1
|
Gerken H, Shetty D, Kern B, Kenney LJ, Misra R. Effects of pleiotropic ompR and envZ alleles of Escherichia coli on envelope stress and antibiotic sensitivity. J Bacteriol 2024; 206:e0017224. [PMID: 38809006 PMCID: PMC11332150 DOI: 10.1128/jb.00172-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
The EnvZ-OmpR two-component system of Escherichia coli regulates the expression of the ompF and ompC porin genes in response to medium osmolarity. However, certain mutations in envZ confer pleiotropy by affecting the expression of genes of the iron and maltose regulons not normally controlled by EnvZ-OmpR. In this study, we obtained two novel envZ and ompR pleiotropic alleles, envZT15P and ompRL19Q, among revertants of a mutant with heightened envelope stress and an outer membrane (OM) permeability defect. Unlike envZ, pleiotropic mutations in ompR have not been described previously. The mutant alleles reduced the expression of several outer membrane proteins (OMPs), overcame the temperature-sensitive growth defect of a protease-deficient (ΔdegP) strain, and lowered envelope stress and OM permeability defects in a background lacking the BamB protein of an essential β-barrel assembly machinery complex. Biochemical analysis showed OmpRL19Q, like wild-type OmpR, is readily phosphorylated by EnvZ, but the EnvZ-dependent dephosphorylation of OmpRL19Q~P was drastically impaired compared to wild-type OmpR. This defect would lead to a prolonged half-life for OmpRL19Q~P, an outcome remarkably similar to what we had previously described for EnvZR397L, resulting in pleiotropy. By employing null alleles of the OMP genes, it was determined that the three pleiotropic alleles lowered envelope stress by reducing OmpF and LamB levels. The absence of LamB was principally responsible for lowering the OM permeability defect, as assessed by the reduced sensitivity of a ΔbamB mutant to vancomycin and rifampin. Possible mechanisms by which novel EnvZ and OmpR mutants influence EnvZ-OmpR interactions and activities are discussed.IMPORTANCEMaintenance of the outer membrane (OM) integrity is critical for the survival of Gram-negative bacteria. Several envelope homeostasis systems are activated when OM integrity is perturbed. Through the isolation and characterization of novel pleiotropic ompR/envZ alleles, this study highlights the involvement of the EnvZ-OmpR two-component system in lowering envelope stress and the OM permeability defect caused by the loss of proteins that are involved in OM biogenesis, envelope homeostasis, and structural integrity.
Collapse
Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dasvit Shetty
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Brea Kern
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
2
|
Eddenden A, Dooda MK, Morrison ZA, Subramanian AS, Howell PL, Troutman JM, Nitz M. Metabolic Usage and Glycan Destinations of GlcNAz in E. coli. ACS Chem Biol 2024; 19:69-80. [PMID: 38146215 PMCID: PMC11138243 DOI: 10.1021/acschembio.3c00501] [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] [Indexed: 12/27/2023]
Abstract
Bacteria use a diverse range of carbohydrates to generate a profusion of glycans, with amino sugars, such as N-acetylglucosamine (GlcNAc), being prevalent in the cell wall and in many exopolysaccharides. The primary substrate for GlcNAc-containing glycans, UDP-GlcNAc, is the product of the bacterial hexosamine pathway and a key target for bacterial metabolic glycan engineering. Using the strategy of expressing NahK, to circumvent the hexosamine pathway, it is possible to directly feed the analogue of GlcNAc, N-azidoacetylglucosamine (GlcNAz), for metabolic labeling in Escherichia coli. The cytosolic production of UDP-GlcNAz was confirmed by using fluorescence-assisted polyacrylamide gel electrophoresis. The key question of where GlcNAz is incorporated was interrogated by analyzing potential sites including peptidoglycan (PGN), the biofilm-related exopolysaccharide poly-β-1,6-N-acetylglucosamine (PNAG), lipopolysaccharide (LPS), and the enterobacterial common antigen (ECA). The highest levels of incorporation were observed in PGN with lower levels in PNAG and no observable incorporation in LPS or ECA. The promiscuity of the PNAG synthase (PgaCD) toward UDP-GlcNAz in vitro and the lack of undecaprenyl-pyrophosphoryl-GlcNAz intermediates generated in vivo confirmed the incorporation preferences. The results of this work will guide the future development of carbohydrate-based probes and metabolic engineering strategies.
Collapse
Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Manoj K. Dooda
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223-0001, United States
| | - Zachary A. Morrison
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Adithya Shankara Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - P. Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223-0001, United States
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| |
Collapse
|
3
|
Li X, Zhou J, Han R, Yu F, Liu K, Zhao M, Liu Y, Xue Z, Zhao S. Phosphatase A1 accessory protein PlaS from Serratia marcescens controls cell membrane permeability, fluidity, hydrophobicity, and fatty acid composition in Escherichia coli BL21. Int J Biol Macromol 2023; 253:126776. [PMID: 37699461 DOI: 10.1016/j.ijbiomac.2023.126776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Phospholipase A1 (PlaA) plays a pivotal role in diverse applications within the food and biochemical medical industries. Herein, we investigate the impact of the accessory protein encoded by plaS from Serratia marcescens on PlaA activity in Escherichia coli. Notably, PlaS demonstrates the ability to enhance PlaA activity while concurrently exhibiting inhibitory effects on the growth of E. coli BL21 (DE3). Our study revolves around probing the inhibitory action of PlaS on E. coli BL21 (DE3). PlaS exhibits a propensity to heighten both the permeability of outer and inner cell membranes, leading to concomitant reductions in membrane fluidity and surface hydrophobicity. This phenomenon is validated through scanning electron microscopy (SEM) analysis, which highlights PlaS's capacity to compromise membrane integrity. Moreover, through a comprehensive comparative transcriptomic sequencing approach, we identify four down-regulated genes (galM, ybhC, ldtC, and kdpB) alongside two up-regulated genes (rbsB and degP). These genes are intricately associated with processes such as cell membrane synthesis and modification, energy metabolism, and transmembrane transport. Our investigation unveils the intricate gene-level mechanisms underpinning PlaS-mediated growth inhibition and membrane disruption. Consequently, our findings serve as a significant reference for the elucidation of membrane protein mechanisms, shedding light on potential avenues for future exploration.
Collapse
Affiliation(s)
- Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Jie Zhou
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Rumeng Han
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Fei Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Kun Liu
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Ming Zhao
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Yan Liu
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China
| | - Zhenglian Xue
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China.
| | - Shiguang Zhao
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic & Food Engineering, Anhui Polytechnic University, 8 Middle Beijing Road, Wuhu 241000, China.
| |
Collapse
|
4
|
Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [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: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
Collapse
Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| |
Collapse
|
5
|
Eddenden A, Dooda MK, Morrison ZA, Subramanian AS, Howell PL, Troutman JM, Nitz M. The Metabolic Usage and Glycan Destinations of GlcNAz in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553294. [PMID: 37645909 PMCID: PMC10462111 DOI: 10.1101/2023.08.17.553294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Bacteria use a diverse range of carbohydrates to generate a profusion of glycans, with amino sugars such as N-acetylglucosamine (GlcNAc) being prevalent in the cell wall and in many exopolysaccharides. The primary substrate for GlcNAc-containing glycans, UDP-GlcNAc, is the product of the bacterial hexosamine pathway, and a key target for bacterial metabolic glycan engineering. Using the strategy of expressing NahK, to circumvent the hexosamine pathway, it is possible to directly feed the analogue of GlcNAc, N-azidoacetylglucosamine (GlcNAz), for metabolic labelling in E. coli. The cytosolic production of UDP-GlcNAz was confirmed using fluorescence assisted polyacrylamide gel electrophoresis. The key question of where GlcNAz is incorporated, was interrogated by analyzing potential sites including: peptidoglycan (PGN), the biofilm-related exopolysaccharide poly-β-1,6-N-acetylglucosamine (PNAG), lipopolysaccharide (LPS) and the enterobacterial common antigen (ECA). The highest levels of incorporation were observed in PGN with lower levels in PNAG and no observable incorporation in LPS or ECA. The promiscuity of the PNAG synthase (PgaCD) towards UDP-GlcNAz in vitro and lack of undecaprenyl-pyrophosphoryl-GlcNAz intermediates generated in vivo confirmed the incorporation preferences. The results of this work will guide the future development of carbohydrate-based probes and metabolic engineering strategies.
Collapse
Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Manoj K Dooda
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, United States
| | - Zachary A Morrison
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Adithya Shankara Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jerry M Troutman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, United States
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
6
|
Amalia L, Tsai SL. Functionalization of OMVs for Biocatalytic Applications. MEMBRANES 2023; 13:membranes13050459. [PMID: 37233521 DOI: 10.3390/membranes13050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Outer membrane vesicles (OMVs) are miniature versions of gram-negative bacteria that contain almost the same content as their parent cells, particularly in terms of membrane composition. Using OMVs as biocatalysts is a promising approach due to their potential benefits, including their ability to be handled similarly to bacteria while lacking potentially pathogenic organisms. To employ OMVs as biocatalysts, they must be functionalized with immobilized enzymes to the OMV platform. Various enzyme immobilization techniques are available, including surface display and encapsulation, each with advantages and disadvantages depending on the objectives. This review provides a concise yet comprehensive overview of these immobilization techniques and their applications in utilizing OMVs as biocatalysts. Specifically, we discuss the use of OMVs in catalyzing the conversion of chemical compounds, their role in polymer degradation, and their performance in bioremediation.
Collapse
Affiliation(s)
- Lita Amalia
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City 10607, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City 10607, Taiwan
| |
Collapse
|
7
|
Young JW, Zhao Z, Wason IS, Duong van Hoa F. A Dual Detergent Strategy to Capture a Bacterial Outer Membrane Proteome in Peptidiscs for Characterization by Mass Spectrometry and Binding Assays. J Proteome Res 2022; 22:1537-1545. [PMID: 36516475 DOI: 10.1021/acs.jproteome.2c00560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outer membrane of Gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics, and therefore is a prime target for antimicrobial discovery. To facilitate the discovery efforts, a precise knowledge of the outer membrane proteome, and possible variations during pathogenesis, is important. Characterization of the bacterial outer membrane remain challenging, however, and low throughput, due to the high hydrophobicity and relatively low abundance of this cell compartment. Here we adapt our peptidisc-based method to selectively isolate the outer membrane proteome before analysis by mass spectrometry. Using a dual detergent membrane solubilization approach, followed by protein purification in peptidiscs, we capture over 70 outer membrane proteins, including 26 integral β-barrels and 26 lipoproteins. Many of these proteins are present at high peptide intensities, indicative of a high abundance in the library sample. We further show that the isolated outer membrane proteome can be employed in downstream ligand-binding assays. This peptidisc library made of outer membrane proteins may therefore be useful to systematically survey other bacterial outer membrane proteomes, but also as a nanoparticle format able to support the discovery of next-generation antimicrobials. Data are available via ProteomeXchange identifier PXD036749.
