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Quan K, Qin Y, Chen K, Liu M, Zhang X, Liu P, van der Mei HC, Busscher HJ, Zhang Z. Lethal puncturing of planktonic Gram-positive and Gram-negative bacteria by magnetically-rotated silica hexapods. J Colloid Interface Sci 2024; 664:275-283. [PMID: 38471190 DOI: 10.1016/j.jcis.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/30/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Planktonic bacterial presence in many industrial and environmental applications and personal health-care products is generally countered using antimicrobials. However, antimicrobial chemicals present an environmental threat, while emerging resistance reduces their efficacy. Suspended bacteria have no defense against mechanical attack. Therefore, we synthesized silica hexapods on an α-Fe2O3 core that can be magnetically-rotated to inflict lethal cell-wall-damage to planktonic Gram-negative and Gram-positive bacteria. Hexapods possessed 600 nm long nano-spikes, composed of SiO2, as shown by FTIR and XPS. Fluorescence staining revealed cell wall damage caused by rotating hexapods. This damage was accompanied by DNA/protein release and bacterial death that increased with increasing rotational frequency up to 500 rpm. Lethal puncturing was more extensive on Gram-negative bacteria than on Gram-positive bacteria, which have a thicker peptidoglycan layer with a higher Young's modulus. Simulations confirmed that cell-wall-puncturing occurs at lower nano-spike penetration levels in the cell walls of Gram-negative bacteria. This approach offers a new way to kill bacteria in suspension, not based on antimicrobial chemicals.
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Affiliation(s)
- Kecheng Quan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China; School of Materials Science and Engineering, Peking University, Beijing 100871, PR China
| | - Yu Qin
- School of Materials Science and Engineering, Peking University, Beijing 100871, PR China
| | - Kai Chen
- School of Materials Science and Engineering, Peking University, Beijing 100871, PR China
| | - Miaomiao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China
| | - Xiaoliang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China
| | - Peng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China
| | - Henny C van der Mei
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, 9713 AV Groningen, The Netherlands
| | - Henk J Busscher
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, 9713 AV Groningen, The Netherlands.
| | - Zexin Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China.
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2
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Lu F, Xia K, Su J, Yi J, Luo Z, Xu J, Gu Q, Chen B, Zhou H. Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria. Eur J Med Chem 2024; 268:116303. [PMID: 38458107 DOI: 10.1016/j.ejmech.2024.116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/27/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 μM (no ATP) to 0.45 μM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.
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Affiliation(s)
- Feihu Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Kaijiang Xia
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jingtian Su
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia Yi
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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3
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Foss S, Sakya SA, Aguinagalde L, Lustig M, Shaughnessy J, Cruz AR, Scheepmaker L, Mathiesen L, Ruso-Julve F, Anthi AK, Gjølberg TT, Mester S, Bern M, Evers M, Bratlie DB, Michaelsen TE, Schlothauer T, Sok D, Bhattacharya J, Leusen J, Valerius T, Ram S, Rooijakkers SHM, Sandlie I, Andersen JT. Human IgG Fc-engineering for enhanced plasma half-life, mucosal distribution and killing of cancer cells and bacteria. Nat Commun 2024; 15:2007. [PMID: 38453922 PMCID: PMC10920689 DOI: 10.1038/s41467-024-46321-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Monoclonal IgG antibodies constitute the fastest growing class of therapeutics. Thus, there is an intense interest to design more potent antibody formats, where long plasma half-life is a commercially competitive differentiator affecting dosing, frequency of administration and thereby potentially patient compliance. Here, we report on an Fc-engineered variant with three amino acid substitutions Q311R/M428E/N434W (REW), that enhances plasma half-life and mucosal distribution, as well as allows for needle-free delivery across respiratory epithelial barriers in human FcRn transgenic mice. In addition, the Fc-engineered variant improves on-target complement-mediated killing of cancer cells as well as both gram-positive and gram-negative bacteria. Hence, this versatile Fc technology should be broadly applicable in antibody design aiming for long-acting prophylactic or therapeutic interventions.
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Affiliation(s)
- Stian Foss
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Siri A Sakya
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Leire Aguinagalde
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marta Lustig
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jutamas Shaughnessy
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ana Rita Cruz
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lisette Scheepmaker
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Line Mathiesen
- Department of Public Health, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fulgencio Ruso-Julve
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Aina Karen Anthi
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Torleif Tollefsrud Gjølberg
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Simone Mester
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Malin Bern
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Mitchell Evers
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Diane B Bratlie
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | - Terje E Michaelsen
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Chemical Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Tilman Schlothauer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Devin Sok
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Jayanta Bhattacharya
- Antibody Translational Research Program, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Jeanette Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Thomas Valerius
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sanjay Ram
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Inger Sandlie
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway.
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway.
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Cho J, Hong HW, Park K, Myung H, Yoon H. Unveiling the mechanism of bactericidal activity of a cecropin A-fused endolysin LNT113. Int J Biol Macromol 2024; 260:129493. [PMID: 38224804 DOI: 10.1016/j.ijbiomac.2024.129493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Endolysins are lytic enzymes produced by bacteriophages at the end of their lytic cycle and degrade the peptidoglycan layer of the bacterial cell wall. Thus, they have been extensively explored as a promising antibacterial agent to replace or supplement current antibiotics. Gram-negative bacteria, however, are prone to resist exogenous endolysins owing to their protective outer membrane. We previously engineered endolysin EC340, encoded by the Escherichia coli phage PBEC131, by substituting its seven amino acids and fusing an antimicrobial peptide cecropin A at its N-terminus. The engineered endolysin LNT113 exerted superior activity to its intrinsic form. This study investigated how cecropin A fusion facilitated the bactericidal activity of LNT113 toward Gram-negative bacteria. Cecropin A of LNT113 markedly increased the interaction with lipopolysaccharides, while the E. coli defective in the core oligosaccharide was less susceptible to endolysins, implicating the interaction between the core oligosaccharide and endolysins. In fact, E. coli with compromised lipid A construction was more vulnerable to LNT113 treatment, suggesting that the integrity of the lipid A layer was important to resist the internalization of LNT113 across the outer membrane. Cecropin A fusion further accelerated the inner membrane destabilization, thereby enabling LNT113 to deconstruct it promptly. Owing to the increased membrane permeability, LNT113 could inactivate some Gram-positive bacteria as well. This study demonstrates that cecropin A fusion is a feasible method to improve the membrane permeability of endolysins in both Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Jeongik Cho
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | - Kyungah Park
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Heejoon Myung
- LyseNTech Co., Ltd., Seongnam, South Korea; Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin, South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea.
