility complex (MHC). Although occasional reports suggest that balancing selection (heterozygote advantage, negative frequency-dependent selection, and fluctuating selection) may act on other immune genes, the current understanding of the phenomenon in non-MHC immune genes is far from solid. In this review, we focus on Toll-like receptors (TLRs), innate immune genes directly involved in pathogen recognition and immune response activation, as there is a growing body of research testing the assumptions of balancing selection in these genes. After reviewing infection- and fitness-based evidence, along with evidence based on population allelic frequencies and heterozygosity levels, we conclude that balancing selection maintains variation in TLRs, though it tends to occur under specific conditions in certain evolutionary lineages rather than being universal and ubiquitous. Our review also identifies key gaps in current knowledge and proposes promising areas for future research. Improving our understanding of host–pathogen interactions and balancing selection in innate immune genes are increasingly important, particularly regarding threats from emerging zoonotic diseases.
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15
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Li Q, Zhou Y, Lu R, Zheng P, Wang Y. Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1. PeerJ 2022; 10:e13241. [PMID: 35433121 PMCID: PMC9012183 DOI: 10.7717/peerj.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles.
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Affiliation(s)
- Qingmei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yingli Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Rui Lu
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zheng
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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16
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Wang Z, Zheng Y, Ji M, Zhang X, Wang H, Chen Y, Wu Q, Chen GQ. Hyperproduction of PHA copolymers containing high fractions of 4-hydroxybutyrate (4HB) by outer membrane-defected Halomonas bluephagenesis grown in bioreactors. Microb Biotechnol 2022; 15:1586-1597. [PMID: 34978757 PMCID: PMC9049619 DOI: 10.1111/1751-7915.13999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/07/2023] Open
Abstract
Bacterial outer membrane (OM) is a self‐protective and permeable barrier, while having many non‐negligible negative effects in industrial biotechnology. Our previous studies revealed enhanced properties of Halomonas bluephagenesis based on positive cellular properties by OM defects. This study further expands the OM defect on membrane compactness by completely deleting two secondary acyltransferases for lipid A modification in H. bluephagenesis, LpxL and LpxM, and found more significant advantages than that of the previous lpxL mutant. Deletions on LpxL and LpxM accelerated poly(3‐hydroxybutyrate) (PHB) production by H. bluephagenesis WZY229, leading to a 37% increase in PHB accumulation and 84‐folds reduced endotoxin production. Enhanced membrane permeability accelerates the diffusion of γ‐butyrolactone, allowing H. bluephagenesis WZY254 derived from H. bluephagenesis WZY229 to produce 82wt% poly(3‐hydroxybutyrate‐co‐23mol%4‐hydroxybutyrate) (P(3HB‐co‐23mol%4HB)) in shake flasks, showing increases of 102% and 307% in P(3HB‐co‐4HB) production and 4HB accumulation, respectively. The 4HB molar fraction in copolymer can be elevated to 32 mol% in the presence of more γ‐butyrolactone. In a 7‐l bioreactor fed‐batch fermentation, H. bluephagenesis WZY254 supported a 84 g l−1 dry cell mass with 81wt% P(3HB‐co‐26mol%4HB), increasing 136% in 4HB molar fraction. This study further demonstrated that OM defects generate a hyperproduction strain for high 4HB containing copolymers.
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Affiliation(s)
- Ziyu Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yifei Zheng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mengke Ji
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuemeng Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China
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17
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Liu D, Chen S, Gou Y, Yu W, Zhou H, Zhang R, Wang J, Ye F, Liu Y, Sun B, Zhang K. Gastrointestinal Microbiota Changes in Patients With Gastric Precancerous Lesions. Front Cell Infect Microbiol 2021; 11:749207. [PMID: 34956928 PMCID: PMC8695999 DOI: 10.3389/fcimb.2021.749207] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background Gastric microbiota may be involved in gastric cancer. The relationship between gastrointestinal microbes and the risk of gastric cancer is unclear. This study aimed to explore the gastric and intestinal bacteria associated with gastritis and gastric precancerous lesions. We conducted a case-control study by performing 16S rRNA gene analysis of gastric biopsies, juices, and stool samples from 148 cases with gastritis or gastric precancerous lesions from Anhui and neighboring provinces, China. And we validated our findings in public datasets. Results Analysis of microbial sequences revealed decreased bacterial alpha diversity in gastric bacteria during the progression of gastritis. Helicobacter pylori was the main contributor to the decreased microbial composition and diversity in the gastric mucosa and had little influence on the microbiota of gastric juice and feces. The gastric mucosal genera Gemella, Veillonella, Streptococcus, Actinobacillus, and Hemophilus had the higher degree of centrality across the progression of gastric precancerous lesions. And Acinetobacter may contribute to the occurrence of intraepithelial neoplasia. In addition, the microbial model of H. pylori-positive gastric biopsies and feces showed value in the prediction of gastric precancerous lesions. Conclusions This study identified associations between gastric precancerous lesions and gastric microbiota, as well as the changes in intestinal microbiota, and explored their values in the prediction of gastric precancerous lesions.
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Affiliation(s)
- Dehua Liu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Si Chen
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yawen Gou
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenyong Yu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hangcheng Zhou
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rutong Zhang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jinghao Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fei Ye
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yingling Liu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Baolin Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Kaiguang Zhang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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18
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Wang Z, Fan F, Wang J, Wang L, Hu H, Wang C, Wang X. Engineering Escherichia coli to produce Bordetella pertussis oligosaccharide with multiple trisaccharide units. Metab Eng 2021; 69:147-162. [PMID: 34863939 DOI: 10.1016/j.ymben.2021.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/18/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022]
Abstract
The immunogenicity of the pertussis vaccine can be significantly improved by adding Bordetella pertussis oligosaccharide with multiple trisaccharide units. The more trisaccharide units there are, the better the efficiency of the immune response induction. However, natural B. pertussis oligosaccharides usually contain only a single terminal trisaccharide unit. In addition, B. pertussis is pathogenic, and there are potential safety hazards when preparing oligosaccharides from B. pertussis. In this study, Escherichia coli MG1655 was engineered to produce B. pertussis oligosaccharides containing multiple trisaccharide units. Fifty-nine genes relevant to the biosynthesis of the O-antigen and core oligosaccharide of lipopolysaccharide, enterobacterial common antigen, and colanic acid were deleted in MG1655, resulting in strain MDCO020. Then, 25 genes relevant to the biosynthesis of the oligosaccharide antigen in B. pertussis and 3 genes relevant to the repeating trisaccharide unit in Pseudomonas aeruginosa PAO1 were overexpressed in MDCO020, resulting in the recombinant E. coli MDCO020/pWpBpD5. The production of B. pertussis oligosaccharide with multiple trisaccharide units by MDCO020/pWpBpD5 was confirmed by SDS-PAGE and 1H NMR analyses, and its immune response-stimulating activity was confirmed by using rabbit anti-pertussis serum.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Fengfeng Fan
- Suzhou Microvac Biotech Co., Ltd., Suzhou, 215021, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Liangjia Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hao Hu
- Suzhou Microvac Biotech Co., Ltd., Suzhou, 215021, China
| | - Chenhui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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19
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Zhang X, Ye L, Liang G, Tang W, Yao L, Huang C. Different microRNAs contribute to the protective effect of mesenchymal stem cell-derived microvesicles in LPS induced acute respiratory distress syndrome. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1702-1708. [PMID: 35432797 PMCID: PMC8976904 DOI: 10.22038/ijbms.2021.56433.12640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES The present study aimed to determine whether bone marrow mesenchymal stem cell-derived microvesicles (MSC MVs) were effective in restoring lung tissue structure, and to assess the potential role of miRNAs in the pathogenesis and progression of acute respiratory distress syndrome (ARDS). MATERIALS AND METHODS ARDS was induced by lipopolysaccharide in male C57BL/6 mice. The degree of lung injury was assessed by histological analysis, lung's wet weight/body weight, and protein levels in the bronchoalveolar lavage fluid (BALF). Sequencing was performed on the BGISEQ-500 platform. Differentially expressed miRNAs (DEMs) were screened with the DEGseq software. The target genes of DEMs were predicted by iRNAhybrid, miRanda, and TargetScan. RESULTS Compared with LPS-injured mice, MSC MVs reduced lung water and total protein levels in the BALF, demonstrating a protective effect. 52 miRNAs were differentially expressed following treatment with MSC MVs in ARDS mice. Among them, miR-532-5p, miR-223-3p, and miR-744-5p were significantly regulated. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed the target genes were mainly located in the cell, organelle, and membrane. Furthermore, KEGG pathways such as ErbB, PI3K-Akt, Ras, MAPK, Toll, and Wnt signaling pathways were the most significant pathways enriched by the target genes. CONCLUSION MSC MVs treatment was involved in alleviating lung injury and promoting lung tissue repair by dysregulated miRNAs.