Collapse
Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
8
|
Pushpker R, Bay DC, Turner RJ. Small multidrug resistance protein EmrE phenotypically associates with OmpW, DcrB and YggM for osmotic stress protection by betaine in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748554 DOI: 10.1099/mic.0.001287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The small multidrug resistance (SMR) protein EmrE resides in the inner membrane and provides resistance against a wide range of antiseptic quaternary cationic compounds (QCCs) for the Gram-negative bacterium Escherichia coli. We have reported previously that overexpression of the emrE gene results in the reduction of pH and osmotic tolerance, likely through EmrE-mediated biological QCC-based osmoprotectant efflux, indicating a potential physiological role for EmrE beyond providing drug resistance. EmrE is the most studied member of SMR transporter family; however, it is not known how the substrates translocated by EmrE move across the periplasm and through the outer membrane (OM). We have shown that the OM protein OmpW participates in the EmrE-mediated substrate efflux process and provided a hypothesis for the present study that additional OM and periplasmic proteins participate in the translocation process. To test the hypothesis, we conducted alkaline pH-based growth phenotype screens under emrE overexpression conditions. This screen identified 10 additional genes that appear to contribute to the EmrE-coupled osmoprotectant efflux: gspD, hofQ, yccZ, acrA, emrA, emrB, proX, osmF, dcrB and yggM. Further screening of these genes using a hyperosmotic growth phenotype assay in the presence and the absence of the osmoprotectant glycine betaine identified ompW and two periplasmic protein genes, dcrB and yggM, are mechanistically linked to EmrE.
Collapse
Affiliation(s)
- Rajnigandha Pushpker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
9
|
Huang Y, Zhu F, Koh J, Stanton D, Chen S, Wang N. Proteomic and bioinformatic analyses of proteins in the outer membrane and extracellular compartments and outer membrane vesicles of Candidatus Liberibacter species. Front Microbiol 2022; 13:977710. [PMID: 36225379 PMCID: PMC9548881 DOI: 10.3389/fmicb.2022.977710] [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: 06/24/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
Citrus Huanglongbing (HLB) is the most devastating citrus disease in the world. Candidatus Liberibacter asiaticus (Las) is the prevalent HLB pathogen, which is yet to be cultivated. A recent study demonstrates that Las does not contain pathogenicity factors that are directly responsible for HLB symptoms. Instead, Las triggers systemic and chronic immune responses, representing a pathogen-triggered immune disease. Importantly, overproduction of reactive oxygen species (ROS) causes systemic cell death of phloem tissues, thus causing HLB symptoms. Because Las resides in the phloem tissues, it is expected that phloem cell might recognize outer membrane proteins, outer membrane vesicle (OMV) proteins and extracellular proteins of Las to contribute to the immune responses. Because Las has not been cultivated, we used Liberibacter crescens (Lcr) as a surrogate to identify proteins in the OM fraction, OMV proteins and extracellular proteins by liquid chromatography with tandem mass spectrometry (LC–MS/MS). We observed OMVs of Lcr under scanning electron microscope, representing the first experimental evidence that Liberibacter can deliver proteins to the extracellular compartment. In addition, we also further analyzed LC–MS/MS data using bioinformatic tools. Our study provides valuable information regarding the biology of Ca. Liberibacter species and identifies many putative proteins that may interact with host proteins in the phloem tissues.
Collapse
Affiliation(s)
- Yixiao Huang
- Department of Plant Pathology, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Fanchao Zhu
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Daniel Stanton
- Department of Plant Pathology, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
- *Correspondence: Nian Wang,
| |
Collapse
|
10
|
Gene Networks and Pathways Involved in Escherichia coli Response to Multiple Stressors. Microorganisms 2022; 10:microorganisms10091793. [PMID: 36144394 PMCID: PMC9501238 DOI: 10.3390/microorganisms10091793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Stress response helps microorganisms survive extreme environmental conditions and host immunity, making them more virulent or drug resistant. Although both reductionist approaches investigating specific genes and systems approaches analyzing individual stress conditions are being used, less is known about gene networks involved in multiple stress responses. Here, using a systems biology approach, we mined hundreds of transcriptomic data sets for key genes and pathways involved in the tolerance of the model microorganism Escherichia coli to multiple stressors. Specifically, we investigated the E. coli K-12 MG1655 transcriptome under five stresses: heat, cold, oxidative stress, nitrosative stress, and antibiotic treatment. Overlaps of transcriptional changes between studies of each stress factor and between different stressors were determined: energy-requiring metabolic pathways, transport, and motility are typically downregulated to conserve energy, while genes related to survival, bona fide stress response, biofilm formation, and DNA repair are mainly upregulated. The transcription of 15 genes with uncharacterized functions is higher in response to multiple stressors, which suggests they may play pivotal roles in stress response. In conclusion, using rank normalization of transcriptomic data, we identified a set of E. coli stress response genes and pathways, which could be potential targets to overcome antibiotic tolerance or multidrug resistance.
Collapse
|
11
|
Du Y, May RC, Cooper HJ. Native ambient mass spectrometry of intact protein assemblies directly from Escherichia coli colonies. Chem Commun (Camb) 2022; 58:6857-6860. [PMID: 35617055 PMCID: PMC9196203 DOI: 10.1039/d2cc02085h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we demonstrate that by combining electroporation with native ambient mass spectrometry, it is possible to detect intact non-covalent protein complexes directly from bacterial colonies growing on agar. Homodimers HdeA and HdeB were identified, together with the 50 kDa Mn-bound superoxide dismutase homodimer, in addition to some previously undetected monomeric proteins.
Collapse
Affiliation(s)
- Yuying Du
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| |
Collapse
|
12
|
Goodall ECA, Isom GL, Rooke JL, Pullela K, Icke C, Yang Z, Boelter G, Jones A, Warner I, Da Costa R, Zhang B, Rae J, Tan WB, Winkle M, Delhaye A, Heinz E, Collet JF, Cunningham AF, Blaskovich MA, Parton RG, Cole JA, Banzhaf M, Chng SS, Vollmer W, Bryant JA, Henderson IR. Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth. PLoS Genet 2021; 17:e1009586. [PMID: 34941903 PMCID: PMC8741058 DOI: 10.1371/journal.pgen.1009586] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/07/2022] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
The cell envelope is essential for viability in all domains of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the best studied organisms, Escherichia coli, there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell division. Here, we used a whole-genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss of yhcB, a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies, we report the comprehensive genetic interaction network of yhcB, revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a ΔyhcB background. Subsequent analyses suggest that YhcB functions at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target. All life depends on a cell envelope to enclose the chemical reactions that make life possible. But how do cell envelopes grow? How each component of the cell envelope is incorporated into the envelope at the correct amount, in the correct place, and at the correct time, to prevent cell death, has been a long-standing question in bacteriology. Using a unique combination of high throughput chemical genetic screens we identified yhcB, a conserved gene of unknown function, required for the maintenance of cell envelope integrity in Escherichia coli. Loss of YhcB results in aberrant cell size driven by the production of excess membrane phospholipids. Subsequent molecular and biochemical analyses suggest YhcB influences the spatiotemporal biogenesis of LPS, peptidoglycan and membrane phospholipids. Our data indicate YhcB is a key regulator of cell envelope growth in Gram-negative bacteria playing a crucial role in coordinating cell width, elongation, and division to maintain cell envelope integrity.
Collapse
Affiliation(s)
- Emily C. A. Goodall
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
- * E-mail: (ECAG); (IRH)
| | - Georgia L. Isom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jessica L. Rooke
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Christopher Icke
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Zihao Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Isabel Warner
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Rochelle Da Costa
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Bing Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - James Rae
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Wee Boon Tan
- Department of Chemistry, National University of Singapore, Singapore
| | - Matthias Winkle
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Antoine Delhaye
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Eva Heinz
- Departments of Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Adam F. Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Mark A. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, Australia
| | - Jeff A. Cole
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jack A. Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
- * E-mail: (ECAG); (IRH)
| |
Collapse
|
13
|
Identification of a specific surface epitope of OmpC for Escherichia coli O157:H7 with protein topology facilitated affinity mass spectrometry. Appl Microbiol Biotechnol 2021; 105:6819-6833. [PMID: 34432131 PMCID: PMC8426304 DOI: 10.1007/s00253-021-11511-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 11/03/2022]
Abstract
Abstract
The goal of this work was to identify the target protein and epitope of a previously reported Escherichia coli O157:H7 (ECO157)–specific monoclonal antibody (mAb) 2G12. mAb 2G12 has shown high specificity for the recovery and detection of ECO157. To achieve this goal, the target protein was first separated by two-dimensional gel electrophoresis (2-DE) and located by Western blot (WB). The protein spots were identified to be the outer membrane protein (Omp) C by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF–MS). After that, the target protein was purified by immunoaffinity chromatography (IAC) and subjected to in situ enzymatic cleavage of the vulnerable peptides. Eight eluted peptides of OmpC identified by liquid chromatography–tandem mass spectrometry (LC–MS/MS) were further mapped onto the homologous protein structure of E. coli OmpC (2IXX). The topology of OmpC showed that three peptides had extracellular loops. Epitope mapping with overlapping peptide library and sequence homology analysis revealed that the epitope consisted of a specific peptide, “LGVING,” and an adjacent conservative peptide, “TQTYNATRVGSLG.” Both peptides loop around the overall structure of the epitope. To test the availability of the epitope when ECO157 was grown under different osmolarity, pH, and nutrition levels, the binding efficacy of mAb 2G12 with ECO157 grown in these conditions was evaluated. Results further demonstrated the good stability of this epitope under potential stressful environmental conditions. In summary, this study revealed that mAb 2G12 targeted one specific and one conservative extracellular loop (peptide) of the OmpC present on ECO157, and the epitope was stable and accessible on ECO157 cells grown in different environment. Key points • OmpC is the target of a recently identified ECO157-specific mAb 2G12. • Eight peptides were identified from the OmpC by using LC–MS/MS. • The specificity of mAb 2G12 is mainly determined by the “LGVING” peptide. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11511-8.