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5
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Cinar MS, Niyas A, Avci FY. Serine-rich repeat proteins: well-known yet little-understood bacterial adhesins. J Bacteriol 2024; 206:e0024123. [PMID: 37975670 PMCID: PMC10810200 DOI: 10.1128/jb.00241-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Serine-rich-repeat proteins (SRRPs) are large mucin-like glycoprotein adhesins expressed by a plethora of pathogenic and symbiotic Gram-positive bacteria. SRRPs play major functional roles in bacterial-host interactions, like adhesion, aggregation, biofilm formation, virulence, and pathogenesis. Through their functional roles, SRRPs aid in the development of host microbiomes but also diseases like infective endocarditis, otitis media, meningitis, and pneumonia. SRRPs comprise shared domains across different species, including two or more heavily O-glycosylated long stretches of serine-rich repeat regions. With loci that can be as large as ~40 kb and can encode up to 10 distinct glycosyltransferases that specifically facilitate SRRP glycosylation, the SRRP loci makes up a significant portion of the bacterial genome. The significance of SRRPs and their glycans in host-microbe communications is becoming increasingly evident. Studies are beginning to reveal the glycosylation pathways and mature O-glycans presented by SRRPs. Here we review the glycosylation machinery of SRRPs across species and discuss the functional roles and clinical manifestations of SRRP glycosylation.
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Affiliation(s)
- Mukaddes S. Cinar
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Afaq Niyas
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Fikri Y. Avci
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
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6
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Xu Y, Wang W, Su W, Wang M, Xu H, Zhang X, Li L. A widespread single amino acid mutation in AcrA reduces tigecycline susceptibility in Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0203023. [PMID: 38032193 PMCID: PMC10782974 DOI: 10.1128/spectrum.02030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Tigecycline, a glycecycline antibiotic with broad-spectrum activity against almost all Gram-positive and Gram-negative bacteria, is a highly concerned "last-resort" antibiotic. In addition to plasmid-hosted mobile tet(X) conferring high-level resistance to tigecycline, there are many reports suggesting increased expression of AcrAB-TolC efflux pump leads to tigecycline non-susceptibility. However, the role of mutations in AcrAB-TolC on tigecycline resistance has not been identified. This study reports a novel T188A mutation of the AcrA subunit of AcrAB-TolC complex in a clinical tigecycline-resistant Klebsiella pneumoniae strain and reveals the role of AcrA mutation on tigecycline resistance in K. pneumoniae. High prevalence of A188 type AcrA in hypervirulent multidrug-resistant K. pneumoniae indicates that mutations of the AcrAB-TolC complex may play a larger role in determining bacterial pathogenesis and antibiotic susceptibility than previously expected.
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Affiliation(s)
- Yingchao Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenjia Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenya Su
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuhua Zhang
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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7
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Tyagi S, Yadav RK, Krishnan V. Determination of the Crystal Structure of the Cell Wall-Anchored Proteins and Pilins. Methods Mol Biol 2024; 2727:159-191. [PMID: 37815717 DOI: 10.1007/978-1-0716-3491-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Surface proteins and pili (or pilus) anchored on the Gram-positive bacterial cell wall play a vital role in adhesion, colonization, biofilm formation, and immunomodulation. The pilus consists of building blocks called pilins or pilus subunits. The surface proteins and pilins share some common sequences and structural features. They contain an N-terminal signal sequence and the C-terminal cell wall sorting region, enabling their transportation across the membrane and covalent attachment to the bacterial cell wall, respectively. The transpeptidase enzymes called sortases facilitate the covalent links between the pilins during the pilus assembly and between surface proteins or basal subunits of pili and peptidoglycan-bridge during the cell wall anchoring. Thus, elucidating three-dimensional structures for the surface proteins and pilins at the atomic level is essential for understanding the mechanism of adhesion, pilus assembly, and host interaction. This chapter aims to provide a general protocol for crystal structure determination of surface proteins and pilins anchored on the Gram-positive bacterial cell wall and substrates for sortases. The protocol involves the production of recombinant protein, crystallization, and structure determination by X-ray crystallography technique.
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Affiliation(s)
- Shivangi Tyagi
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Rajnesh Kumari Yadav
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.
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8
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Scaffidi SJ, Yu W. Tracking Cell Wall-Anchored Proteins in Gram-Positive Bacteria. Methods Mol Biol 2024; 2727:193-204. [PMID: 37815718 DOI: 10.1007/978-1-0716-3491-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Cell wall-anchored surface proteins are integral components of Gram-positive bacterial cell envelope and vital for bacterial survival in different environmental niches. To fulfill their functions, surface protein precursors translocate from cytoplasm to bacterial cell surface in three sequential steps: secretion across the cytoplasmic membrane, covalently anchoring to the cell wall precursor lipid II by sortase A, and incorporation of the lipid II-linked precursors into mature cell wall peptidoglycan. Here, we describe a series of immunofluorescence microscopy methods to track the subcellular localization of cell wall-anchored proteins along the sorting pathway. While the protocols are tailored to Staphylococcus aureus, they can be readily adapted to localize cell wall-anchored proteins as well as membrane proteins in other Gram-positive bacteria.