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Affiliation(s)
- Xingcai Zhang
- Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China
| | - Lifang Ye
- Department of Anesthesiology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Guojin Liang
- Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China
| | - Wan Tang
- Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China
| | - Lifeng Yao
- Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China
| | - Changshun Huang
- Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China,Corresponding author: Changshun Huang. Department of Anesthesiology, Ningbo First Hospital, No. 59 Liuting Street, Haishu District, Ningbo 315010, Zhejiang, China. Tel/ Fax: +86-13957882779;
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20
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Engineering the Outer Membrane Could Facilitate Better Bacterial Performance and Effectively Enhance Poly-3-Hydroxybutyrate Accumulation. Appl Environ Microbiol 2021; 87:e0138921. [PMID: 34550763 DOI: 10.1128/aem.01389-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly-3-hydroxybutyrate (PHB) is an environmentally friendly polymer and can be produced in Escherichia coli cells after overexpression of the heterologous gene cluster phaCAB. The biosynthesis of the outer membrane (OM) consumes many nutrients and influences cell morphology. Here, we engineered the OM by disrupting all gene clusters relevant to the polysaccharide portion of lipopolysaccharide (LPS), colanic acid (CA), flagella, and/or fimbria in E. coli W3110. All these disruptions benefited PHB production. Especially, disrupting all these OM components increased the PHB content to 83.0 wt% (PHB content percentage of dry cell weight), while the wild-type control produced only 1.5 wt% PHB. The increase was mainly due to the LPS truncation to Kdo2 (3-deoxy-d-manno-octulosonic acid)-lipid A, which resulted in 82.0 wt% PHB with a 25-fold larger cell volume, and disrupting CA resulted in 57.8 wt% PHB. In addition, disrupting LPS facilitated advantageous fermentation features, including 69.1% less acetate, a 550% higher percentage of autoaggregated cells among the total culture cells, 69.1% less biofilm, and a higher broken cell ratio. Further detailed mechanism investigations showed that disrupting LPS caused global changes in envelope and cellular metabolism: (i) a sharp decrease in flagella, fimbria, and secretions; (ii) more elastic cells; (iii) much greater carbon flux toward acetyl coenzyme A (acetyl-CoA) and supply of cofactors, including NADP, NAD, and ATP; and (iv) a decrease in by-product acids but increase in γ-aminobutyric acid by activating σE factor. Disrupting CA, flagella, and fimbria also improved the levels of acetyl-CoA and cofactors. The results indicate that engineering the OM is an effective strategy to enhance PHB production and highlight the applicability of OM engineering to increase microbial cell factory performance. IMPORTANCE Understanding the detailed influence of the OM on the cell envelope and cellular metabolism is important for optimizing the E. coli cell factory and many other microorganisms. This study revealed the applicability of remodeling the OM to enhance PHB accumulation as representative inclusion bodies. The results generated in this study give essential information for producing other inclusion bodies or chemicals which need more acetyl-CoA and cofactors but less by-product acids. This study is promising to provide new ideas for the improvement of microbial cell factories.
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21
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Tan X, Qiao J, Li H, Huang D, Hu X, Wang X. Global metabolic regulation in Vibrio parahaemolyticus under polymyxin B stimulation. Microb Pathog 2021; 161:105260. [PMID: 34688850 DOI: 10.1016/j.micpath.2021.105260] [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: 06/29/2021] [Revised: 09/25/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022]
Abstract
Vibrio parahaemolyticus is responsible for infection diseases of people who consume the contaminated seafood, but its metabolic regulation profile in response to colistin, the last treatment option for multidrug-resistant Gram-negative bacteria, remains unclear. In this study, the metabolic regulation profile of V. parahaemolyticus ATCC33846 under polymyxin B stimulation has been investigated. V. parahaemolyticus exposed to polymyxin B resulted in 4597 differentially transcribed genes, including 673 significantly up-regulated genes and 569 significantly down-regulated genes. In V. parahaemolyticus under polymyxin B stimulation, the cellular antioxidant systems to prevent bacteria from oxidant stress was activated, the synthesis of some nonessential macromolecules was reduced, and the assembly and modification of lipopolysaccharide and peptidoglycan to resist the attack from other antibiotics were promoted. These findings provide new insights into polymyxin B-related stress response in V. parahaemolyticus which should be useful for developing novel drugs for infection.
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Affiliation(s)
- Xin Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hedan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Danyang Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
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22
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Extraction of ADP-Heptose and Kdo2-Lipid A from E. coli Deficient in the Heptosyltransferase I Gene. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11188314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enzymes involved in lipopolysaccharide (LPS) biosynthesis, including Heptosyltransferase I (HepI), are critical for maintaining the integrity of the bacterial cell wall, and therefore these LPS biosynthetic enzymes are validated targets for drug discovery to treat Gram-negative bacterial infections. Enzymes involved in the biosynthesis of lipopolysaccharides (LPSs) utilize substrates that are synthetically complex, with numerous stereocenters and site-specific glycosylation patterns. Due to the relatively complex substrate structures, characterization of these enzymes has necessitated strategies to generate bacterial cells with gene disruptions to enable the extraction of these substrates from large scale bacterial growths. Like many LPS biosynthetic enzymes, Heptosyltransferase I binds two substrates: the sugar acceptor substrate, Kdo2-Lipid A, and the sugar donor substrate, ADP-l-glycero-d-manno-heptose (ADPH). HepI characterization experiments require copious amounts of Kdo2-Lipid A and ADPH, and unsuccessful extractions of these two substrates can lead to serious delays in collection of data. While there are papers and theses with protocols for extraction of these substrates, they are often missing small details essential to the success of the extraction. Herein detailed protocols are given for extraction of ADPH and Kdo2-Lipid A (KLA) from E. coli, which have had proven success in the Taylor lab. Key steps in the extraction of ADPH are clearing the extract through ultracentrifugation and keeping all water that touches anything in the extraction, including filters, at a pH of 8.0. Key steps in the extraction of KLA are properly lysing the dried down cells before starting the extraction, maximizing yield by allowing precipitate to form overnight, appropriately washing the pellet with phenol and dissolving the KLA in 1% TEA using visual cues, rather than a specific volume. These protocols led to increased yield and a higher success rate of extractions thereby enabling the characterization of HepI.