Collapse
|
14
|
Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. Antioxidants (Basel) 2021; 10:antiox10060861. [PMID: 34072091 PMCID: PMC8228696 DOI: 10.3390/antiox10060861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023] Open
Abstract
The use of oxidizing agents is one of the most favorable approaches to kill bacteria in daily life. However, bacteria have been evolving to survive in the presence of different oxidizing agents. In this study, we aimed to obtain a comprehensive list of genes whose expression can make Escherichiacoli cells resistant to different oxidizing agents. For this purpose, we utilized the ASKA library and performed a genome-wide screening of ~4200 E. coli genes. Hydrogen peroxide (H2O2) and hypochlorite (HOCl) were tested as representative oxidizing agents in this study. To further validate our screening results, we used different E. coli strains as host cells to express or inactivate selected resistance genes individually. More than 100 genes obtained in this screening were not known to associate with oxidative stress responses before. Thus, this study is expected to facilitate both basic studies on oxidative stress and the development of antibacterial agents.
Collapse
|
15
|
Karthik R, Pandiselvi K, Mariyappan K, Park K, Kwak IS, Sivakamavalli J. Synthesis of Biogenic Chitosan Biopolymer-Functionalized Zinc-Doped Bi2O3 Nanoneedles and Its Bio-applications: In Vitro Antibacterial and Anticancer activity. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-020-05099-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
16
|
Monteiro R, Chafsey I, Ageorges V, Leroy S, Chambon C, Hébraud M, Livrelli V, Pizza M, Pezzicoli A, Desvaux M. The Secretome landscape of Escherichia coli O157:H7: Deciphering the cell-surface, outer membrane vesicle and extracellular subproteomes. J Proteomics 2020; 232:104025. [PMID: 33160105 DOI: 10.1016/j.jprot.2020.104025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 12/14/2022]
Abstract
Among diarrheagenic E. coli (DEC), enterohaemorrhagic E. coli (EHEC) are the most virulent anthropozoonotic agents. The ability of bacterial cells to functionally interact with their surrounding essentially relies on the secretion of different protein effectors. To experimentally determine the repertoire of extracytoproteins in E. coli O157:H7, a subproteomic analysis was performed not only considering the extracellular milieu but the cell surface and outer membrane vesicles. Following a secretome-based approach, the proteins trafficking from the interior to the exterior of the cell were depicted considering cognate protein transport systems and subcellular localisation. Label-free quantitative analysis of the proteosurfaceome, proteovesiculome and exoproteome from E. coli O157:H7 grown in three different nutrient media revealed differential protein expression profiles and allowed defining the core and variant subproteomes. Network analysis further revealed the higher abundance of some protein clusters in chemically defined medium over rich complex medium, especially related to some outer membrane proteins, ABC transport and Type III secretion systems. This first comprehensive study of the EHEC secretome unravels the profound influence of environmental conditions on the extracytoplasmic proteome, provides new insight in the physiology of E. coli O157:H7 and identifies potentially important molecular targets for the development of preventive strategies against EHEC/STEC. SIGNIFICANCE: Escherichia coli O157:H7 is responsible for severe diarrhoea especially in young children. Despite years of investigations, the global view of the extracytoplasmic proteins expressed in this microorganism was eluded. To provide the first comprehensive view of the secretome landscape of E. coli O157:H7, the exoproteome, proteosurfaceome and proteovesiculome were profiled using growth conditions most likely to induce changes in bacterial protein secretion. The profound influence of growth conditions on the extracytoplasmic proteome was unravelled and allowed identifying the core and variant subproteomes. Besides new insight in the physiology of enterohaemorrhagic E. coli, these proteins potentially constitute important molecular targets for the development of preventive strategies.
Collapse
Affiliation(s)
- Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France; GSK, Siena, Italy
| | - Ingrid Chafsey
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Christophe Chambon
- INRAE, Plate-Forme d'Exploration du Métabolisme, QuaPA, F-63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France; INRAE, Plate-Forme d'Exploration du Métabolisme, QuaPA, F-63122 Saint-Genès Champanelle, France
| | - Valérie Livrelli
- Université Clermont-Auvergne, INSERM, INRAE, M2ISH, F-63000 Clermont-ferrand, France
| | | | | | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.
| |
Collapse
|
17
|
Pankratov D, Bendixen M, Shipovskov S, Gosewinkel U, Ferapontova EE. Cellulase-Linked Immunomagnetic Microbial Assay on Electrodes: Specific and Sensitive Detection of a Single Bacterial Cell. Anal Chem 2020; 92:12451-12459. [PMID: 32799451 DOI: 10.1021/acs.analchem.0c02262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogen-associated infections represent one of the major threats to human health and require reliable methods for immediate and robust identification of pathogenic microorganisms. Here, an inexpensive cellulase-linked immunomagnetic methodology was developed for the specific and ultrasensitive analysis of bacteria at their single-cell levels within a 3 h procedure. Detection of a model bacterium, Escherichia coli, was performed in a sandwich reaction with E. coli-specific either aptamer or antibody (Ab)-modified magnetic beads (MBs) and Ab/aptamer reporter molecules linked to cellulase. The cellulase-labeled immuno-aptamer sandwich applied onto nitrocellulose-film-modified electrodes digested the film and changed its electrical conductivity. Electrode's chronocoulometric responses at 0.3 V, in the absence of any redox indicators, allowed a single E. coli cell detection and from 1 to 4 × 104 CFU mL-1 E. coli quantification. No interference/cross-reactivity from Salmonella enteritidis, Enterobacter agglomerans, Pseudomonas putida, Staphylococcus aureus, and Bacillus subtilis was observed when the assay was performed on Ab-modified MBs, and E. coli could be quantified in tap water and milk. This electrochemically label-free methodology is sufficiently fast, highly specific, and sensitive to be used in direct in-field applications. The assay can be adapted for specific detection of other bacterial strains of either the same or different species and offers new analytical tools for fast, specific, and reliable analysis of bacteria in the clinic, food, and environment.
Collapse
Affiliation(s)
- Dmitrii Pankratov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Mads Bendixen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Stepan Shipovskov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| |
Collapse
|
18
|
Han MJ. Novel Bacterial Surface Display System Based on the Escherichia coli Protein MipA. J Microbiol Biotechnol 2020; 30:1097-1103. [PMID: 32325544 PMCID: PMC9728377 DOI: 10.4014/jmb.2001.01053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/19/2020] [Indexed: 12/15/2022]
Abstract
Bacterial surface display systems have been developed for various applications in biotechnology and industry. Particularly, the discovery and design of anchoring motifs is highly important for the successful display of a target protein or peptide on the surface of bacteria. In this study, an efficient display system on Escherichia coli was developed using novel anchoring motifs designed from the E. coli mipA gene. Using the C-terminal fusion system of an industrial enzyme, Pseudomonas fluorescens lipase, six possible fusion sites, V140, V176, K179, V226, V232, and K234, which were truncated from the C-terminal end of the mipA gene (MV140, MV176, MV179, MV226, MV232, and MV234) were examined. The whole-cell lipase activities showed that MV140 was the best among the six anchoring motifs. Furthermore, the lipase activity obtained using MV140 as the anchoring motif was approximately 20-fold higher than that of the previous anchoring motifs FadL and OprF but slightly higher than that of YiaTR232. Western blotting and confocal microscopy further confirmed the localization of the fusion lipase displayed on the E. coli surface using the truncated MV140. Additionally the MV140 motif could be used for successfully displaying another industrial enzyme, α-amylase from Bacillus subtilis. These results showed that the fusion proteins using the MV140 motif had notably high enzyme activities and did not exert any adverse effects on either cell growth or outer membrane integrity. Thus, this study shows that MipA can be used as a novel anchoring motif for more efficient bacterial surface display in the biotechnological and industrial fields.
Collapse
Affiliation(s)
- Mee-Jung Han
- Department of Biomolecular and Chemical Engineering, and Department of Nursing, Dongyang University, Yeongju 36040, Republic of Korea,Corresponding author Phone: +82-54-630-1148 Fax: +82-54-630-1275 E-mail:
| |
Collapse
|
19
|
Hu R, Li J, Zhao Y, Lin H, Liang L, Wang M, Liu H, Min Y, Gao Y, Yang M. Exploiting bacterial outer membrane vesicles as a cross-protective vaccine candidate against avian pathogenic Escherichia coli (APEC). Microb Cell Fact 2020; 19:119. [PMID: 32493405 PMCID: PMC7268718 DOI: 10.1186/s12934-020-01372-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022] Open
Abstract
Background The well-known fact that avian pathogenic Escherichia coli (APEC) is harder to prevent due to its numerous serogroups has promoted the development of biological immunostimulatory materials as new vaccine candidates in poultry farms. Bacterial outer membrane vesicles (OMVs), known as spherical nanovesicles enriched with various immunostimulants, are naturally secreted by Gram-negative bacteria, and have gained much attention for developing effective vaccine candidates. Recent report has demonstrated that OMVs of APEC O78 can induce protective immunity in chickens. Here, a novel multi-serogroup OMVs (MOMVs) vaccine was developed to achieve cross-protection against APEC infection in broiler chickens. Results In this study, OMVs produced by three APEC strains were isolated, purified and prepared into MOMVs by mixing these three OMVs. By using SDS-PAGE and LC–MS/MS, 159 proteins were identified in MOMVs and the subcellular location and biological functions of 20 most abundant proteins were analyzed. The immunogenicity of MOMVs was evaluated, and the results showed that MOMVs could elicit innate immune responses, including internalization by chicken macrophage and production of immunomodulatory cytokines. Vaccination with MOMVs induced specific broad-spectrum antibodies as well as Th1 and Th17 immune responses. The animal experiment has confirmed that immunization with an appropriate dose of MOMVs could not cause any adverse effect and was able to reduce bacteria loads and pro-inflammatory cytokines production, thus providing effective cross-protection against lethal infections induced by multi-serogroup APEC strains in chickens. Further experiments indicated that, although vesicular proteins were able to induce stronger protective efficiency than lipopolysaccharide, both vesicular proteins and lipopolysaccharide are crucial in MOMVs-mediated protection. Conclusions The multi-serogroup nanovesicles produced by APEC strains will open up a new way for the development of next generation vaccines with low toxicity and broad protection in the treatment and control of APEC infection.