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Affiliation(s)
- Salvatore J Scaffidi
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Wenqi Yu
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA.
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9
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Han J, Zhao X, Zhao X, Li P, Gu Q. Insight into the structure, biosynthesis, isolation method and biological function of teichoic acid in different gram-positive microorganisms: A review. Int J Biol Macromol 2023; 253:126825. [PMID: 37696369 DOI: 10.1016/j.ijbiomac.2023.126825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Teichoic acid (TA) is a weakly anionic polymer present in the cell walls of Gram-positive bacteria. It can be classified into wall teichoic acid (WTA) and lipoteichoic acid (LTA) based on its localization in the cell wall. The structure and biosynthetic pathway of TAs are strain-specific and have a significant role in maintaining cell wall stability. TAs have various beneficial functions, such as immunomodulatory, anticancer and antioxidant activities. However, the purity and yield of TAs are generally not high, and different isolation methods may even affect their structural integrity, which limits the research progress on the probiotic functions of TA. This paper reviews an overview of the structure and biosynthetic pathway of TAs in different strains, as well as the research progress of the isolation and purification methods of TAs. Furthermore, this review also highlights the current research status on the biological functions of TAs. Through a comprehensive understanding of this review, it is expected to pave the way for advancements in isolating and purifying high-quality TAs and, in turn, lay a foundation for contributing to the development of targeted probiotic therapies.
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Affiliation(s)
- Jiarun Han
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Xin Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Xilian Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, People's Republic of China
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310018, People's Republic of China.
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10
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Upender I, Yoshida O, Schrecengost A, Ranson H, Wu Q, Rowley DC, Kishore S, Cywes C, Miller EL, Whalen KE. A marine-derived fatty acid targets the cell membrane of Gram-positive bacteria. J Bacteriol 2023; 205:e0031023. [PMID: 37905811 PMCID: PMC10662121 DOI: 10.1128/jb.00310-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE With the lack of new antibiotics in the drug discovery pipeline, coupled with accelerated evolution of antibiotic resistance, new sources of antibiotics that target pathogens of clinical importance are paramount. Here, we use bacterial cytological profiling to identify the mechanism of action of the monounsaturated fatty acid (Z)-13-methyltetra-4-decenoic acid isolated from the marine bacterium Olleya marilimosa with antibacterial effects against Gram-positive bacteria. The fatty acid antibiotic was found to rapidly destabilize the cell membrane by pore formation and membrane aggregation in Bacillus subtilis, suggesting that this fatty acid may be a promising adjuvant used in combination to enhance antibiotic sensitivity.
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Affiliation(s)
- Isha Upender
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Olivia Yoshida
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Anna Schrecengost
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Hilary Ranson
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Qihao Wu
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Shreya Kishore
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Claire Cywes
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Kristen E. Whalen
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
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11
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Watkins D, Arya D. Models of Hfq interactions with small non-coding RNA in Gram-negative and Gram-positive bacteria. Front Cell Infect Microbiol 2023; 13:1282258. [PMID: 37942477 PMCID: PMC10628458 DOI: 10.3389/fcimb.2023.1282258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Hfq is required by many Gram-negative bacteria to chaperone the interaction between small non-coding RNA (sRNA) and mRNA to facilitate annealing. Conversely and despite the presence of Hfq in many Gram-positive bacteria, sRNAs in Gram-positive bacteria bind the mRNA target independent of Hfq. Details provided by the Hfq structures from both Gram-negative and Gram-positive bacteria have demonstrated that despite a conserved global structure of the protein, variations of residues on the binding surfaces of Hfq results in the recognition of different RNA sequences as well as the ability of Hfq to facilitate the annealing of the sRNA to the mRNA target. Additionally, a subset of Gram-negative bacteria has an extended C-terminal Domain (CTD) that has been shown to affect the stability of the Hfq hexamer and increase the rate of release of the annealed sRNA-mRNA product. Here we review the structures of Hfq and biochemical data that have defined the interactions of the Gram-negative and Gram-positive homologues to highlight the similarities and differences in the interactions with RNA. These interactions provided a deeper understanding of the how Hfq functions to facilitate the annealing of sRNA-mRNA, the selectivity of the interactions with RNA, and the role of the CTD of Hfq in the interactions with sRNA.