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23
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Yin W, Ling Z, Dong Y, Qiao L, Shen Y, Liu Z, Wu Y, Li W, Zhang R, Walsh TR, Dai C, Li J, Yang H, Liu D, Wang Y, Gao GF, Shen J. Mobile Colistin Resistance Enzyme MCR-3 Facilitates Bacterial Evasion of Host Phagocytosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101336. [PMID: 34323389 PMCID: PMC8456205 DOI: 10.1002/advs.202101336] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/12/2021] [Indexed: 05/10/2023]
Abstract
Mobile colistin resistance enzyme MCR-3 is a phosphoethanolamine transferase modifying lipid A in Gram-negative bacteria. MCR-3 generally mediates low-level (≤8 mg L-1 ) colistin resistance among Enterobacteriaceae, but occasionally confers high-level (>128 mg L-1 ) resistance in aeromonads. Herein, it is determined that MCR-3, together with another lipid A modification mediated by the arnBCADTEF operon, may be responsible for high-level colistin resistance in aeromonads. Lipid A is the critical site of pathogens for Toll-like receptor 4 recognizing. However, it is unknown whether or how MCR-3-mediated lipid A modification affects the host immune response. Compared with the wild-type strains, increased mortality is observed in mice intraperitoneally-infected with mcr-3-positive Aeromonas salmonicida and Escherichia coli strains, along with sepsis symptoms. Further, mcr-3-positive strains show decreased clearance rates than wild-type strains, leading to bacterial accumulation in organs. The increased mortality is tightly associated with the increased tissue hypoxia, injury, and post-inflammation. MCR-3 expression also impairs phagocytosis efficiency both in vivo and in vitro, contributing to the increased persistence of mcr-3-positive bacteria in tissues compared with parental strains. This study, for the first time, reveals a dual function of MCR-3 in bacterial resistance and pathogenicity, which calls for caution in treating the infections caused by mcr-positive pathogens.
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Affiliation(s)
- Wenjuan Yin
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
- College of Basic Medical ScienceKey Laboratory of Pathogenesis Mechanism and Control of Inflammatory‐Autoimmune Diseases of Hebei ProvinceHebei UniversityBaoding071002China
| | - Zhuoren Ling
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yanjun Dong
- Department of Basic Veterinary MedicineCollege of Veterinary MedicineChina Agricultural UniversityHaidianBeijing100193China
| | - Lu Qiao
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yingbo Shen
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of Sciences (CAS)Beijing100101China
| | - Zhihai Liu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
- Agricultural Bio‐Pharmaceutical LaboratoryCollege of Chemistry and Pharmaceutical SciencesQingdao Agricultural UniversityQingdao266109China
| | - Yifan Wu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Wan Li
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhou310009China
| | | | - Chongshan Dai
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and ControlNational Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionChangpingBeijing102206China
| | - Hui Yang
- NHC Key Laboratory of Food Safety Risk AssessmentChina National Center for Food Safety Risk AssessmentNo. 7 Panjiayuan NanliBeijing100021China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of Sciences (CAS)Beijing100101China
- College of Veterinary MedicineChina Agricultural UniversityHaidianBeijing100193China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal‐Derived Food SafetyCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193China
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Fan Z, Pathak JL, Ge L. The Potential Role of RP105 in Regulation of Inflammation and Osteoclastogenesis During Inflammatory Diseases. Front Cell Dev Biol 2021; 9:713254. [PMID: 34414191 PMCID: PMC8369417 DOI: 10.3389/fcell.2021.713254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammatory diseases have a negative impact on bone homeostasis via exacerbated local and systemic inflammation. Bone resorbing osteoclasts are mainly derived from hematopoietic precursors and bone marrow monocytes. Induced osteoclastogenesis during inflammation, autoimmunity, metabolic diseases, and cancers is associated with bone loss and osteoporosis. Proinflammatory cytokines, pathogen-associated molecular patterns, or endogenous pathogenic factors induce osteoclastogenic differentiation by binding to the Toll-like receptor (TLR) family expressed on surface of osteoclast precursors. As a non-canonical member of the TLRs, radioprotective 105 kDa (RP105 or CD180) and its ligand, myeloid differentiation protein 1 (MD1), are involved in several bone metabolic disorders. Reports from literature had demonstrated RP105 as an important activator of B cells, bone marrow monocytes, and macrophages, which regulates inflammatory cytokines release from immune cells. Reports from literature had shown the association between RP105 and other TLRs, and the downstream signaling mechanisms of RP105 with different “signaling-competent” partners in immune cells during different disease conditions. This review is focused to summarize: (1) the role of RP105 on immune cells’ function and inflammation regulation (2) the potential regulatory roles of RP105 in different disease-mediated osteoclast activation and the underlying mechanisms, and (3) the different “signaling-competent” partners of RP105 that regulates osteoclastogenesis.
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Affiliation(s)
- Zhou Fan
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Janak L Pathak
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Linhu Ge
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China.,Institute of Oral Disease, Guangzhou Medical University, Guangzhou, China
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25
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Stevens BR, Roesch L, Thiago P, Russell JT, Pepine CJ, Holbert RC, Raizada MK, Triplett EW. Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome. Mol Psychiatry 2021; 26:4277-4287. [PMID: 31988436 DOI: 10.1038/s41380-020-0652-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Single nucleotide exact amplicon sequence variants (ASV) of the human gut microbiome were used to evaluate if individuals with a depression phenotype (DEPR) could be identified from healthy reference subjects (NODEP). Microbial DNA in stool samples obtained from 40 subjects were characterized using high throughput microbiome sequence data processed via DADA2 error correction combined with PIME machine-learning de-noising and taxa binning/parsing of prevalent ASVs at the single nucleotide level of resolution. Application of ALDEx2 differential abundance analysis with assessed effect sizes and stringent PICRUSt2 predicted metabolic pathways. This multivariate machine-learning approach significantly differentiated DEPR (n = 20) vs. NODEP (n = 20) (PERMANOVA P < 0.001) based on microbiome taxa clustering and neurocircuit-relevant metabolic pathway network analysis for GABA, butyrate, glutamate, monoamines, monosaturated fatty acids, and inflammasome components. Gut microbiome dysbiosis using ASV prevalence data may offer the diagnostic potential of using human metaorganism biomarkers to identify individuals with a depression phenotype.