Collapse
Affiliation(s)
- Rujiu Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Li
- Department of Animal Engineering, Yangling Vocation and Technical College, Yangling, 712100, Shaanxi, China
| | - Yuezhen Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hua Lin
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Liu Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mimi Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haojing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuna Min
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yupeng Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Mingming Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
20
|
Su YC, Mattsson E, Singh B, Jalalvand F, Murphy TF, Riesbeck K. The Laminin Interactome: A Multifactorial Laminin-Binding Strategy by Nontypeable Haemophilus influenzae for Effective Adherence and Colonization. J Infect Dis 2020; 220:1049-1060. [PMID: 31034569 DOI: 10.1093/infdis/jiz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
Laminin is a well-defined component of the airway basement membrane (BM). Efficient binding of laminin via multiple interactions is important for nontypeable Haemophilus influenzae (NTHi) colonization in the airway mucosa. In this study, we identified elongation factor thermo-unstable (EF-Tu), l-lactate dehydrogenase (LDH), protein D (PD), and peptidoglycan-associated lipoprotein P6 as novel laminin-binding proteins (Lbps) of NTHi. In parallel with other well-studied Lbps (protein 4 [P4], protein E [PE], protein F [PF], and Haemophilus adhesion and penetration protein [Hap]), EF-Tu, LDH, PD, and P6 exhibited interactions with laminin, and mediated NTHi laminin-dependent adherence to pulmonary epithelial cell lines. More importantly, the NTHi laminin interactome consisting of the well-studied and novel Lbps recognized laminin LG domains from the subunit α chains of laminin-111 and -332, the latter isoform of which is the main laminin in the airway BM. The NTHi interactome mainly targeted multiple heparin-binding domains of laminin. In conclusion, the NTHi interactome exhibited a high plasticity of interactions with different laminin isoforms via multiple heparin-binding sites.
Collapse
Affiliation(s)
- Yu-Ching Su
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Emma Mattsson
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Birendra Singh
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Farshid Jalalvand
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Timothy F Murphy
- Clinical and Translational Research Center, University at Buffalo, the State University of New York
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| |
Collapse
|
21
|
Nguyen LP, Pinto NA, Vu TN, Lee H, Cho YL, Byun JH, D’Souza R, Yong D. In Vitro Activity of a Novel Siderophore-Cephalosporin, GT-1 and Serine-Type β-Lactamase Inhibitor, GT-055, against Escherichia coli, Klebsiella pneumoniae and Acinetobacter spp. Panel Strains. Antibiotics (Basel) 2020; 9:antibiotics9050267. [PMID: 32443875 PMCID: PMC7277296 DOI: 10.3390/antibiotics9050267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
This study investigates GT-1 (also known as LCB10-0200), a novel-siderophore cephalosporin, inhibited multidrug-resistant (MDR) Gram-negative pathogen, via a Trojan horse strategy exploiting iron-uptake systems. We investigated GT-1 activity and the role of siderophore uptake systems, and the combination of GT-1 and a non-β-lactam β-lactamase inhibitor (BLI) of diazabicyclooctane, GT-055, (also referred to as LCB18-055) against molecularly characterised resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter spp. isolates. GT-1 and GT-1/GT-055 were tested in vitro against comparators among three different characterised panel strain sets. Bacterial resistome and siderophore uptake systems were characterised to elucidate the genetic basis for GT-1 minimum inhibitory concentrations (MICs). GT-1 exhibited in vitro activity (≤2 μg/mL MICs) against many MDR isolates, including extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing E. coli and K. pneumoniae and oxacillinase (OXA)-producing Acinetobacter spp. GT-1 also inhibited strains with mutated siderophore transporters and porins. Although BLI GT-055 exhibited intrinsic activity (MIC 2-8 μg/mL) against most E. coli and K. pneumoniae isolates, GT-055 enhanced the activity of GT-1 against many GT-1-resistant strains. Compared with CAZ-AVI, GT-1/GT-055 exhibited lower MICs against E. coli and K. pneumoniae isolates. GT-1 demonstrated potent in vitro activity against clinical panel strains of E. coli, K. pneumoniae and Acinetobacter spp. GT-055 enhanced the in vitro activity of GT-1 against many GT-1-resistant strains.
Collapse
Affiliation(s)
- Le Phuong Nguyen
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul 03722, Korea
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul 03722, Korea
| | - Thao Nguyen Vu
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul 03722, Korea
| | - Hyunsook Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul 03722, Korea
| | | | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Gyeongsang National University Hospital, Jinju 52727, Korea;
| | - Roshan D’Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- J. Craig Venter Institute, Rockville, MD 20850, USA
- Correspondence: (R.D.); (D.Y.); Tel.: +1-301-795-7342 (R.D.); +82-2-2228-2442 (D.Y.); Fax: +82-2-364-1583 (D.Y.)
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul 03722, Korea; (L.P.N.); (N.A.P.); (T.N.V.); (H.L.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul 03722, Korea
- Correspondence: (R.D.); (D.Y.); Tel.: +1-301-795-7342 (R.D.); +82-2-2228-2442 (D.Y.); Fax: +82-2-364-1583 (D.Y.)
| |
Collapse
|
22
|
Hirschi S, Fotiadis D. Purification of Membrane Proteins by Affinity Chromatography with On-Column Protease Cleavage. Methods Mol Biol 2020; 2127:139-150. [PMID: 32112320 DOI: 10.1007/978-1-0716-0373-4_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A protocol is described for the isolation of recombinant polyhistidine-tagged membrane proteins from overexpressing Escherichia coli cells. The gene encoding a target membrane protein is cloned into an expression plasmid and then introduced into E. coli cells for overexpression. Membranes from bacterial cells are isolated and the tagged target membrane protein is solubilized in detergent and subsequently bound to an affinity matrix. Tagged proteins are commonly eluted by an excess of a solute that competes for the binding to the matrix. Alternatively, amino acid sequence-specific proteases can be used to cleave off the affinity purification tag directly on the purification column (i.e., on-column cleavage). This selectively releases the target protein and allows subsequent elution. Importantly, this step represents an additional purification step and can significantly increase the purity of the isolated protein.
Collapse
Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
| |
Collapse
|
23
|
Lama R, Pereiro P, Novoa B, Coll J. Sea Bass Immunization to Downsize the Betanodavirus Protein Displayed in the Surface of Inactivated Repair-Less Bacteria. Vaccines (Basel) 2019; 7:E94. [PMID: 31434322 PMCID: PMC6789578 DOI: 10.3390/vaccines7030094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/20/2023] Open
Abstract
: This work describes immunization of European sea bass (Dicentrarchus labrax) juveniles against viral nervous necrosis virus (VNNV), a betanodavirus causing worldwide mortalities in many fish species. Protection was obtained with the so-called spinycterin vehicles consisting of irreversibly DNA-damaged DNA-repair-less Escherichia coli displaying at their surface a downsized VNNV coat antigen. In this work we have i) maximized bacterial expression levels by downsizing the coat protein of VNNV to a fragment (frgC91-220) containing most of its previously determined antigenicity, ii) developed a scalable autoinduction culture media for E.coli based in soy-bean rather than in casein hydrolysates, iii) enriched surface expression by screening different anchors from several prokaryotic sources (anchor + frgC91-220 recombinant products), iv) preserved frgC91-220 antigenicity by inactivating bacteria by irreversible DNA-damage by means of Ciprofloxacin, and v) increased safety using a repair-less E.coli strain as chassis for the spinycterins. These spinycterins protected fish against VNNV challenge with partial (Nmistic + frgC91-220) or total (YBEL + frgC91-220) levels of protection, in contrast to fish immunized with frgC91-220 spinycterins. The proposed spinycterin platform has high levels of environmental safety and cost effectiveness and required no adjuvants, thus providing potential to further develop VNNV vaccines for sustainable aquaculture.
Collapse
Affiliation(s)
- Raquel Lama
- Institute of Marine Research (IIM). Spanish National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | | | - Beatriz Novoa
- Institute of Marine Research (IIM). Spanish National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Julio Coll
- National Institute for Agricultural and Food Research and Technology (INIA), Biotechnology Department, La Coruña road, 28040 Madrid, Spain.
| |
Collapse
|
24
|
Pagnout C, Sohm B, Razafitianamaharavo A, Caillet C, Offroy M, Leduc M, Gendre H, Jomini S, Beaussart A, Bauda P, Duval JFL. Pleiotropic effects of rfa-gene mutations on Escherichia coli envelope properties. Sci Rep 2019; 9:9696. [PMID: 31273247 PMCID: PMC6609704 DOI: 10.1038/s41598-019-46100-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/17/2019] [Indexed: 01/18/2023] Open
Abstract
Mutations in the rfa operon leading to severely truncated lipopolysaccharide (LPS) structures are associated with pleiotropic effects on bacterial cells, which in turn generates a complex phenotype termed deep-rough. Literature reports distinct behavior of these mutants in terms of susceptibility to bacteriophages and to several antibacterial substances. There is so far a critical lack of understanding of such peculiar structure-reactivity relationships mainly due to a paucity of thorough biophysical and biochemical characterizations of the surfaces of these mutants. In the current study, the biophysicochemical features of the envelopes of Escherichia coli deep-rough mutants are identified from the molecular to the single cell and population levels using a suite of complementary techniques, namely microelectrophoresis, Atomic Force Microscopy (AFM) and Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) for quantitative proteomics. Electrokinetic, nanomechanical and proteomic analyses evidence enhanced mutant membrane destabilization/permeability, and differentiated abundances of outer membrane proteins involved in the susceptibility phenotypes of LPS-truncated mutants towards bacteriophages, antimicrobial peptides and hydrophobic antibiotics. In particular, inner-core LPS altered mutants exhibit the most pronounced heterogeneity in the spatial distribution of their Young modulus and stiffness, which is symptomatic of deep damages on cell envelope likely to mediate phage infection process and antibiotic action.