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Affiliation(s)
- Derrick Watkins
- Department of Math and Science, University of Tennessee Southern, Pulaski, TN, United States
| | - Dev Arya
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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12
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Jeong GJ, Khan F, Tabassum N, Cho KJ, Kim YM. Controlling biofilm and virulence properties of Gram-positive bacteria by targeting wall teichoic acid and lipoteichoic acid. Int J Antimicrob Agents 2023; 62:106941. [PMID: 37536571 DOI: 10.1016/j.ijantimicag.2023.106941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
Wall teichoic acid (WTA) and lipoteichoic acid (LTA) are structural components of Gram-positive bacteria's peptidoglycan and cell membrane, which are mostly anionic glycopolymers. WTA confers numerous physiological, virulence, and pathogenic features to bacterial pathogens. It controls cell shape, cell division, and the localisation of autolytic enzymes and ion homeostasis. In the context of virulence and pathogenicity, it aids bacterial cell attachment and colonisation and protects against the host defence system and antibiotics. Having such a broad function in pathogenic bacteria's lifecycle, WTA/LTA become one of the potential targets for antibacterial agents to reduce bacterial infection in the host. The number of reports for targeting the WTA/LTA pathway has risen, mostly by focusing on three distinct targets: antivirulence targets, β-lactam potentiator targets, and essential targets. The current review looked at the role of WTA/LTA in biofilm development and virulence in a range of Gram-positive pathogenic bacteria. Furthermore, alternate strategies, such as the application of natural and synthetic compounds that target the WTA/LTA pathway, have been thoroughly discussed. Moreover, the application of nanomaterials and a combination of drugs have also been discussed as a viable method for targeting the WTA/LTA in numerous Gram-positive bacteria. In addition, a future perspective for controlling bacterial infection by targeting the WTA/LTA is proposed.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyung-Jin Cho
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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13
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Madhu B, Lakdawala MF, Gumienny TL. The DBL-1/TGF-β signaling pathway tailors behavioral and molecular host responses to a variety of bacteria in Caenorhabditis elegans. eLife 2023; 12:e75831. [PMID: 37750680 PMCID: PMC10567113 DOI: 10.7554/elife.75831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/25/2023] [Indexed: 09/27/2023] Open
Abstract
Generating specific, robust protective responses to different bacteria is vital for animal survival. Here, we address the role of transforming growth factor β (TGF-β) member DBL-1 in regulating signature host defense responses in Caenorhabditis elegans to human opportunistic Gram-negative and Gram-positive pathogens. Canonical DBL-1 signaling is required to suppress avoidance behavior in response to Gram-negative, but not Gram-positive bacteria. We propose that in the absence of DBL-1, animals perceive some bacteria as more harmful. Animals activate DBL-1 pathway activity in response to Gram-negative bacteria and strongly repress it in response to select Gram-positive bacteria, demonstrating bacteria-responsive regulation of DBL-1 signaling. DBL-1 signaling differentially regulates expression of target innate immunity genes depending on the bacterial exposure. These findings highlight a central role for TGF-β in tailoring a suite of bacteria-specific host defenses.
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Affiliation(s)
- Bhoomi Madhu
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Mohammed Farhan Lakdawala
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- AbbVie (United States)WorcesterUnited States
| | - Tina L Gumienny
- Department of Biology, Texas Woman’s UniversityDentonUnited States
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14
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Elshami FI, Shereef HA, El-Mehasseb IM, Shaban SY, van Eldik R. Hydroxychloroquine-Loaded Chitosan Nanoparticles Induce Anticancer Activity in A549 Lung Cancer Cells: Design, BSA Binding, Molecular Docking, Mechanistic, and Biological Evaluation. Int J Mol Sci 2023; 24:14103. [PMID: 37762406 PMCID: PMC10531786 DOI: 10.3390/ijms241814103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The current study describes the encapsulation of hydroxychloroquine, widely used in traditional medicine due to its diverse pharmacological and medicinal uses, in chitosan nanoparticles (CNPs). This work aims to combine the HCQ drug with CS NPs to generate a novel nanocomposite with improved characteristics and bioavailability. HCQ@CS NPs are roughly shaped like roadways and have a smooth surface with an average size of 159.3 ± 7.1 nm, a PDI of 0.224 ± 0.101, and a zeta potential of +46.6 ± 0.8 mV. To aid in the development of pharmaceutical systems for use in cancer therapy, the binding mechanism and affinity of the interaction between HCQ and HCQ@CS NPs and BSA were examined using stopped-flow and other spectroscopic approaches, supplemented by molecular docking analysis. HCQ and HCQ@CS NPs binding with BSA is driven by a ground-state complex formation that may be accompanied by a non-radiative energy transfer process, and binding constants indicate that HCQ@CS NPs-BSA was more stable than HCQ-BSA. The stopped-flow analysis demonstrated that, in addition to increasing BSA affinity, the nanoformulation HCQ@CS NPS changes the binding process and may open new routes for interaction. Docking experiments verified the development of the HCQ-BSA complex, with HCQ binding to site I on the BSA structure, primarily with the amino acids, Thr 578, Gln 579, Gln 525, Tyr 400, and Asn 404. Furthermore, the nanoformulation HCQ@CS NPS not only increased cytotoxicity against the A549 lung cancer cell line (IC50 = 28.57 ± 1.72 μg/mL) compared to HCQ (102.21 ± 0.67 μg/mL), but also exhibited higher antibacterial activity against both Gram-positive and Gram-negative bacteria when compared to HCQ and chloramphenicol, which is in agreement with the binding constants. The nanoformulation developed in this study may offer a viable therapy option for A549 lung cancer.
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Affiliation(s)
- Fawzia I. Elshami
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (F.I.E.); (I.M.E.-M.)
| | - Hadeer A. Shereef
- Clinical Pathology Department, University Hospital, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Ibrahim M. El-Mehasseb
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (F.I.E.); (I.M.E.-M.)
| | - Shaban Y. Shaban
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (F.I.E.); (I.M.E.-M.)
| | - Rudi van Eldik
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland
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15
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Kiani P, Soozanipour A, Rezayat A, Taheri-Kafrani A. Lysozyme-immobilized bandage contact lens inhibits the growth and biofilm formation of common eye pathogens in vitro. Exp Eye Res 2023; 234:109601. [PMID: 37488008 DOI: 10.1016/j.exer.2023.109601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Bandage contact lenses have an increased affinity to accumulate tear film proteins and bacteria during wear. Among the wide variety of tear film proteins, lysozyme has attracted the most attention for several reasons, including the fact that it is found at a high concentration in the tear film, has exceptional antibacterial and antibiofilm properties, and its significant deposits onto contact lenses. This study aims to evaluate the effect of lysozyme on bacterial biofilm formation on bandage contact lenses. For this purpose, several methods, including microtiter plate test and Colony Forming Unit (CFU) assay have been used to determine antibacterial and antibiofilm characteristics of lysozyme against the two most frequent contact lens-induced bacterial ocular infections, Staphylococcus aureus, and Pseudomonas aeruginosa. The results of these assays demonstrate lysozyme potential to inhibit 57.9% and 80.7% of the growth of S. aureus and P. aeruginosa, respectively. In addition, biofilm formations of P. aeruginosa and S. aureus reduced by 38.3% and 62.7%, respectively due to the antibiofilm effect of lysozyme. SEM and AFM imaging were utilized to visualize lysozyme antibacterial activity and topography changes of the contact lens surface, respectively, in the presence/absence of lysozyme. The results indicated that lysozyme can efficiently attack both gram-positive and gram-negative bacteria and consequently lysozyme-functionalized bandage contact lenses can reduce the risk of ocular infection after eye surgery.