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Affiliation(s)
- Bruce R Stevens
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA. .,Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA. .,Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
| | - Luiz Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.,Centro Interdisciplinar de Pesquisas em Biotecnologia-CIP-Biotec, Universidade Federal do Pampa, São Gabriel, Bagé, Brazil
| | - Priscila Thiago
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jordan T Russell
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Richard C Holbert
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mohan K Raizada
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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26
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Core oligosaccharide portion of lipopolysaccharide plays important roles on multiple antibiotic resistance in Escherichia coli. Antimicrob Agents Chemother 2021; 65:e0034121. [PMID: 34310209 DOI: 10.1128/aac.00341-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative bacteria are intrinsically resistant to antibiotics due to the presence of the cell envelope, but mechanisms are still not fully understood. In this study, a series of mutants that lack one or more major components associated with the cell envelope were constructed from Escherichia coli K-12 W3110. WJW02 can only synthesize Kdo2-lipid A which lacks the core oligosaccharide portion of lipopolysaccharide. WJW04, WJW07 and WJW08 were constructed from WJW02 by deleting the gene clusters relevant to the biosynthesis of exopolysaccharide, flagella and fimbria, respectively. WJW09, WJW010 and WJW011 cells cannot synthesize exopolysaccharide, flagella and fimbria, respectively. Comparing to the wild type W3110, mutants WJW02, WJW04, WJW07 and WJW08 cells showed decreased resistance to more than 10 different antibacterial drugs, but not the mutants WJW09, WJW010 and WJW011. This indicates that the core oligosaccharide portion of lipopolysaccharide plays important roles on multiple antibiotic resistance in E. coli and the 1st heptose in core oligosaccharide portion is critical. Furthermore, the removal of the core oligosaccharide of LPS leads to influences on cell wall morphology, cell phenotypes, porins, efflux systems, and the respond behaviors to antibiotic stimulation. The results demonstrated the important role of lipopolysaccharide on the antibiotic resistance of Gram-negative bacteria.
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27
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Tan X, Qiao J, Zhou Q, Huang D, Li H, Wang J, Wang X. Identification of a phosphoethanolamine transferase for lipid A modification in Vibrio parahaemolyticus. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Williams TJ, Allen MA, Ivanova N, Huntemann M, Haque S, Hancock AM, Brazendale S, Cavicchioli R. Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake. Front Microbiol 2021; 12:674758. [PMID: 34140946 PMCID: PMC8204192 DOI: 10.3389/fmicb.2021.674758] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/23/2021] [Indexed: 01/25/2023] Open
Abstract
Organic Lake in Antarctica is a marine-derived, cold (−13∘C), stratified (oxic-anoxic), hypersaline (>200 gl–1) system with unusual chemistry (very high levels of dimethylsulfide) that supports the growth of phylogenetically and metabolically diverse microorganisms. Symbionts are not well characterized in Antarctica. However, unicellular eukaryotes are often present in Antarctic lakes and theoretically could harbor endosymbionts. Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenome-assembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al., 2020). At 158,228 bp (encoding 194 genes), the genome of Ca. Organicella extenuata is among the smallest known bacterial genomes and similar to the genome of Ca. Pinguicoccus supinus (163,218 bp, 205 genes). Ca. Organicella extenuata retains a capacity for replication, transcription, translation, and protein-folding while lacking any capacity for the biosynthesis of amino acids or vitamins. Notably, the endosymbiont retains a capacity for fatty acid synthesis (type II) and iron–sulfur (Fe-S) cluster assembly. Metagenomic analysis of 150 new metagenomes from Organic Lake and more than 70 other Antarctic aquatic locations revealed a strong correlation in abundance between Ca. Organicella extenuata and a novel ciliate of the genus Euplotes. Like Ca. Pinguicoccus supinus, we infer that Ca. Organicella extenuata is an endosymbiont of Euplotes and hypothesize that both Ca. Organicella extenuata and Ca. Pinguicocccus supinus provide fatty acids and Fe-S clusters to their Euplotes host as the foundation of a mutualistic symbiosis. The discovery of Ca. Organicella extenuata as possessing genetic code 4 illustrates that in addition to identifying endosymbionts by sequencing known symbiotic communities and searching metagenome data using reference endosymbiont genomes, the potential exists to identify novel endosymbionts by searching for unusual coding parameters.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Natalia Ivanova
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
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29
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Wang Z, Qin Q, Zheng Y, Li F, Zhao Y, Chen GQ. Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties. Metab Eng 2021; 67:53-66. [PMID: 34098101 DOI: 10.1016/j.ymben.2021.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022]
Abstract
Bacterial outer membrane (OM), an asymmetric lipid bilayer functioning as a self-protective barrier with reduced permeability for Gram-negative bacteria, yet wasting nutrients and energy to synthesize, has not been studied for its effect on bioproduction. Here we construct several OM-defected halophile Halomonas bluephagenesis strains to investigate the effects of OM on bioproduction. We achieve enhanced chassis properties of H. bluephagenesis based on positive cellular properties among several OM-defected strains. The OM-defected H. bluephagenesis WZY09 demonstrates better adaptation to lower salinity, increasing 28%, 30% and 12% on dry cell mass (DCM), poly(3-hydroxybutyrate) (PHB) accumulation and glucose to PHB conversion rate, respectively, including enlarged cell sizes and 21-folds reduced endotoxin. Interestingly, a poly(3-hydroxybutyrate-co-21mol%4-hydroxybutyrate) (P(3HB-co-21mol%4HB)) is produced by H. bluephagenesis WZY09 derivate WZY249, increasing 60% and 260% on polyhydroxyalkanoate (PHA) production and 4HB content, respectively. Furthermore, increased electroporation efficiency, more sensitive isopropyl β-D-1-thio-galactopyranoside (IPTG) induction, better oxygen uptake, enhanced antibiotics sensitivity and ectoine secretion due to better membrane permeability are observed if OM defected, demonstrating significant OM defection impacts for further metabolic engineering, synthetic biology studies and industrial applications.
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Affiliation(s)
- Ziyu Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qin Qin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yifei Zheng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fajin Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yiqing Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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30
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Chen S, Chen S, Wang J, Zhan Y, Wang Z, Fang Y, Wang X. Characterization of a gene cluster containing four genes relevant to biosynthesis of inner core of lipopolysaccharide in Cronobacter sakazakii. Biotechnol Appl Biochem 2021; 69:1080-1093. [PMID: 33928676 DOI: 10.1002/bab.2179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/20/2021] [Indexed: 11/08/2022]
Abstract
Many genes in the biosynthetic pathway of lipopolysaccharide in Cronobacter sakazakii have not been identified. In this study, we demonstrate that an operon containing four genes ESA_RS18945, ESA_RS18950, ESA_RS18955, and ESA_RS18960 is responsible for L-glycero-D-mannoheptose addition on the inner core of lipopolysaccharide in C. sakazakii. The proteins encoded by these four genes are homologous to E. coli WaaQ, WaaC, WaaF, and WaaD. Lipopolysaccharide from the deletion mutants of ESA_RS18945, ESA_RS18950, ESA_RS18955, and ESA_RS18960 (named as △RS18945, △RS18950, △RS18955 and △RS18960, respectively) were analyzed by SDS-PAGE. △RS18945 synthesized lipopolysaccharide with similar length to the wildtype BAA-894, whereas △RS18950, △RS18955, and △RS18960 synthesized much shorter lipopolysaccharide. This suggests that the enzyme encoded by ESA_RS18945 might function as E. coli WaaQ on the sidechain of lipopolysaccharide. When E. coli WaaC, WaaF, and WaaD were overexpressed in △RS18950, △RS18955, and △RS18960, respectively, the full length of lipopolysaccharide was recovered. Mass spectrometry analysis indicates that △RS18950 and △RS18960 only synthesized Kdo2 -lipid A, confirming that enzymes encoded by ESA_RS18950 and ESA_RS18960 have similar functions to E. coli WaaC and WaaD, respectively. Hep-Kdo2 -lipid A with a phosphoethanolamine was produced in △RS18955, suggesting that the enzyme encoded by ESA_RS18955 has similar function to E. coli WaaF.