Collapse
Affiliation(s)
- Christophe Pagnout
- Université de Lorraine, LIEC, UMR7360, Campus Bridoux, Metz, F-57070, France.
| | - Bénédicte Sohm
- Université de Lorraine, LIEC, UMR7360, Campus Bridoux, Metz, F-57070, France
| | | | - Céline Caillet
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, F-54000, France
| | - Marc Offroy
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, F-54000, France
| | - Marjorie Leduc
- Plateforme protéomique 3P5, Inserm U1016-Institut Cochin, Université Paris Descartes, MICUSPC, Paris, France
| | - Héloïse Gendre
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, F-54000, France
| | | | - Audrey Beaussart
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, F-54000, France
| | - Pascale Bauda
- Université de Lorraine, LIEC, UMR7360, Campus Bridoux, Metz, F-57070, France
| | - Jérôme F L Duval
- Université de Lorraine, LIEC, UMR7360, Vandoeuvre-lès-Nancy, F-54000, France
| |
Collapse
|
25
|
Suryaletha K, Narendrakumar L, John J, Radhakrishnan MP, George S, Thomas S. Decoding the proteomic changes involved in the biofilm formation of Enterococcus faecalis SK460 to elucidate potential biofilm determinants. BMC Microbiol 2019; 19:146. [PMID: 31253082 PMCID: PMC6599329 DOI: 10.1186/s12866-019-1527-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/20/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Enterococcus faecalis is a major clinically relevant nosocomial bacterial pathogen frequently isolated from polymicrobial infections. The biofilm forming ability of E. faecalis attributes a key role in its virulence and drug resistance. Biofilm cells are phenotypically and metabolically different from their planktonic counterparts and many aspects involved in E. faecalis biofilm formation are yet to be elucidated. The strain E. faecalis SK460 used in the present study is esp (Enterococcal surface protein) and fsr (two-component signal transduction system) negative non-gelatinase producing strong biofilm former isolated from a chronic diabetic foot ulcer patient. We executed a label-free quantitative proteomic approach to elucidate the differential protein expression pattern at planktonic and biofilm stages of SK460 to come up with potential determinants associated with Enterococcal biofilm formation. RESULTS The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of proteomic data revealed that biofilm cells expressed higher levels of proteins which are associated with glycolysis, amino acid biosynthesis, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and stress response factors. Besides these basic survival pathways, LuxS-mediated quorum sensing, arginine metabolism, rhamnose biosynthesis, pheromone and adhesion associated proteins were found to be upregulated during the biofilm transit from planktonic stages. The selected subsets were validated by quantitative real-time PCR. In silico functional interaction analysis revealed that the genes involved in upregulated pathways pose a close molecular interaction thereby coordinating the regulatory network to thrive as a biofilm community. CONCLUSIONS The present study describes the first report of the quantitative proteome analysis of an esp and fsr negative non gelatinase producing E. faecalis. Proteome analysis evidenced enhanced expression of glycolytic pathways, stress response factors, LuxS quorum signaling system, rhamnopolysaccharide synthesis and pheromone associated proteins in biofilm phenotype. We also pointed out the relevance of LuxS quorum sensing and pheromone associated proteins in the biofilm development of E. faecalis which lacks the Fsr quorum signaling system. These validated biofilm determinants can act as potential inhibiting targets in Enterococcal infections.
Collapse
Affiliation(s)
- Karthika Suryaletha
- Cholera and Biofilm Research Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, (National Institute under the Department of Biotechnology, Government of India), Trivandrum, Kerala, 695014, India
| | - Lekshmi Narendrakumar
- Cholera and Biofilm Research Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, (National Institute under the Department of Biotechnology, Government of India), Trivandrum, Kerala, 695014, India
| | - Joby John
- Department of Surgery, Government Medical College Hospital, Trivandrum, Kerala, 695011, India
| | - Megha Periyappilly Radhakrishnan
- Cholera and Biofilm Research Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, (National Institute under the Department of Biotechnology, Government of India), Trivandrum, Kerala, 695014, India
| | - Sanil George
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Sabu Thomas
- Cholera and Biofilm Research Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, (National Institute under the Department of Biotechnology, Government of India), Trivandrum, Kerala, 695014, India.
| |
Collapse
|
26
|
Influence of Mg doping on the structural, morphological, optical, thermal, and visible-light responsive antibacterial properties of ZnO nanoparticles synthesized via co-precipitation. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 98:717-725. [DOI: 10.1016/j.msec.2019.01.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 12/06/2018] [Accepted: 01/08/2019] [Indexed: 11/30/2022]
|
27
|
Slouka C, Kopp J, Spadiut O, Herwig C. Perspectives of inclusion bodies for bio-based products: curse or blessing? Appl Microbiol Biotechnol 2019; 103:1143-1153. [PMID: 30569219 PMCID: PMC6394472 DOI: 10.1007/s00253-018-9569-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022]
Abstract
The bacterium Escherichia coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant protein can be located intracellularly, which often leads to protein aggregates inside of the cytoplasm, forming so the called inclusion bodies (IBs). When compared to other protein expression strategies, inclusion body formation allows high product titers and also the possibility of expressing proteins being toxic for the host. In the past years, the comprehension of inclusion bodies being only inactive protein aggregates changed, and the new term of non-classical inclusion bodies emerged. These inclusion bodies are believed to contain a reasonable amount of active protein within their structure. However, subsequent downstream processing, such as homogenisation of cells, centrifugation or solubilisation of IBs, is prone to variable process performance and is often known to result in low extraction yields. It is hypothesised that variations in IB quality attributes are responsible for those effects and that such attributes can be controlled by upstream process conditions. In this review, we address the impact of process design (process parameters) in the upstream on defined inclusion body quality attributes. The following topics are therefore addressed: (i) an overview of the range of inclusion body applications (including emerging technologies); (ii) analytical methods to determine quality attributes; and (iii) screws in process engineering to achieve the desired quality attributes for different inclusion body-based applications. Process parameters in the upstream can be used to trigger different quality attributes including protein activity, but are not exploited to a satisfying content yet. Design by quality approaches in the upstream are already considered for a multitude of existing processes. Further intensifying this approach may pave the industrial application for new IB-based products and improves IB processing, as discussed within this review.
Collapse
Affiliation(s)
- Christoph Slouka
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria.
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße, 1a, 1060, Vienna, Austria.
| |
Collapse
|
28
|
Singhal N, Maurya AK, Virdi JS. Bacterial Whole Cell Protein Profiling: Methodology, Applications and Constraints. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666180905102253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:In the era of modern microbiology, several methods are available for identification and typing of bacteria, including whole genome sequencing. However, in microbiological laboratories or hospitals where genomic based molecular typing methods and/or trained manpower are unavailable, whole cell protein profiling using sodium dodecyl sulfate polyacrylamide gel electrophoresis might be a useful alternative/supplementary method for bacterial identification, strain typing and epidemiology. Whole cell protein profiling by SDS-PAGE is based on the principle that under standard growth conditions, a bacterial strain expresses the same set of proteins, the pattern of which can be used for bacterial identification.Objective:The objective of this review is to assess the current status of whole cell protein profiling by SDS-PAGE and its advantages and constraints for bacterial identification and typing.Results and Conclusions:Several earlier and recent studies prove the potential and utility of this technique as an adjunct or supplementary method for bacterial identification, strain typing and epidemiology. There is no denying the fact that utility of this technique as an adjunct or supplementary method for bacterial identification and typing has already been demonstrated and its practical applications need to be evaluated further.
Collapse
Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
| | - Anay Kumar Maurya
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
| | - Jugsharan Singh Virdi
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
| |
Collapse
|
29
|
Slouka C, Kopp J, Hutwimmer S, Strahammer M, Strohmer D, Eitenberger E, Schwaighofer A, Herwig C. Custom made inclusion bodies: impact of classical process parameters and physiological parameters on inclusion body quality attributes. Microb Cell Fact 2018; 17:148. [PMID: 30236107 PMCID: PMC6148765 DOI: 10.1186/s12934-018-0997-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/14/2018] [Indexed: 01/21/2023] Open
Abstract
Background The bacterium E. coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant protein can be located intracellularly. In many cases the formation of inclusion bodies (IBs), protein aggregates inside of the cytoplasm of the cell, is favored in order to achieve high productivities and to cope with toxic products. However, subsequent downstream processing, including homogenization of the cells, centrifugation or solubilization of the IBs, is prone to variable process performance or can be characterized by low extraction yields as published elsewhere. It is hypothesized that variations in IB quality attributes (QA) are responsible for those effects and that such attributes can be controlled by upstream process conditions. This contribution is aimed at analyzing how standard process parameters, such as pH and temperature (T) as well as different controlled levels of physiological parameters, such as specific substrate uptake rates, can vary IB quality attributes. Results Classical process parameters like pH and T influence the expression of analyzed IB. The effect on the three QAs titer, size and purity could be successfully revealed. The developed data driven model showed that low temperatures and low pH are favorable for the expression of the two tested industrially relevant proteins. Based on this knowledge, physiological control using specific substrate feeding rate (of glucose) qs,Glu is altered and the impact is tested for one protein. Conclusions Time dependent monitoring of IB QA—titer, purity, IB bead size—showed a dependence on classical process parameters pH and temperature. These findings are confirmed using a second industrially relevant strain. Optimized process conditions for pH and temperature were used to determine dependence on the physiological parameters, the specific substrate uptake rate (qs,Glu). Higher qs,Glu were shown to have a strong influence on the analyzed IB QAs and drastically increase the titer and purity in early time stages. We therefore present a novel approach to modulate—time dependently—quality attributes in upstream processing to enable robust downstream processing. Electronic supplementary material The online version of this article (10.1186/s12934-018-0997-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Christoph Slouka
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Michael Strahammer
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Daniel Strohmer
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Elisabeth Eitenberger
- Institute of Chemical Technology and Analytics, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Andreas Schwaighofer
- Institute of Chemical Technology and Analytics, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria. .,Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| |
Collapse
|
30
|
Xu D, Liao C, Zhang B, Tolbert WD, He W, Dai Z, Zhang W, Yuan W, Pazgier M, Liu J, Yu J, Sansonetti PJ, Bevins CL, Shao Y, Lu W. Human Enteric α-Defensin 5 Promotes Shigella Infection by Enhancing Bacterial Adhesion and Invasion. Immunity 2018; 48:1233-1244.e6. [PMID: 29858013 PMCID: PMC6051418 DOI: 10.1016/j.immuni.2018.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/18/2018] [Accepted: 04/13/2018] [Indexed: 01/07/2023]
Abstract
Shigella is a Gram-negative bacterium that causes bacillary dysentery worldwide. It invades the intestinal epithelium to elicit intense inflammation and tissue damage, yet the underlying mechanisms of its host selectivity and low infectious inoculum remain perplexing. Here, we report that Shigella co-opts human α-defensin 5 (HD5), a host defense peptide important for intestinal homeostasis and innate immunity, to enhance its adhesion to and invasion of mucosal tissues. HD5 promoted Shigella infection in vitro in a structure-dependent manner. Shigella, commonly devoid of an effective host-adhesion apparatus, preferentially targeted HD5 to augment its ability to colonize the intestinal epithelium through interactions with multiple bacterial membrane proteins. HD5 exacerbated infectivity and Shigella-induced pathology in a culture of human colorectal tissues and three animal models. Our findings illuminate how Shigella exploits innate immunity by turning HD5 into a virulence factor for infection, unveiling a mechanism of action for this highly proficient human pathogen.