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Affiliation(s)
- Pardis Kiani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Asieh Soozanipour
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran
| | - Azam Rezayat
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran; Department of Chemistry, Faculty of Science, Lorestan University, Khorramabad, Iran
| | - Asghar Taheri-Kafrani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, 81746-73441, Iran.
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16
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Saathoff M, Kosol S, Semmler T, Tedin K, Dimos N, Kupke J, Seidel M, Ghazisaeedi F, Jonske MC, Wolf SA, Kuropka B, Czyszczoń W, Ghilarov D, Grätz S, Heddle JG, Loll B, Süssmuth RD, Fulde M. Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria. PLoS Biol 2023; 21:e3002186. [PMID: 37561817 PMCID: PMC10414762 DOI: 10.1371/journal.pbio.3002186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/07/2023] [Indexed: 08/12/2023] Open
Abstract
Antibiotic resistance is a continuously increasing concern for public healthcare. Understanding resistance mechanisms and their emergence is crucial for the development of new antibiotics and their effective use. The peptide antibiotic albicidin is such a promising candidate that, as a gyrase poison, shows bactericidal activity against a wide range of gram-positive and gram-negative bacteria. Here, we report the discovery of a gene amplification-based mechanism that imparts an up to 1000-fold increase in resistance levels against albicidin. RNA sequencing and proteomics data show that this novel mechanism protects Salmonella Typhimurium and Escherichia coli by increasing the copy number of STM3175 (YgiV), a transcription regulator with a GyrI-like small molecule binding domain that traps albicidin with high affinity. X-ray crystallography and molecular docking reveal a new conserved motif in the binding groove of the GyrI-like domain that can interact with aromatic building blocks of albicidin. Phylogenetic studies suggest that this resistance mechanism is ubiquitous in gram-negative bacteria, and our experiments confirm that STM3175 homologs can confer resistance in pathogens such as Vibrio vulnificus and Pseudomonas aeruginosa.
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Affiliation(s)
- Mareike Saathoff
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Dimos
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Johannes Kupke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Micela Condor Jonske
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Silver A. Wolf
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Benno Kuropka
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bernhard Loll
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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17
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Barringer R, Parnell AE, Lafita A, Monzon V, Back CR, Madej M, Potempa J, Nobbs AH, Burston SG, Bateman A, Race PR. Domain shuffling of a highly mutable ligand-binding fold drives adhesin generation across the bacterial kingdom. Proteins 2023; 91:1007-1020. [PMID: 36912614 PMCID: PMC10952558 DOI: 10.1002/prot.26487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023]
Abstract
Bacterial fibrillar adhesins are specialized extracellular polypeptides that promote the attachment of bacteria to the surfaces of other cells or materials. Adhesin-mediated interactions are critical for the establishment and persistence of stable bacterial populations within diverse environmental niches and are important determinants of virulence. The fibronectin (Fn)-binding fibrillar adhesin CshA, and its paralogue CshB, play important roles in host colonization by the oral commensal and opportunistic pathogen Streptococcus gordonii. As paralogues are often catalysts for functional diversification, we have probed the early stages of structural and functional divergence in Csh proteins by determining the X-ray crystal structure of the CshB adhesive domain NR2 and characterizing its Fn-binding properties in vitro. Despite sharing a common fold, CshB_NR2 displays an ~1.7-fold reduction in Fn-binding affinity relative to CshA_NR2. This correlates with reduced electrostatic charge in the Fn-binding cleft. Complementary bioinformatic studies reveal that homologues of CshA/B_NR2 domains are widely distributed in both Gram-positive and Gram-negative bacteria, where they are found housed within functionally cryptic multi-domain polypeptides. Our findings are consistent with the classification of Csh adhesins and their relatives as members of the recently defined polymer adhesin domain (PAD) family of bacterial proteins.