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Affiliation(s)
- Shanshan Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Si Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yi Zhan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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31
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Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry. Metabolites 2021; 11:metabo11040197. [PMID: 33810392 PMCID: PMC8065654 DOI: 10.3390/metabo11040197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Lipid A is a characteristic molecule of Gram-negative bacteria that elicits an immune response in mammalian cells. The presence of structurally diverse lipid A types in the human gut bacteria has been suggested before, and this appears associated with the immune response. However, lipid A structures and their quantitative heterogeneity have not been well characterized. In this study, a method of analysis for lipid A using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) was developed and applied to the analyses of Escherichia coli and Bacteroidetes strains. In general, phosphate compounds adsorb on stainless-steel piping and cause peak tailing, but the use of an ammonia-containing alkaline solvent produced sharp lipid A peaks with high sensitivity. The method was applied to E. coli strains, and revealed the accumulation of lipid A with abnormal acyl side chains in knockout strains as well as known diphosphoryl hexa-acylated lipid A in a wild-type strain. The analysis of nine representative strains of Bacteroidetes showed the presence of monophosphoryl penta-acylated lipid A characterized by a highly heterogeneous main acyl chain length. Comparison of the structures and amounts of lipid A among the strains suggested a relationship between lipid A profiles and the phylogenetic classification of the strains.
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32
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Wang J, Ma W, Wang X. Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories. Microb Cell Fact 2021; 20:73. [PMID: 33743682 PMCID: PMC7980664 DOI: 10.1186/s12934-021-01565-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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33
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Xu Z, Liu Z, Soteyome T, Hua J, Zhang L, Yuan L, Ye Y, Cai Z, Yang L, Chen L, Harro JM, Kjellerup BV, Liu J, Li Y. Impact of pmrA on Cronobacter sakazakii planktonic and biofilm cells: A comprehensive transcriptomic study. Food Microbiol 2021; 98:103785. [PMID: 33875213 DOI: 10.1016/j.fm.2021.103785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 12/30/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Cronobacter sakazakii is an emerging opportunistic foodborne pathogen causing rare but severe infections in neonates. Furthermore, the formation of biofilm allows C. sakazakii to persist in different environments. We have demonstrated that the mutator phenotype ascribed to deficiency of the pmrA gene results in more biomass in the first 24 h but less during the post maturation stage (7-14 d) compared with BAA 894. The present study aimed to investigate the regulatory mechanism modulating biofilm formation due to pmrA mutation. The transcriptomic analyses of BAA 894 and s-3 were performed by RNA-sequencing on planktonic and biofilm cells collected at different time points. According to the results, when comparing biofilm to planktonic cells, expression of genes encoding outer membrane proteins, lysozyme, etc. were up-regulated, with LysR family transcriptional regulators, periplasmic proteins, etc. down-regulated. During biofilm formation, cellulose synthase operon genes, flagella-related genes, etc. played essential roles in different stages. Remarkably, pmrA varies the expression of a number of genes related to motility, biofilm formation, and antimicrobial resistance, including srfB, virK, mviM encoding virulence factor, flgF, fliN, etc. encoding flagellar assembly, and marA, ramA, etc. encoding AraC family transcriptional regulators in C. sakazakii. This study provides valuable insights into transcriptional regulation of C. sakazakii pmrA mutant during biofilm formation.
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Affiliation(s)
- Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China; Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38103, USA; Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand; National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, 510640, China
| | - Ziqi Liu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Thanapop Soteyome
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - Jingjing Hua
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yanrui Ye
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Zhao Cai
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Janette M Harro
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA
| | - Birthe Veno Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yanyan Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China.
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34
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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35
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Singh V, Hwang N, Ko G, Tatsuya U. Effects of digested Cheonggukjang on human microbiota assessed by in vitro fecal fermentation. J Microbiol 2021; 59:217-227. [PMID: 33527320 DOI: 10.1007/s12275-021-0525-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/16/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
In vitro fecal fermentation is an assay that uses fecal microbes to ferment foods, the results of which can be used to evaluate the potential of prebiotic candidates. To date, there have been various protocols used for in vitro fecal fermentation-based assessments of food substances. In this study, we investigated how personal gut microbiota differences and external factors affect the results of in vitro fecal fermentation assays. We used Cheonggukjang (CGJ), a Korean traditional fermented soybean soup that is acknowledged as healthy functional diet. CGJ was digested in vitro using acids and enzymes, and then fermented with human feces anaerobically. After fecal fermentation, the microbiota was analyzed using MiSeq, and the amount of short chain fatty acids (SCFAs) were measured using GC-MS. Our results suggest that CGJ was effectively metabolized by fecal bacteria to produce SCFAs, and this process resulted in an increase in the abundance of Coprococcus, Ruminococcus, and Bifidobacterium and a reduction in the growth of Sutterella, an opportunistic pathogen. The metabolic activities predicted from the microbiota shifts indicated enhanced metabolism linked to methionine biosynthesis and depleted chondroitin sulfate degradation. Moreover, the amount of SCFAs and microbiota shifts varied depending on personal microbiota differences. Our findings also suggest that in vitro fecal fermentation of CGJ for longer durations may partially affect certain fecal microbes. Overall, the study discusses the usability of in vitro gastrointestinal digestion and fecal fermentation (GIDFF) to imitate the effects of diet-induced microbiome modulation and its impact on the host.
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Affiliation(s)
- Vineet Singh
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea
| | - Nakwon Hwang
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea
| | - Gwangpyo Ko
- Subtropical/tropical Organism Gene Bank, Jeju National University, Jeju, 63243, Republic of Korea
| | - Unno Tatsuya
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea.
- Subtropical/tropical Organism Gene Bank, Jeju National University, Jeju, 63243, Republic of Korea.
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36
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Nguyen TT, Kosciolek T, Daly RE, Vázquez-Baeza Y, Swafford A, Knight R, Jeste DV. Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk. Brain Behav Immun 2021; 91:245-256. [PMID: 33098964 PMCID: PMC8023565 DOI: 10.1016/j.bbi.2020.10.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging evidence has linked the gut microbiome changes to schizophrenia. However, there has been limited research into the functional pathways by which the gut microbiota contributes to the phenotype of persons with chronic schizophrenia. We characterized the composition and functional potential of the gut microbiota in 48 individuals with chronic schizophrenia and 48 matched (sequencing plate, age, sex, BMI, and antibiotic use) non-psychiatric comparison subjects (NCs) using 16S rRNA sequencing. Patients with schizophrenia demonstrated significant beta-diversity differences in microbial composition and predicted genetic functional potential compared to NCs. Alpha-diversity of taxa and functional pathways were not different between groups. Random forests analyses revealed that the microbiome predicts differentiation of patients with schizophrenia from NCs using taxa (75% accuracy) and functional profiles (67% accuracy for KEGG orthologs, 70% for MetaCyc pathways). We utilized a new compositionally-aware method incorporating reference frames to identify differentially abundant microbes and pathways, which revealed that Lachnospiraceae is associated with schizophrenia. Functional pathways related to trimethylamine-N-oxide reductase and Kdo2-lipid A biosynthesis were altered in schizophrenia. These metabolic pathways were associated with inflammatory cytokines and risk for coronary heart disease in schizophrenia. Findings suggest potential mechanisms by which the microbiota may impact the pathophysiology of the disease through modulation of functional pathways related to immune signaling/response and lipid and glucose regulation to be further investigated in future studies.