Collapse
Affiliation(s)
- Dan Xu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China,Center for Translational Medicine, Frontier Institute of Science and Technology, Xi’an Jiaotong University,Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Chongbing Liao
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China,Center for Translational Medicine, Frontier Institute of Science and Technology, Xi’an Jiaotong University
| | - Bing Zhang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - W. David Tolbert
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Wangxiao He
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China,Center for Translational Medicine, Frontier Institute of Science and Technology, Xi’an Jiaotong University,Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Zhijun Dai
- The Second Affiliated Hospital, Xi’an Jiaotong University School of Medicine
| | - Wei Zhang
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Weirong Yuan
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marzena Pazgier
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jiankang Liu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jun Yu
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | | | - Charles L. Bevins
- Department of Microbiology and Immunology, University of California, School of Medicine, Davis, California, USA
| | - Yongping Shao
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China,Center for Translational Medicine, Frontier Institute of Science and Technology, Xi’an Jiaotong University,Correspondence to: (lead contact) or
| | - Wuyuan Lu
- Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China,Center for Translational Medicine, Frontier Institute of Science and Technology, Xi’an Jiaotong University,Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA,Correspondence to: (lead contact) or
| |
Collapse
|
31
|
Uppuluri P, Lin L, Alqarihi A, Luo G, Youssef EG, Alkhazraji S, Yount NY, Ibrahim BA, Bolaris MA, Edwards JE, Swidergall M, Filler SG, Yeaman MR, Ibrahim AS. The Hyr1 protein from the fungus Candida albicans is a cross kingdom immunotherapeutic target for Acinetobacter bacterial infection. PLoS Pathog 2018; 14:e1007056. [PMID: 29746596 PMCID: PMC5963808 DOI: 10.1371/journal.ppat.1007056] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/22/2018] [Accepted: 04/26/2018] [Indexed: 11/21/2022] Open
Abstract
Different pathogens share similar medical settings and rely on similar virulence strategies to cause infections. We have previously applied 3-D computational modeling and bioinformatics to discover novel antigens that target more than one human pathogen. Active and passive immunization with the recombinant N-terminus of Candida albicans Hyr1 (rHyr1p-N) protect mice against lethal candidemia. Here we determine that Hyr1p shares homology with cell surface proteins of the multidrug resistant Gram negative bacterium, Acinetobacter baumannii including hemagglutinin (FhaB) and outer membrane protein A (OmpA). The A. baumannii OmpA binds to C. albicans Hyr1p, leading to a mixed species biofilm. Deletion of HYR1, or blocking of Hyr1p using polyclonal antibodies, significantly reduce A. baumannii binding to C. albicans hyphae. Furthermore, active vaccination with rHyr1p-N or passive immunization with polyclonal antibodies raised against specific peptide motifs of rHyr1p-N markedly improve survival of diabetic or neutropenic mice infected with A. baumannii bacteremia or pneumonia. Antibody raised against one particular peptide of the rHyr1p-N sequence (peptide 5) confers majority of the protection through blocking A. baumannii invasion of host cells and inducing death of the bacterium by a putative iron starvation mechanism. Anti-Hyr1 peptide 5 antibodies also mitigate A. baumannii /C. albicans mixed biofilm formation in vitro. Consistent with our bioinformatic analysis and structural modeling of Hyr1p, anti-Hyr1p peptide 5 antibodies bound to A. baumannii FhaB, OmpA, and an outer membrane siderophore binding protein. Our studies highlight the concept of cross-kingdom vaccine protection against high priority human pathogens such as A. baumannii and C. albicans that share similar ecological niches in immunocompromised patients.
Collapse
Affiliation(s)
- Priya Uppuluri
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Lin Lin
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Abdullah Alqarihi
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - Guanpingsheng Luo
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - Eman G. Youssef
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt
| | - Sondus Alkhazraji
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - Nannette Y. Yount
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - Belal A. Ibrahim
- Portola High School, Irvine, California, United States of America
| | - Michael Anthony Bolaris
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - John E. Edwards
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Marc Swidergall
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
| | - Scott G. Filler
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Michael R. Yeaman
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Ashraf S. Ibrahim
- Department of Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles (UCLA) Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| |
Collapse
|
32
|
Kleiner-Grote GRM, Risse JM, Friehs K. Secretion of recombinant proteins from E. coli. Eng Life Sci 2018; 18:532-550. [PMID: 32624934 DOI: 10.1002/elsc.201700200] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 11/10/2022] Open
Abstract
The microorganism Escherichia coli is commonly used for recombinant protein production. Despite several advantageous characteristics like fast growth and high protein yields, its inability to easily secrete recombinant proteins into the extracellular medium remains a drawback for industrial production processes. To overcome this limitation, a multitude of approaches to enhance the extracellular yield and the secretion efficiency of recombinant proteins have been developed in recent years. Here, a comprehensive overview of secretion mechanisms for recombinant proteins from E. coli is given and divided into three main sections. First, the structure of the E. coli cell envelope and the known natural secretion systems are described. Second, the use and optimization of different one- or two-step secretion systems for recombinant protein production, as well as further permeabilization methods are discussed. Finally, the often-overlooked role of cell lysis in secretion studies and its analysis are addressed. So far, effective approaches for increasing the extracellular protein concentration to more than 10 g/L and almost 100% secretion efficiency exist, however, the large range of optimization methods and their combinations suggests that the potential for secretory protein production from E. coli has not yet been fully realized.
Collapse
Affiliation(s)
| | - Joe M Risse
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Karl Friehs
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| |
Collapse
|
33
|
Duong DA, Jensen RV, Stevens AM. Discovery of Pantoea stewartii ssp. stewartii genes important for survival in corn xylem through a Tn-Seq analysis. MOLECULAR PLANT PATHOLOGY 2018; 19:1929-1941. [PMID: 29480976 PMCID: PMC6638119 DOI: 10.1111/mpp.12669] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 05/29/2023]
Abstract
The bacterium Pantoea stewartii ssp. stewartii causes Stewart's wilt disease in corn. Pantoea stewartii is transmitted to plants via corn flea beetles, where it first colonizes the apoplast causing water-soaked lesions, and then migrates to the xylem and forms a biofilm that blocks water transport. Bacterial quorum sensing ensures that the exopolysaccharide production necessary for biofilm formation occurs only at high cell density. A genomic-level transposon sequencing (Tn-Seq) analysis was performed to identify additional bacterial genes essential for survival in planta and to provide insights into the plant-microbe interactions occurring during wilt disease. A mariner transposon library of approximately 40 000 mutants was constructed and used to inoculate corn seedlings through a xylem infection model. Cultures of the library grown in Luria-Bertani (LB) broth served as the in vitro pre-inoculation control. Tn-Seq analysis showed that the number of transposon mutations was reduced by more than 10-fold for 486 genes in planta compared with the library that grew in LB, suggesting that they are important for xylem survival. Interestingly, a small set of genes had a higher abundance of mutants in planta versus in vitro conditions, indicating enhanced strain fitness with loss of these genes inside the host. In planta competition assays retested the trends of the Tn-Seq data for several genes, including two outer membrane proteins, Lon protease and two quorum sensing-associated transcription factors, RcsA and LrhA. Virulence assays were performed to check for correlation between growth/colonization and pathogenicity. This study demonstrates the capacity of a Tn-Seq approach to advance our understanding of P. stewartii-corn interactions.
Collapse
Affiliation(s)
- Duy An Duong
- Department of Biological SciencesVirginia TechBlacksburgVA 24061USA
| | | | - Ann M. Stevens
- Department of Biological SciencesVirginia TechBlacksburgVA 24061USA
| |
Collapse
|
34
|
Fu X, Zhang J, Li T, Zhang M, Li J, Kan B. The Outer Membrane Protein OmpW Enhanced V. cholerae Growth in Hypersaline Conditions by Transporting Carnitine. Front Microbiol 2018; 8:2703. [PMID: 29403450 PMCID: PMC5786537 DOI: 10.3389/fmicb.2017.02703] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/29/2017] [Indexed: 11/13/2022] Open
Abstract
Pathogenic marine bacteria are found in environments and food sources with high salt concentrations, which the bacteria must effectively manage for their survival. Several mechanisms, such as the transport of ions and compatible solutes as well as changes in aerobic and anaerobic respiration, confer salt tolerance to bacteria. In this study, we found that the outer membrane protein OmpW was related to salt stress in Vibrio cholerae and that ompW gene transcription and expression were up-regulated in cultures containing high NaCl concentrations. Deletion of ompW resulted in reduced V. cholerae growth in hypersaline culture conditions. Supplements of the compatible solutes betaine, L-carnitine, or L-lysine enhanced the growth of V. cholerae in hypersaline media. Supplements of betaine or L-lysine had the same growth enhancement effect on the ompW-deletion mutant cultured in hypersaline media, whereas L-carnitine supplementation did not restore mutant growth. In addition, the uptake of L-carnitine was decreased in the ompW-deletion mutant. Our study showed that among the multiplex factors that enhance the hypersaline tolerance of V. cholerae, OmpW also plays a role by transporting L-carnitine.
Collapse
Affiliation(s)
- Xiuping Fu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tianyi Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mei Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| |
Collapse
|
35
|
Effect of isoquercitrin on membrane dynamics and apoptosis-like death in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:357-363. [PMID: 29155212 DOI: 10.1016/j.bbamem.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022]
Abstract
Minimum inhibitory concentration (MIC) is defined as the lowest concentration of a compound that completely inhibits microbial growth. Antibacterial mechanisms of compounds have been investigated at their sub-MICs as well as at their MIC. In this study, the effects of sub-MIC and MIC of isoquercitrin on Escherichia coli were investigated. The antibacterial effect of isoquercitrin was tested using the microdilution method. Sub-MICs of isoquercitrin induced the production of reactive oxygen species and depletion of glutathione. The oxidative effects induced by sub-MICs of isoquercitrin could be prolonged, finally resulting in apoptosis-like death. DNA fragmentation and phosphatidylserine externalization, which are regarded as the hallmarks of apoptosis, were evaluated using the TUNEL assay and Annexin V staining, respectively. Furthermore, isoquercitrin induced the peroxidation of membrane lipids and inner membrane permeabilization at both its sub-MIC and MIC. This suggested membrane damage in response to lipid oxidation. The uptake of membrane impermeable dyes, propidium iodide and calcein, demonstrated that isoquercitrin damaged the cell membrane at concentrations higher than its MIC. Thus, isoquercitrin induced apoptosis-like death and dysregulation of cell membrane dynamics.