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Affiliation(s)
- Rob Barringer
- School of BiochemistryUniversity of Bristol, University WalkBristolBS8 1TDUK
| | - Alice E. Parnell
- School of BiochemistryUniversity of Bristol, University WalkBristolBS8 1TDUK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Aleix Lafita
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Genome CampusHinxtonCB10 1SDUK
| | - Vivian Monzon
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Genome CampusHinxtonCB10 1SDUK
| | - Catherine R. Back
- School of BiochemistryUniversity of Bristol, University WalkBristolBS8 1TDUK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian UniversityKrakowPoland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and BiotechnologyJagiellonian UniversityKrakowPoland
- Department of Oral Immunology and Infectious DiseasesUniversity of Louisville School of DentistryLouisvilleKentuckyUSA
| | - Angela H. Nobbs
- Bristol Dental School, University of BristolLower Maudlin StreetBristolBS1 2LYUK
| | - Steven G. Burston
- School of BiochemistryUniversity of Bristol, University WalkBristolBS8 1TDUK
| | - Alex Bateman
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Genome CampusHinxtonCB10 1SDUK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol, University WalkBristolBS8 1TDUK
- BrisSynBio Synthetic Biology Research CentreUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
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18
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Hasan S, Kayed K, Ghemrawi R, Bataineh NA, Mahgoub RE, Audeh R, Aldulaymi R, Atatreh N, Ghattas MA. Molecular Modelling Study and Antibacterial Evaluation of Diphenylmethane Derivatives as Potential FabI Inhibitors. Molecules 2023; 28:molecules28073000. [PMID: 37049763 PMCID: PMC10095751 DOI: 10.3390/molecules28073000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The need for new antibiotics has become a major worldwide challenge as bacterial strains keep developing resistance to the existing drugs at an alarming rate. Enoyl-acyl carrier protein reductases (FabI) play a crucial role in lipids and fatty acid biosynthesis, which are essential for the integrity of the bacterial cell membrane. Our study aimed to discover small FabI inhibitors in continuation to our previously found hit MN02. The process was initially started by conducting a similarity search to the NCI ligand database using MN02 as a query. Accordingly, ten compounds were chosen for the computational assessment and antimicrobial testing. Most of the compounds showed an antibacterial activity against Gram-positive strains, while RK10 exhibited broad-spectrum activity against both Gram-positive and Gram-negative bacteria. All tested compounds were then docked into the saFabI active site followed by 100 ns MD simulations (Molecular Dynamics) and MM-GBSA (Molecular Mechanics with Generalised Born and Surface Area Solvation) calculations in order to understand their fitting and estimate their binding energies. Interestingly, and in line with the experimental data, RK10 was able to exhibit the best fitting with the target catalytic pocket. To sum up, RK10 is a small compound with leadlike characteristics that can indeed act as a promising candidate for the future development of broad-spectrum antibacterial agents.
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Affiliation(s)
- Shaima Hasan
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Kawthar Kayed
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Nezar Al Bataineh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Radwa E. Mahgoub
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rola Audeh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Raghad Aldulaymi
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- Correspondence: ; Tel.: +971-26133275
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19
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Huang J, Lou Y, Liu J, Bulet P, Cai C, Ma K, Jiao R, Hoffmann JA, Liégeois S, Li Z, Ferrandon D. A Toll pathway effector protects Drosophila specifically from distinct toxins secreted by a fungus or a bacterium. Proc Natl Acad Sci U S A 2023; 120:e2205140120. [PMID: 36917667 PMCID: PMC10041126 DOI: 10.1073/pnas.2205140120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/09/2023] [Indexed: 03/16/2023] Open
Abstract
The Drosophila systemic immune response against many Gram-positive bacteria and fungi is mediated by the Toll pathway. How Toll-regulated effectors actually fulfill this role remains poorly understood as the known Toll-regulated antimicrobial peptide (AMP) genes are active only against filamentous fungi and not against Gram-positive bacteria or yeasts. Besides AMPs, two families of peptides secreted in response to infectious stimuli that activate the Toll pathway have been identified, namely Bomanins and peptides derived from a polyprotein precursor known as Baramicin A (BaraA). Unexpectedly, the deletion of a cluster of 10 Bomanins phenocopies the Toll mutant phenotype of susceptibility to infections. Here, we demonstrate that BaraA is required specifically in the host defense against Enterococcus faecalis and against the entomopathogenic fungus Metarhizium robertsii, albeit the fungal burden is not altered in BaraA mutants. BaraA protects the fly from the action of distinct toxins secreted by these Gram-positive and fungal pathogens, respectively, Enterocin V and Destruxin A. The injection of Destruxin A leads to the rapid paralysis of flies, whether wild type (WT) or mutant. However, a larger fraction of wild-type than BaraA flies recovers from paralysis within 5 to 10 h. BaraAs' function in protecting the host from the deleterious action of Destruxin is required in glial cells, highlighting a resilience role for the Toll pathway in the nervous system against microbial virulence factors. Thus, in complement to the current paradigm, innate immunity can cope effectively with the effects of toxins secreted by pathogens through the secretion of dedicated peptides, independently of xenobiotics detoxification pathways.
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Affiliation(s)
- Jianqiong Huang
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Yanyan Lou
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Jiyong Liu
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Philippe Bulet
- Université Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, 38000Grenoble, France
- Platform BioPark Archamps, 74160Archamps, France
| | - Chuping Cai
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
- Université de Strasbourg, Faculté des Sciences de la Vie, 67000Strasbourg, France
- Modèles Insectes d'Immunité Innée, Unité Propre de Recherche 9022 du CNRS, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084Strasbourg, France
| | - Kaiyu Ma
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Renjie Jiao
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Jules A. Hoffmann
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
- Université de Strasbourg, Faculté des Sciences de la Vie, 67000Strasbourg, France
- Modèles Insectes d'Immunité Innée, Unité Propre de Recherche 9022 du CNRS, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084Strasbourg, France
- Université de Strasbourg Institute for Advanced Study, 67000Strasbourg, France
| | - Samuel Liégeois
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
- Université de Strasbourg, Faculté des Sciences de la Vie, 67000Strasbourg, France
- Modèles Insectes d'Immunité Innée, Unité Propre de Recherche 9022 du CNRS, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084Strasbourg, France
| | - Zi Li
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
| | - Dominique Ferrandon
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou511436, China
- Université de Strasbourg, Faculté des Sciences de la Vie, 67000Strasbourg, France
- Modèles Insectes d'Immunité Innée, Unité Propre de Recherche 9022 du CNRS, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084Strasbourg, France
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20
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Arthi P, Dharmasivam M, Kaya B, Rahiman AK. Multi-target activity of copper complexes: Antibacterial, DNA binding, and molecular docking with SARS-CoV-2 receptor. Chem Biol Interact 2023; 373:110349. [PMID: 36639010 PMCID: PMC9831667 DOI: 10.1016/j.cbi.2023.110349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
A series of pendant-armed mixed-ligand copper(II) complexes of the type [CuL1-3(diimine)] (1-6) have been synthesized by the reaction of pendant-armed ligands N,N-bis(2-(((E)-2-hydroxy-5-methylbenzylidene)amino)ethyl)benzamide (H2L1), N,N-bis(2-(((E)-2-hydroxy-5-methylbenzylidene)amino)ethyl)-4-nitrobenzamide (H2L2) and N,N-bis(2-(((E)-2-hydroxy-5-methylbenzylidene)amino)ethyl)-3,5-dinitrobenzamide (H2L3) with diimine = 2,2'-bipyridyl (bpy) or 1,10-phenanthroline (phen) in the presence of copper(II) chloride and analyzed using various spectroscopic methods. All the spectroscopic results support that the complexes adopt a pentagonal-bipyramidal shape around the copper ion. Gram-positive and Gram-negative bacteria were used to test all the complexes for antibacterial activity and all the complexes had greater potency against gram-negative pathogens. DNA-binding experiments of complexes with calf thymus DNA revealed a major-groove binding pattern, further supported by molecular docking studies. Complexes have significantly interacted with SARS-CoV-2 receptor via π-π, π-σ, π-alkyl, π-anion, π-cation, alkyl, hydrogen bond, van der Waals, and electrostatic interactions. The estimated binding energy and inhibition constant of these complexes are higher than standard drugs, chloroquine, and molnupiravir.