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Affiliation(s)
- Tanya T Nguyen
- Department of Psychiatry, University of California, San Diego, CA, United States; Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, CA, United States.
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California, San Diego, CA, United States; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rebecca E Daly
- Sam and Rose Stein Institute for Research on Aging, University of California, San Diego, CA, United States
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, CA, United States
| | - Austin Swafford
- Center for Microbiome Innovation, University of California, San Diego, CA, United States
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA, United States; Center for Microbiome Innovation, University of California, San Diego, CA, United States; Department of Computer Science and Engineering, University of California, San Diego, CA, United States; Department of Computer Science and Engineering, University of California, San Diego, CA, United States
| | - Dilip V Jeste
- Department of Psychiatry, University of California, San Diego, CA, United States; Department of Pediatrics, University of California, San Diego, CA, United States; Center for Microbiome Innovation, University of California, San Diego, CA, United States; Department of Neurosciences, University of California, San Diego, CA, United States
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37
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Těšický M, Velová H, Novotný M, Kreisinger J, Beneš V, Vinkler M. Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae). Mol Ecol 2020; 29:3056-3070. [PMID: 32652716 DOI: 10.1111/mec.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 01/04/2023]
Abstract
Despite widespread variability and redundancy abounding animal immunity, little is currently known about the rate of evolutionary convergence (functionally analogous traits not inherited from a common ancestor) in host molecular adaptations to parasite selective pressures. Toll-like receptors (TLRs) provide the molecular interface allowing hosts to recognize pathogenic structures and trigger early danger signals initiating an immune response. Using a novel combination of bioinformatic approaches, here we explore genetic variation in ligand-binding regions of bacteria-sensing TLR4 and TLR5 in 29 species belonging to the tit family of passerine birds (Aves: Paridae). Three out of the four consensual positively selected sites in TLR4 and six out of 14 positively selected positions in TLR5 were located on the receptor surface near the functionally important sites, and based on the phylogenetic pattern evolved in a convergent (parallel) manner. This type of evolution was also seen at one N-glycosylation site and two positively selected phosphorylation sites, providing the first evidence of convergence in post-translational modifications in evolutionary immunology. Finally, the overall mismatch between phylogeny and the clustering of surface charge distribution demonstrates that convergence is common in overall TLR4 and TLR5 molecular phenotypes involved in ligand binding. Our analysis did not reveal any broad ecological traits explaining the convergence observed in electrostatic potentials, suggesting that information on microbial symbionts may be needed to explain TLR evolution. Adopting state-of-the-art predictive structural bionformatics, we have outlined a new broadly applicable methodological approach to estimate the functional significance of positively selected variation and test for the adaptive molecular convergence in protein-coding polymorphisms.
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Affiliation(s)
- Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hana Velová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Beneš
- European Molecular Laboratory Heidelberg, Heidelberg, Germany
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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38
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Hua J, Jia X, Zhang L, Li Y. The Characterization of Two-Component System PmrA/PmrB in Cronobacter sakazakii. Front Microbiol 2020; 11:903. [PMID: 32655500 PMCID: PMC7326031 DOI: 10.3389/fmicb.2020.00903] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/16/2020] [Indexed: 01/12/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic Gram-negative pathogen that could cause meningitis and necrotizing enterocolitis. Several Gram-negative bacteria use the PmrA/PmrB system to sense and adapt to environmental change by resistance to cationic antimicrobial peptides of host immune systems. The PmrA/PmrB two-component system regulates several genes to modify LPS structure in the bacterial outer membrane. The role of PmrA/PmrB of C. sakazakii has been studied within the current study. The results suggest that PmrA/PmrB plays a crucial role in modifying LPS structure, cationic antimicrobial peptide susceptibility, cell membrane permeability and hydrophobicity, and invading macrophage.
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Affiliation(s)
- Jingjing Hua
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Xiangyin Jia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Yanyan Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
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39
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Zhang Y, Liu Y, Zhang S, Ma W, Wang J, Yin L, Wang X. Metabolic engineering of Corynebacterium glutamicum WM001 to improve l-isoleucine production. Biotechnol Appl Biochem 2020; 68:568-584. [PMID: 32474971 DOI: 10.1002/bab.1963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/29/2020] [Indexed: 01/02/2023]
Abstract
In this study, l-isoleucine production in Corynebacterium glutamicum WM001 was improved by deleting three genes in the genome, replacing the native promoter of ilvA in the genome, and overexpression of five genes in an alr-based auxotrophic complementation expression system. The three genes deleted in the genome are alaT, brnQ, and alr. Deletion of alaT improved l-isoleucine production by increasing the supply of pyruvate, whereas deletion of brnQ improved l-isoleucine production by blocking the uptake of extracellular l-isoleucine. Exchange of the native promoter of ilvA with promoter tac or tacM could contribute to l-isoleucine production by increasing 2-ketobutyric acid; tac is better than tacM for improving l-isoleucine yield. Different combinations of the genes ilvBN, ppnK, lrp, and brnFE were overexpressed in an alr-based auxotrophic complementation expression system to further improve l-isoleucine production, and the best yield after 72-H flask fermentation was obtained from the strain WM005/pYCW-1-ilvBN2-ppnK1. Without addition of any antibiotics, WM005/pYCW-1-ilvBN2-ppnK1 could produce 32.1 g/L l-isoleucine after 72-H fed-batch fermentation, which is 34.3% increase compared with the original strain WM001.
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Affiliation(s)
- Yanchao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, People's Republic of China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, People's Republic of China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, People's Republic of China
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40
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Wang J, Ma W, Fang Y, Zhang H, Liang H, Li Y, Wang X. Truncating the Structure of Lipopolysaccharide in Escherichia coli Can Effectively Improve Poly-3-hydroxybutyrate Production. ACS Synth Biol 2020; 9:1201-1215. [PMID: 32302096 DOI: 10.1021/acssynbio.0c00071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Poly-3-hydroxybutyrate is an environmentally friendly polymer with many promising applications and can be produced in Escherichia coli cells after overexpressing the heterologous gene cluster phaCAB. In this study, we found that truncating the structure of lipopolysaccharide in E. coli can effectively enhance poly-3-hydroxybutyrate production. E. coli mutant strains WJW00, WJD00, and WJJ00 were constructed by deleting rfaD from E. coli strain W3110, DH5α, and JM109, respectively. Compared to the controls W3110/pDXW-8-phaCAB, DH5a/pDXW-8-phaCAB, and JM109/pDXW-8-phaCAB, the yield of poly-3-hydroxybutyrate in WJW00/pDXW-8-phaCAB, WJD00/pDXW-8-phaCAB, and WJJ00/pDXW-8-phaCAB cells increased by 200%, 81.5%, and 75.6%, respectively, and the conversion rate of glucose to poly-3-hydroxybutyrate was increased by ∼250%. Further analysis revealed that LPS truncation in E. coli rebalanced carbon and nitrogen metabolism, increased the levels of acetyl-CoA, γ-aminobutyric acid, NADPH, NADH, and ATP, and decreased the levels of organic acids and flagella, resulting in the high ratio of carbon to nitrogen. These metabolic changes in these E. coli mutants led to the significant increase of poly-3-hydroxybutyrate production.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biotechnology Engineering, College of Life Science, Yantai University, Shandong, 264005, China
| | - Hao Liang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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41
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Glasl B, Robbins S, Frade PR, Marangon E, Laffy PW, Bourne DG, Webster NS. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME JOURNAL 2020; 14:1435-1450. [PMID: 32123297 PMCID: PMC7242418 DOI: 10.1038/s41396-020-0622-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 01/06/2023]
Abstract
Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.