Collapse
|
36
|
Dong X, Awak MA, Tomlinson N, Tang Y, Sun YP, Yang L. Antibacterial effects of carbon dots in combination with other antimicrobial reagents. PLoS One 2017; 12:e0185324. [PMID: 28934346 PMCID: PMC5608398 DOI: 10.1371/journal.pone.0185324] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022] Open
Abstract
This study was designed to investigate the antimicrobial effects of CDots in combination with other antimicrobial reagents, including H2O2, Na2CO3, and AcOH (acetic acid). CDots were synthesized and passivated with 2,2'-(ethylenedioxy)bis(ethylamine) (EDA). The minimal inhibitory concentration (MIC) of CDots was 64 μg/mL on both Gram negative bacteria E.coli cells and Gram positive bacteria Bacillus subtilis cells. When CDots were combined with H2O2, antibacterial synergistic effects were observed based on the fractional inhibitory concentration (FIC) index, and further confirmed by an isobologram analysis and viable cell number counting methods. With the combination treatment of 10 μg/mL CDots with 8.82 mM H2O2, the viable E.coli cell numbers decreased 2.46 log, which was significant lower than the log reduction from 8.82 mM H2O2 (1.57 log) or 10 μg/mL CDots (0.14 log) treatment alone. However, the combination of CDots with Na2CO3 or AcOH did not show synergistic effects, instead, exhibiting indifference effects according to the FIC index. This study indicated that the combination of CDots with their synergistic antimicrobial reagents, such as H2O2, could reach the goal of inhibiting bacteria growth by using lower concentration of each individual chemical in the combination than using one chemical treatment alone, reduce the risks imposed on environmental health and the possibilities of the development of microbial resistances.
Collapse
Affiliation(s)
- Xiuli Dong
- Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, North Carolina, United States of America
| | - Mohamad Al Awak
- Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, North Carolina, United States of America
| | - Nicholas Tomlinson
- Department of Chemistry and Laboratory for Emerging Materials and Technology, Clemson University, Clemson, South Carolina, United States of America
| | - Yongan Tang
- Department of Mathematics and Physics, North Carolina Central University, Durham, North Carolina, United States of America
| | - Ya-Ping Sun
- Department of Chemistry and Laboratory for Emerging Materials and Technology, Clemson University, Clemson, South Carolina, United States of America
| | - Liju Yang
- Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, North Carolina, United States of America
| |
Collapse
|
37
|
Hsu PC, Bruininks BMH, Jefferies D, Cesar Telles de Souza P, Lee J, Patel DS, Marrink SJ, Qi Y, Khalid S, Im W. CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J Comput Chem 2017; 38:2354-2363. [PMID: 28776689 DOI: 10.1002/jcc.24895] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/03/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022]
Abstract
A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Pin-Chia Hsu
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Damien Jefferies
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Paulo Cesar Telles de Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Jumin Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Yifei Qi
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| |
Collapse
|
38
|
Chourabi K, Campoy S, Rodriguez JA, Kloula S, Landoulsi A, Chatti A. UV-C Adaptation of Shigella: Morphological, Outer Membrane Proteins, Secreted Proteins, and Lipopolysaccharides Effects. Curr Microbiol 2017; 74:1261-1269. [PMID: 28744569 DOI: 10.1007/s00284-017-1311-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/14/2017] [Indexed: 11/29/2022]
Abstract
Water UV disinfection remains extremely important, particularly in developing countries where drinking and reclaimed crop irrigation water may spread devastating infectious diseases. Enteric bacterial pathogens, among which Shigella, are possible contaminants of drinking and bathing water and foods. To study the effect of UV light on Shigella, four strains were exposed to different doses in a laboratory-made irradiation device, given that the ultraviolet radiation degree of inactivation is directly related to the UV dose applied to water. Our results showed that the UV-C rays are effective against all the tested Shigella strains. However, UV-C doses appeared as determinant factors for Shigella eradication. On the other hand, Shigella-survived strains changed their outer membrane protein profiles, secreted proteins, and lipopolysaccharides. Also, as shown by electron microscopy transmission, morphological alterations were manifested by an internal cytoplasm disorganized and membrane envelope breaks. Taken together, the focus of interest of our study is to know the adaptive mechanism of UV-C resistance of Shigella strains.
Collapse
Affiliation(s)
- Kalthoum Chourabi
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technology Centre, Technopole of Borj-Cédria, BP 273, Soliman, 8020, Tunisia.
| | - Susana Campoy
- Department of Genetics and Microbiology, Autonomous University of Barcelona, 08290, Barcelona, Spain
| | - Jesus A Rodriguez
- Department of Genetics and Microbiology, Autonomous University of Barcelona, 08290, Barcelona, Spain
| | - Salma Kloula
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technology Centre, Technopole of Borj-Cédria, BP 273, Soliman, 8020, Tunisia
| | - Ahmed Landoulsi
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, 7021, Tunisia
| | - Abdelwaheb Chatti
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technology Centre, Technopole of Borj-Cédria, BP 273, Soliman, 8020, Tunisia
| |
Collapse
|
39
|
Identification of membrane proteome of Paracoccidioides lutzii and its regulation by zinc. Future Sci OA 2017; 3:FSO232. [PMID: 29134119 PMCID: PMC5676091 DOI: 10.4155/fsoa-2017-0044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/21/2017] [Indexed: 01/09/2023] Open
Abstract
Aim: During infection development in the host, Paracoccidioides spp. faces the deprivation of micronutrients, a mechanism called nutritional immunity. This condition induces the remodeling of proteins present in different metabolic pathways. Therefore, we attempted to identify membrane proteins and their regulation by zinc in Paracoccidioides lutzii. Materials & methods: Membranes enriched fraction of yeast cells of P. lutzii were isolated, purified and identified by 2D LC–MS/MS detection and database search. Results & conclusion: Zinc deprivation suppressed the expression of membrane proteins such as glycoproteins, those involved in cell wall synthesis and those related to oxidative phosphorylation. This is the first study describing membrane proteins and the effect of zinc deficiency in their regulation in one member of the genus Paracoccidioides. The methodology of protein identification allows the characterization of biological processes performed by those molecules. Therefore, we performed a membrane proteomic analysis of Paracoccidioides lutzii and further evaluated the responses of the fungus to zinc deprivation. The results obtained in the work allowed the characterization of membrane proteins present in organelles that are related to different cellular functions. Zinc deprivation changes processes related to cellular physiology and metabolism. These results help us to understand the process of pathogen–host interaction, since zinc deprivation is a condition present during infection.
Collapse
|
40
|
Meropenem selection induced overproduction of the intrinsic carbapenemase as well as phenotype divergence in Acinetobacter baumannii. Int J Antimicrob Agents 2017; 50:419-426. [PMID: 28669829 DOI: 10.1016/j.ijantimicag.2017.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 01/24/2023]
Abstract
Acinetobacter baumannii 37662 is a carbapenem-susceptible isolate with blaOXA-51-like as the sole carbapenemase gene. Following selection with meropenem (MEM) at a subinhibitory concentration, two morphologically different mutants, designated 37662RM1 and 37662RM2, were obtained and characterised. Compared with the parent strain, resistant mutant 37662RM1 grew at a slower rate and had impaired capsule synthesis, whereas 37662RM2 grew fast and abolished capsule synthesis. In addition, the latter resistant mutant also lost pathogenicity but showed significantly enhanced biofilm formation. Transposition of the insertion sequence ISAba1 and formation of ISAba1-blaOXA-51-like was responsible for the upregulated expression of blaOXA-51-like. The blaOXA-51-like gene of A. baumannii 37662 is a close variant of blaOXA-138 and has been designated blaOXA-508. Overproduction of OXA-508 conferred major carbapenem resistance to these two mutants. Overall, these results indicate that a subinhibitory concentration of MEM can induce phenotype divergence together with carbapenem resistance in A. baumannii.
Collapse
|
41
|
Dugovich BS, Peel MJ, Palmer AL, Zielke RA, Sikora AE, Beechler BR, Jolles AE, Epps CW, Dolan BP. Detection of bacterial-reactive natural IgM antibodies in desert bighorn sheep populations. PLoS One 2017; 12:e0180415. [PMID: 28662203 PMCID: PMC5491220 DOI: 10.1371/journal.pone.0180415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/29/2017] [Indexed: 12/25/2022] Open
Abstract
Ecoimmunology is a burgeoning field of ecology which studies immune responses in wildlife by utilizing general immune assays such as the detection of natural antibody. Unlike adaptive antibodies, natural antibodies are important in innate immune responses and often recognized conserved epitopes present in pathogens. Here, we describe a procedure for measuring natural antibodies reactive to bacterial antigens that may be applicable to a variety of organisms. IgM from desert bighorn sheep plasma samples was tested for reactivity to outer membrane proteins from Vibrio coralliilyticus, a marine bacterium to which sheep would have not been exposed. Immunoblotting demonstrated bighorn sheep IgM could bind to a variety of bacterial cell envelope proteins while ELISA analysis allowed for rapid determination of natural antibody levels in hundreds of individual animals. Natural antibody levels were correlated with the ability of plasma to kill laboratory strains of E. coli bacteria. Finally, we demonstrate that natural antibody levels varied in two distinct populations of desert bighorn sheep. These data demonstrate a novel and specific measure of natural antibody function and show that this varies in ecologically relevant ways.
Collapse
Affiliation(s)
- Brian S. Dugovich
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Melanie J. Peel
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Amy L. Palmer
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Brianna R. Beechler
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Anna E. Jolles
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Clinton W. Epps
- Department of Fisheries and Wildlife, College of Agricultural Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Brian P. Dolan
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
42
|
Maffei B, Francetic O, Subtil A. Tracking Proteins Secreted by Bacteria: What's in the Toolbox? Front Cell Infect Microbiol 2017; 7:221. [PMID: 28620586 PMCID: PMC5449463 DOI: 10.3389/fcimb.2017.00221] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/15/2017] [Indexed: 01/14/2023] Open
Abstract
Bacteria have acquired multiple systems to expose proteins on their surface, release them in the extracellular environment or even inject them into a neighboring cell. Protein secretion has a high adaptive value and secreted proteins are implicated in many functions, which are often essential for bacterial fitness. Several secreted proteins or secretion machineries have been extensively studied as potential drug targets. It is therefore important to identify the secretion substrates, to understand how they are specifically recognized by the secretion machineries, and how transport through these machineries occurs. The purpose of this review is to provide an overview of the biochemical, genetic and imaging tools that have been developed to evaluate protein secretion in a qualitative or quantitative manner. After a brief overview of the different tools available, we will illustrate their advantages and limitations through a discussion of some of the current open questions related to protein secretion. We will start with the question of the identification of secreted proteins, which for many bacteria remains a critical initial step toward a better understanding of their interactions with the environment. We will then illustrate our toolbox by reporting how these tools have been applied to better understand how substrates are recognized by their cognate machinery, and how secretion proceeds. Finally, we will highlight recent approaches that aim at investigating secretion in real time, and in complex environments such as a tissue or an organism.