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Affiliation(s)
- Padmanathan Arthi
- Department of Chemistry, SRM Institute of Science and Technology, Ramapuram, Chennai, 600 089, India
| | - Mahendiran Dharmasivam
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, 4111, Australia
| | - Busra Kaya
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, 4111, Australia; Department of Chemistry, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Turkey
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, 600 014, India.
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21
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Wingfield LK, Jitprasitporn N, Che-alee N. Isolation and characterization of halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. PLoS One 2023; 18:e0281623. [PMID: 36780513 PMCID: PMC9925087 DOI: 10.1371/journal.pone.0281623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
The present study explored culturable halophilic and halotolerant fungi from man-made solar salterns in Pattani Province, Thailand. A total of 24 fungal isolates were discovered and characterized using morphological and molecular identification. Production of extracellular enzymes, secondary metabolites and mycoviruses was examined. Growth was observed in salinity and temperature ranges between 0%-20% and 28-40°C, respectively. Growth in different environmental conditions confirmed the halophilic or halotolerant nature of some strains. Fungal isolates were phylogenetically classified into seven different genera belonging to Aspergillus, Cladosporium, Curvularia, Diaporthe, Ectophoma, Fusarium and Penicillium. An enzymatic production test revealed that thirteen isolates could produce proteases and amylases at different levels. The presence of mycoviruses was detected in three isolates. Seventeen of the 24 isolates produced antimicrobial metabolites. The majority of these active isolates were identified as Aspergillus and Penicillium species. Crude extracts of the fungal mycelia and culture broths from these isolates had an inhibitory effect on both Gram-positive and Gram-negative bacteria and human pathogenic fungi. Research into fungi from saline environments could reveal fungal strains of biotechnological and industrial interest.
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Affiliation(s)
- Lakkhana Kanhayuwa Wingfield
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- * E-mail:
| | - Ninadia Jitprasitporn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Nureeda Che-alee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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22
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Keestra-Gounder AM, Nagao PE. Inflammasome activation by Gram-positive bacteria: Mechanisms of activation and regulation. Front Immunol 2023; 14:1075834. [PMID: 36761775 PMCID: PMC9902775 DOI: 10.3389/fimmu.2023.1075834] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
The inflammasomes are intracellular multimeric protein complexes consisting of an innate immune sensor, the adapter protein ASC and the inflammatory caspases-1 and/or -11 and are important for the host defense against pathogens. Activaton of the receptor leads to formation of the inflammasomes and subsequent processing and activation of caspase-1 that cleaves the proinflammatory cytokines IL-1β and IL-18. Active caspase-1, and in some instances caspase-11, cleaves gasdermin D that translocates to the cell membrane where it forms pores resulting in the cell death program called pyroptosis. Inflammasomes can detect a range of microbial ligands through direct interaction or indirectly through diverse cellular processes including changes in ion fluxes, production of reactive oxygen species and disruption of various host cell functions. In this review, we will focus on the NLRP3, NLRP6, NLRC4 and AIM2 inflammasomes and how they are activated and regulated during infections with Gram-positive bacteria, including Staphylococcus spp., Streptococcus spp. and Listeria monocytogenes.
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Affiliation(s)
- A. Marijke Keestra-Gounder
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Prescilla Emy Nagao
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Brazil
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23
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Martinez-Goikoetxea M, Lupas AN. A conserved motif suggests a common origin for a group of proteins involved in the cell division of Gram-positive bacteria. PLoS One 2023; 18:e0273136. [PMID: 36662698 PMCID: PMC9858780 DOI: 10.1371/journal.pone.0273136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/29/2022] [Indexed: 01/21/2023] Open
Abstract
DivIVA, GpsB, FilP, and Scy are all involved in bacterial cell division. They have been reported to interact with each other, and although they have been the subject of considerable research interest, not much is known about the molecular basis for their biological activity. Although they show great variability in taxonomic occurrence, phenotypic profile, and molecular properties, we find that they nevertheless share a conserved N-terminal sequence motif, which points to a common evolutionary origin. The motif always occurs N-terminally to a coiled-coil helix that mediates dimerization. We define the motif and coiled coil jointly as a new domain, which we name DivIVA-like. In a large-scale survey of this domain in the protein sequence database, we identify a new family of proteins potentially involved in cell division, whose members, unlike all other DivIVA-like proteins, have between 2 and 8 copies of the domain in tandem. AlphaFold models indicate that the domains in these proteins assemble within a single chain, therefore not mediating dimerization.