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Affiliation(s)
- Bettina Glasl
- Australian Institute of Marine Science, Townsville, QLD, Australia. .,College of Science and Engineering, James Cook University, Townsville, QLD, Australia. .,AIMS@JCU, Townsville, QLD, Australia.
| | - Steven Robbins
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Pedro R Frade
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Emma Marangon
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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42
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Chakrabarty JK, Sadananda SC, Bhat A, Naik AJ, Ostwal DV, Chowdhury SM. High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:173-182. [PMID: 32031390 DOI: 10.1021/jasms.9b00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cleavable cross-linking technology requires further MS/MS of the cleavable fragments for unambiguous identification of cross-linked peptides. These spectra are sometimes very ambiguous due to the sensitivity and complex fragmentation pattern of the peptides with the cross-linked residues. We recently reported a dual cleavable cross-linking technology (DUCCT), which can enhance the confidence in the identification of cross-linked peptides. The heart of this strategy is a novel dual mass spectrometry cleavable cross linker that can be cleaved preferentially by two differential tandem mass spectrometry methods, collision induced dissociation and electron transfer dissociation (CID and ETD). Different signature ions from two different mass spectra for the same cross-linked peptide helped identify the cross-linked peptides with high confidence. In this study, we developed an enrichment-based photocleavable DUCCT (PC-DUCCT-biotin), where cross-linked products were enriched from biological samples using affinity purification, and subsequently, two sequential tandem (CID and ETD) mass spectrometry processes were utilized. Furthermore, we developed a prototype software called Cleave-XL to analyze cross-linked products generated by DUCCT. Photocleavable DUCCT was demonstrated in standard peptides and proteins. Efficiency of the software tools to search and compare CID and ETD data of photocleavable DUCCT biotin in standard peptides and proteins as well as regular DUCCT in protein complexes from immune cells were tested. The software is efficient in pinpointing cross-linked sites using CID and ETD cross-linking data. We believe this new DUCCT and associated software tool Cleave-XL will advance high confidence identification of protein cross-linking sites and automated identification of low-resolution protein structures.
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Affiliation(s)
- Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Sandhya C Sadananda
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Apeksha Bhat
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Aishwarya J Naik
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Dhanashri V Ostwal
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
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43
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Xu Z, Li M, Li Y, Cao H, Miao L, Xu Z, Higuchi Y, Yamasaki S, Nishino K, Woo PC, Xiang H, Yan A. Native CRISPR-Cas-Mediated Genome Editing Enables Dissecting and Sensitizing Clinical Multidrug-Resistant P. aeruginosa. Cell Rep 2019; 29:1707-1717.e3. [DOI: 10.1016/j.celrep.2019.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/09/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
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Kroeck KG, Sacco MD, Smith EW, Zhang X, Shoun D, Akhtar A, Darch SE, Cohen F, Andrews LD, Knox JE, Chen Y. Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography. Sci Rep 2019; 9:15450. [PMID: 31664082 PMCID: PMC6820557 DOI: 10.1038/s41598-019-51844-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022] Open
Abstract
The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.
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Affiliation(s)
- Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Michael D Sacco
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Daniel Shoun
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Sophie E Darch
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Frederick Cohen
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Logan D Andrews
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - John E Knox
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States.
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45
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Zhao L, Hu X, Li Y, Wang Z, Wang X. Construction of a novel Escherichia coli expression system: relocation of lpxA from chromosome to a constitutive expression vector. Appl Microbiol Biotechnol 2019; 103:7177-7189. [PMID: 31317228 DOI: 10.1007/s00253-019-10013-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/22/2019] [Accepted: 07/05/2019] [Indexed: 11/26/2022]
Abstract
The selective marker in the plasmid-based expression system is usually a gene that encodes an antibiotic-resistant protein; therefore, the antibiotic has to add to maintain the plasmid when growing the bacteria. This antibiotic addition would lead to increase of production cost and the environment contamination. In this study, a novel Escherichia coli expression system, the lpxA deletion mutant harboring an lpxA-carrying vector, was developed. To develop this system, three plasmids pCas9Cre, pTF-A-UD, and pRSFCmlpxA were constructed. The plasmid pCas9Cre produces enzymes Cas9, λ-Red, and Cre and can be cured by growing at 42 °C; pTF-A-UD contains several DNA fragments required for deleting the chromosomal lpxA and can be cured by adding isopropyl-D-thiogalactopyranoside; pRSFCmlpxA contains the lpxA mutant lpxA123 and CamR. When E. coli were transformed with these three plasmids, the chromosomal lpxA and the CamR in pRSFCmlpxA can be efficiently removed, resulting in an E. coli lpxA mutant harboring pRSFlpxA. The lpxA is essential for the growth of E. coli; its relocation from chromosome to a constitutive expression vector is an ideal strategy to maintain the vector without antibiotic addition. The lpxA123 in pRSFlpxA can complement the deletion of the chromosomal lpxA and provide a strong selective pressure to maintain the plasmid pRSFlpxA. This study provides an experimental evidence that this novel expression system is convenient and efficient to use and can be used to improve L-threonine biosynthesis in the wild type E. coli MG1655 and an L-threonine producing E. coli TWF006.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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46
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de Oliveira MTP, de Sá Coutinho D, Tenório de Souza É, Stanisçuaski Guterres S, Pohlmann AR, Silva PMR, Martins MA, Bernardi A. Orally delivered resveratrol-loaded lipid-core nanocapsules ameliorate LPS-induced acute lung injury via the ERK and PI3K/Akt pathways. Int J Nanomedicine 2019; 14:5215-5228. [PMID: 31371957 PMCID: PMC6636190 DOI: 10.2147/ijn.s200666] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022] Open
Abstract
Background Resveratrol (RSV) has attracted interest as an alternative drug for the treatment of acute lung injury (ALI) and other pulmonary diseases, but its poor oral bioavailability is a limitation. In this study, we employed drug delivery nanotechnology to improve the stability, lung localization and efficacy of orally administered resveratrol to control lung damage leading to ALI. Methods and materials RSV-loaded lipid-core nanocapsules (RSV-LNCs), prepared by interfacial deposition of biodegradable polymers, were given orally to A/J mice prior to lipopolysaccharide (LPS) intranasal instillation. Inflammatory changes, oxidative stress and lung tissue elastance were assessed 24 h after LPS challenge. Results RSV-LNCs (5 mg/kg), given 1, 4, 6 or 12 h but not 24 h before provocation, inhibited LPS-induced leukocyte accumulation in the bronchoalveolar fluid (BALF), whereas unloaded nanocapsules (ULNCs) or free RSV (5 mg/kg) were ineffective. RSV-LNCs (2.5–10 mg/kg) but not ULNCs or RSV improved lung function and prevented total leukocyte and neutrophil accumulation equally in both BALF and lung tissue when given 4 h before LPS challenge. Similar findings were seen concerning the generation of a range of pro-inflammatory cytokines such as IL-6, KC, MIP-1α, MIP-2, MCP-1 and RANTES in lung tissue. In addition, only RSV-LNCs inhibited MDA levels and SOD activity in parallel with blockade of the ERK and PI3K/Akt pathways following LPS provocation. Conclusion Nanoformulation of RSV in biodegradable oil-core polymers is an effective strategy to improve the anti-ALI activity of RSV, suggesting that the modified-release formulation of this plant polyphenol may be of great value in clinical conditions associated with ALI and respiratory failure.