Collapse
Affiliation(s)
- Benoit Maffei
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut PasteurParis, France.,Centre National de la Recherche Scientifique UMR3691Paris, France
| | - Olivera Francetic
- Unité de Biochimie des Interactions Macromoléculaires, Institut PasteurParis, France.,Centre National de la Recherche Scientifique ERL6002Paris, France
| | - Agathe Subtil
- Unité de Biologie Cellulaire de l'Infection Microbienne, Institut PasteurParis, France.,Centre National de la Recherche Scientifique UMR3691Paris, France
| |
Collapse
|
43
|
Chen Q, Rozovsky S, Chen W. Engineering multi-functional bacterial outer membrane vesicles as modular nanodevices for biosensing and bioimaging. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc04246a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report here a one-pot synthesis approach to engineer multi-functionalized OMV-based sensors for both antigen binding and signal generation. A virtually unlimited combination of capturing and reporting moieties can be created for a wide range of biosensing and bioimaging applications.
Collapse
Affiliation(s)
- Qi Chen
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark
- USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
| |
Collapse
|
44
|
Yun SH, Lee SY, Choi CW, Lee H, Ro HJ, Jun S, Kwon YM, Kwon KK, Kim SJ, Kim GH, Kim SI. Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1. J Microbiol 2016; 55:56-62. [PMID: 28035602 DOI: 10.1007/s12275-017-6581-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25-70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.
Collapse
Affiliation(s)
- Sung Ho Yun
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Sang-Yeop Lee
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Chi-Won Choi
- Tunneling Nanotube Research Center, Division of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hayoung Lee
- Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun-Joo Ro
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Sangmi Jun
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Yong Min Kwon
- National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sang-Jin Kim
- Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea.,National Marine Biodiversity Institute of Korea, Seocheon, 33662, Republic of Korea
| | - Gun-Hwa Kim
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea
| | - Seung Il Kim
- Drug and Disease Target Team, Korea Basic Science Institute, Daejeon, 34133, Republic of Korea. .,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| |
Collapse
|
45
|
Khalilpour A, Kilic T, Khalilpour S, Álvarez MM, Yazdi IK. Proteomic-based biomarker discovery for development of next generation diagnostics. Appl Microbiol Biotechnol 2016; 101:475-491. [PMID: 28013407 DOI: 10.1007/s00253-016-8029-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/09/2023]
Abstract
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers. This review covers a selection of widely used proteomic technologies for biomarker discovery. In addition, we describe the most commonly used approaches for diagnosis based on proteomic biomarkers and further discuss trends and critical challenges during development of cost-effective rapid diagnostic tests and microfluidic diagnostic systems based on proteomic biomarkers.
Collapse
Affiliation(s)
- Akbar Khalilpour
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA. .,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Tugba Kilic
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620, Izmir, Turkey.,Department of Biotechnology, Institute of Science, Ege University, 35100, Izmir, Turkey
| | - Saba Khalilpour
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Mario Moisés Álvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Iman K Yazdi
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02139, USA
| |
Collapse
|
46
|
Bayraç C, Öktem HA. Evaluation of Staphylococcus aureus DNA aptamer by enzyme-linked aptamer assay and isothermal titration calorimetry. J Mol Recognit 2016; 30. [PMID: 27696554 DOI: 10.1002/jmr.2583] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/06/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
To monitor the specificity of Staphylococcus aureus aptamer (SA-31) against its target cell, we used enzyme-linked aptamer assay. In the presence of target cell, horseradish peroxidase-conjugated streptavidin bound to biotin-labeled SA-31 showed specific binding to S aureus among 3 different bacteria with limit of detection of 103 colony-forming unit per milliliter. The apparent Ka was 1.39 μM-1 ± 0.3 μM-1 . The binding of SA-31 to membrane proteins extracted from cell surface was characterized using isothermal titration calorimetry, and the effect of changes in binding temperature and salt concentrations of binding buffer was evaluated based on thermodynamic parameters (Ka , ΔH, and ΔG). Since binding of aptamer to its targets solely depends on its 3-dimensional structure under experimental conditions used in selection process, the change in temperature and ion concentration changed the affinity of SA-31 to its target on surface of bacteria. At 4°C, SA-31 did not show an affinity to its target with poor heat change upon injection of membrane fraction to aptamer solution. However, the apparent association constants of SA-31 slightly varied from Ka = 1.56 μM-1 ± 0.69 μM-1 at 25°C to Ka = 1.03 μM-1 ± 0.9 μM-1 at 37°C. At spontaneously occurring exothermic binding reactions, affinities of S aureus aptamer to its target were also 9.44 μM-1 ± 0.38 μM-1 at 50mM, 1.60 μM-1 ± 0.11 μM-1 at 137mM, and 3.28 μM-1 ± 0.46 μM-1 at 200 mM of salt concentration. In this study, it was demonstrated that enzyme-linked aptamer assay and isothermal titration calorimetry were useful tools for studying the fundamental binding mechanism between a DNA aptamer and its target on the outer surface of S aureus.
Collapse
Affiliation(s)
- Ceren Bayraç
- Bioengineering Department, Karamanoğlu Mehmetbey University, Yunus Emre Campus, Karaman, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Hüseyin Avni Öktem
- Konya Food & Agriculture University, Dedekorkut Mah. Beyşehir Cad. No. 9, Konya, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| |
Collapse
|
47
|
Parada C, Orruño M, Kaberdin V, Bravo Z, Barcina I, Arana I. Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater. MICROBIAL ECOLOGY 2016; 72:549-558. [PMID: 27324654 DOI: 10.1007/s00248-016-0802-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.
Collapse
Affiliation(s)
- Claudia Parada
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Maite Orruño
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Vladimir Kaberdin
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
- Department of Immunology, Microbiology and Parasitology, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Zaloa Bravo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Barcina
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Inés Arana
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain.
| |
Collapse
|
48
|
Dehghani B, Mottamedifar M, Khoshkharam-Roodmajani H, Hassanzadeh A, Zomorrodian K, Rahimi A. SDS-PAGE Analysis of the Outer Membrane Proteins of Uropathogenic Escherichia coli Isolated from Patients in Different Wards of Nemazee Hospital, Shiraz, Iran. IRANIAN JOURNAL OF MEDICAL SCIENCES 2016; 41:399-405. [PMID: 27582589 PMCID: PMC4967484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Outer membrane proteins (OMPs) constitute the main structure and about half of the cell wall of Gram-negative bacteria. The OMPs of Escherichia coli (E. coli) play an important role in its drug resistance. Previous studies have shown that the OMPs of E. coli enhance its pathogenic effects by helping the bacterium to evade the immune defense and promote its adsorption to host cells. We sought to compare E. coli isolates collected from different hospital wards and to perform a primary investigation of the association between the serotypes and profiles of their OMPs. We also aimed to detect the diversity of the E. coli isolates from the hospitalized patients. METHODS A total of 115 isolates of E. coli were collected from patients hospitalized in Nemazee Hospital, Shiraz, Iran. After biochemical and serological tests, OMPs were extracted by using glass beads and N-Lauroylsarcosine sodium. OMP typing was done by 10% SDS-PAGE and Coomassie brilliant blue staining. In terms of the number of protein bands, OMP-I was detected with 2 bands, OMP-α with 3 bands, and OMP-β with1 band. RESULTS Of the 115 isolates, 103 were OMP-I and 12 were OMP-α; none of the isolates belonged to OMP-β. Our statistical analyses showed a relationship between OMP patterns and other factors, including hospital wards and source of samples. Serotyping showed that the majority of the isolates were O128. CONCLUSION Our results demonstrated some similarities between the OMP band patterns of the analyzed groups of E. coli. Of all the OMPs in the isolates from the hospitalized and outpatient department patients, OmpA and OmpC were the most prevalent proteins in the outer membrane of the studied uropathogenic E. coli.
Collapse
Affiliation(s)
- Behzad Dehghani
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Mottamedifar
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran,Shiraz HIV/AIDS Research Center Shiraz University of Medical Sciences, Shiraz, Iran,Correspondence: Mohammad Motamedifar, PhD; Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Zip Code: 71348-45794, Shiraz, Iran Tel/Fax: +98 71 32304356 .
| | | | - Amir Hassanzadeh
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamyar Zomorrodian
- Basic Sciences in Infectious Disease Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Rahimi
- Department of Molecular Medicine, School of Advanced Medical Science and Technology, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
49
|
Secretome, surfome and immunome: emerging approaches for the discovery of new vaccine candidates against bacterial infections. World J Microbiol Biotechnol 2016; 32:155. [DOI: 10.1007/s11274-016-2107-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
|
50
|
Ottman N, Huuskonen L, Reunanen J, Boeren S, Klievink J, Smidt H, Belzer C, de Vos WM. Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. Front Microbiol 2016; 7:1157. [PMID: 27507967 PMCID: PMC4960237 DOI: 10.3389/fmicb.2016.01157] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/12/2016] [Indexed: 12/26/2022] Open
Abstract
Akkermansia muciniphila is a common member of the human gut microbiota and belongs to the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. Decreased levels of A. muciniphila have been associated with many diseases, and thus it is considered to be a beneficial resident of the intestinal mucus layer. Surface-exposed molecules produced by this organism likely play important roles in colonization and communication with other microbes and the host, but the protein composition of the outer membrane (OM) has not been characterized thus far. Herein we set out to identify and characterize A. muciniphila proteins using an integrated approach of proteomics and computational analysis. Sarkosyl extraction and sucrose density-gradient centrifugation methods were used to enrich and fractionate the OM proteome of A. muciniphila. Proteins from these fractions were identified by LC-MS/MS and candidates for OM proteins derived from the experimental approach were subjected to computational screening to verify their location in the cell. In total we identified 79 putative OM and membrane-associated extracellular proteins, and 23 of those were found to differ in abundance between cells of A. muciniphila grown on the natural substrate, mucin, and those grown on the non-mucus sugar, glucose. The identified OM proteins included highly abundant proteins involved in secretion and transport, as well as proteins predicted to take part in formation of the pili-like structures observed in A. muciniphila. The most abundant OM protein was a 95-kD protein, termed PilQ, annotated as a type IV pili secretin and predicted to be involved in the production of pili in A. muciniphila. To verify its location we purified the His-Tag labeled N-terminal domain of PilQ and generated rabbit polyclonal antibodies. Immunoelectron microscopy of thin sections immunolabeled with these antibodies demonstrated the OM localization of PilQ, testifying for its predicted function as a type IV pili secretin in A. muciniphila. As pili structures are known to be involved in the modulation of host immune responses, this provides support for the involvement of OM proteins in the host interaction of A. muciniphila. In conclusion, the characterization of A. muciniphila OM proteome provides valuable information that can be used for further functional and immunological studies.
Collapse
Affiliation(s)
- Noora Ottman
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Metapopulation Research Centre, University of HelsinkiHelsinki, Finland
| | - Laura Huuskonen
- Department of Veterinary Biosciences, University of Helsinki Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of HelsinkiHelsinki, Finland
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | - Judith Klievink
- Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of Helsinki Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of HelsinkiHelsinki, Finland
| |
Collapse
|