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Affiliation(s)
| | - Diego de Sá Coutinho
- Laboratory of Inflammation, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Éverton Tenório de Souza
- Laboratory of Inflammation, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Sílvia Stanisçuaski Guterres
- Pharmaceutical Sciences Post-Graduation Program, College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriana Raffin Pohlmann
- Department of Organic Chemistry, Institute of Chemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Marco Aurélio Martins
- Laboratory of Inflammation, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Andressa Bernardi
- Laboratory of Inflammation, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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47
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Strategy for improving L-isoleucine production efficiency in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:2101-2111. [DOI: 10.1007/s00253-019-09632-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 01/25/2023]
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48
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Buettner MJ, Shah SR, Saeui CT, Ariss R, Yarema KJ. Improving Immunotherapy Through Glycodesign. Front Immunol 2018; 9:2485. [PMID: 30450094 PMCID: PMC6224361 DOI: 10.3389/fimmu.2018.02485] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/08/2018] [Indexed: 01/04/2023] Open
Abstract
Immunotherapy is revolutionizing health care, with the majority of high impact "drugs" approved in the past decade falling into this category of therapy. Despite considerable success, glycosylation-a key design parameter that ensures safety, optimizes biological response, and influences the pharmacokinetic properties of an immunotherapeutic-has slowed the development of this class of drugs in the past and remains challenging at present. This article describes how optimizing glycosylation through a variety of glycoengineering strategies provides enticing opportunities to not only avoid past pitfalls, but also to substantially improve immunotherapies including antibodies and recombinant proteins, and cell-based therapies. We cover design principles important for early stage pre-clinical development and also discuss how various glycoengineering strategies can augment the biomanufacturing process to ensure the overall effectiveness of immunotherapeutics.
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Affiliation(s)
- Matthew J Buettner
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Sagar R Shah
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Christopher T Saeui
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States.,Pharmacology/Toxicology Branch I, Division of Clinical Evaluation and Pharmacology/Toxicology, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Bethesda, MD, United States
| | - Ryan Ariss
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
| | - Kevin J Yarema
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, MD, United States
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49
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Borio A, Holgado A, Garate JA, Beyaert R, Heine H, Zamyatina A. Disaccharide-Based Anionic Amphiphiles as Potent Inhibitors of Lipopolysaccharide-Induced Inflammation. ChemMedChem 2018; 13:2317-2331. [PMID: 30276970 DOI: 10.1002/cmdc.201800505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/18/2018] [Indexed: 01/08/2023]
Abstract
Despite significant advances made in the last decade in the understanding of molecular mechanisms of sepsis and in the development of clinically relevant therapies, sepsis remains the leading cause of mortality in intensive care units with increasing incidence worldwide. Toll-like receptor 4 (TLR4)-a transmembrane pattern-recognition receptor responsible for propagating the immediate immune response to Gram-negative bacterial infection-plays a central role in the pathogenesis of sepsis and chronic inflammation-related disorders. TLR4 is complexed with the lipopolysaccharide (LPS)-sensing protein myeloid differentiation-2 (MD-2) which represents a preferred target for establishing new anti-inflammatory treatment strategies. Herein we report the development, facile synthesis, and biological evaluation of novel disaccharide-based TLR4⋅MD-2 antagonists with potent anti-endotoxic activity at micromolar concentrations. A series of synthetic anionic glycolipids entailing amide-linked β-ketoacyl lipid residues was prepared in a straightforward manner by using a single orthogonally protected nonreducing diglucosamine scaffold. Suppression of the LPS-induced release of interleukin-6 and tumor necrosis factor was monitored and confirmed in human immune cells (MNC and THP1) and mouse macrophages. Structure-activity relationship studies and molecular dynamics simulations revealed the structural basis for the high-affinity interaction between anionic glycolipids and MD-2, and highlighted two compounds as leads for the development of potential anti-inflammatory therapeutics.
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Affiliation(s)
- Alessio Borio
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Aurora Holgado
- Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation, Ghent University, Center for Inflammation Research, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Jose Antonio Garate
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
| | - Rudi Beyaert
- Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation, Ghent University, Center for Inflammation Research, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Holger Heine
- Research Group Innate Immunity, Research Center Borstel-Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Disease (DZL), Parkallee 22, 23845, Borstel, Germany
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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50
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Chen S, Zhou Q, Tan X, Li Y, Ren G, Wang X. The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency. Front Microbiol 2018; 9:1875. [PMID: 30154778 PMCID: PMC6102319 DOI: 10.3389/fmicb.2018.01875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 07/25/2018] [Indexed: 12/29/2022] Open
Abstract
Cronobacter species can cause necrotizing enterocolitis and meningitis in neonates and infants, their infection is closely relevant to their responses to extreme growth conditions. In this study, the response of Cronobacter species to amino acid deficiency has been investigated. Four Cronobacter species formed smooth colonies when grown on the solid LB medium, but formed mucoid colonies when grown on the amino acid deficient M9 medium. When the mucoid colonies were stained with tannin mordant, exopolysaccharide around the cells could be discerned. The exopolysaccharide was isolated, analyzed, and identified as colanic acid. When genes wcaD and wcaE relevant to colanic acid biosynthesis were deleted in Cronobacter sakazakii BAA-894, no exopolysaccharide could be produced, confirming the exopolysaccharide formed in C. sakazakii grown in M9 is colanic acid. On the other hand, when genes rcsA, rcsB, rcsC, rcsD, or rcsF relevant to Rcs phosphorelay system was deleted in C. sakazakii BAA-894, colanic acid could not be produced, suggesting that the production of colanic acid in C. sakazakii is regulated by Rcs phosphorelay system. Furthermore, C. sakazakii BAA-894 grown in M9 supplemented with amino acids could not produce exopolysaccharide. Transcriptomes of C. sakazakii BAA-894 grown in M9 or LB were analyzed. A total of 3956 genes were differentially expressed in M9, of which 2339 were up-regulated and 1617 were down-regulated. When C. sakazakii BAA-894 was grown in M9, the genes relevant to the biosynthesis of exopolysaccharide were significantly up-regulated; on the other hand, the genes relevant to the flagellum formation and chemotaxis were significantly down-regulated; in addition, most genes relevant to various amino acid biosynthesis were also significantly regulated. The results demonstrate that amino acid deficiency has a global impact on C. sakazakii cells.
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Affiliation(s)
- Si Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qing Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xin Tan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Ge Ren
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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