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Affiliation(s)
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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24
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Matosinhos RD, Cesca K, Carciofi BAM, de Oliveira D, de Andrade CJ. Mannosylerythritol lipids as green pesticides and plant biostimulants. J Sci Food Agric 2023; 103:37-47. [PMID: 35775374 DOI: 10.1002/jsfa.12100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/03/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Biosurfactants can be applied in the formulation of personal care products, as food additives, and as biocontrol agents in the agricultural sector. Glycolipids and lipopeptides represent an important group of microbial-based biosurfactants with biostimulating properties. Among them, the mannosylerythritol lipids also presented antimicrobial activity, mostly against Gram-positive bacteria and phytopathogenic fungi. In this sense, mannosylerythritol lipids are a potential safer green alternative for partially replacing synthetic pesticides. This review aimed to critically discuss the current state of the art and future trends of mannosylerythritol lipids as green pesticides and biostimulants for seed germination and plant growth. Due to their chemical structure, mannosylerythritol lipids are likely related to energy pathways such as glycolysis and Krebs cycle, i.e. a direct cellular biostimulant potential. In this case, experimental evidence from other glycolipids indicated that structural and chemical changes as a potential drug vehicle due to morphological changes caused by biosurfactant-membrane interaction. In addition, like other biosurfactants, mannosylerythritol lipids can trigger self-defense mechanisms, leading to a lower frequency of phytopathogen infections. Therefore, mannosylerythritol lipids have the potential for biostimulation and antiphytopathogenic action, despite that to date no data are available on mannosylerythritol lipids as biostimulants and green pesticides simultaneously. Based on the current state of the art, mannosylerythritol lipids have great potential for a biotechnological advance toward more sustainable agriculture. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Renato Dias Matosinhos
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Karina Cesca
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Débora de Oliveira
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Cristiano José de Andrade
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
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25
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Kong G, Yang Y, Luo Y, Liu F, Song D, Sun G, Li D, Guo J, Dong M, Xu M. Cysteine-Mediated Extracellular Electron Transfer of Lysinibacillus varians GY32. Microbiol Spectr 2022; 10:e0279822. [PMID: 36318024 PMCID: PMC9769522 DOI: 10.1128/spectrum.02798-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Microbial extracellular electron transfer (EET) is essential in many natural and engineering processes. Compared with the versatile EET pathways of Gram-negative bacteria, the EET of Gram-positive bacteria has been studied much less and is mainly limited to the flavin-mediated pathway. Here, we investigate the EET pathway of a Gram-positive filamentous bacterium Lysinibacillus varians GY32. Strain GY32 has a wide electron donor spectrum (including lactate, acetate, formate, and some amino acids) in electrode respiration. Transcriptomic, proteomic, and electrochemical analyses show that the electrode respiration of GY32 mainly depends on electron mediators, and c-type cytochromes may be involved in its respiration. Fluorescent sensor and electrochemical analyses demonstrate that strain GY32 can secrete cysteine and flavins. Cysteine added shortly after inoculation into microbial fuel cells accelerated EET, showing cysteine is a new endogenous electron mediator of Gram-positive bacteria, which provides novel information to understand the EET networks in natural environments. IMPORTANCE Extracellular electron transport (EET) is a key driving force in biogeochemical element cycles and microbial chemical-electrical-optical energy conversion on the Earth. Gram-positive bacteria are ubiquitous and even dominant in EET-enriched environments. However, attention and knowledge of their EET pathways are largely lacking. Gram-positive bacterium Lysinibacillus varians GY32 has extremely long cells (>1 mm) and conductive nanowires, promising a unique and enormous role in the microenvironments where it lives. Its capability to secrete cysteine renders it not only an EET pathway to respire and survive, but also an electrochemical strategy to connect and shape the ambient microbial community at a millimeter scale. Moreover, its incapability of using flavins as an electron mediator suggests that the common electron mediator is species-dependent. Therefore, our results are important to understanding the EET networks in natural and engineering processes.
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Affiliation(s)
- Guannan Kong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yeshen Luo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Da Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Daobo Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meijun Dong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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26
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Megaly AMA, Miyashita M, Abdel-Wahab M, Nakagawa Y, Miyagawa H. Molecular Diversity of Linear Peptides Revealed by Transcriptomic Analysis of the Venom Gland of the Spider Lycosa poonaensis. Toxins (Basel) 2022; 14:toxins14120854. [PMID: 36548751 PMCID: PMC9788040 DOI: 10.3390/toxins14120854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Spider venom is a complex mixture of bioactive components. Previously, we identified two linear peptides in Lycosa poonaensis venom using mass spectrometric analysis and predicted the presence of more linear peptides therein. In this study, a transcriptomic analysis of the L. poonaensis venom gland was conducted to identify other undetermined linear peptides in the venom. The results identified 87 contigs encoding peptides and proteins in the venom that were similar to those in other spider venoms. The number of contigs identified as neurotoxins was the highest, and 15 contigs encoding 17 linear peptide sequences were identified. Seven peptides that were representative of each family were chemically synthesized, and their biological activities were evaluated. All peptides showed significant antibacterial activity against Gram-positive and Gram-negative bacteria, although their selectivity for bacterial species differed. All peptides also exhibited paralytic activity against crickets, but none showed hemolytic activity. The secondary structure analysis based on the circular dichroism spectroscopy showed that all these peptides adopt an amphiphilic α-helical structure. Their activities appear to depend on the net charge, the arrangement of basic and acidic residues, and the hydrophobicity of the peptides.
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Affiliation(s)
- Alhussin Mohamed Abdelhakeem Megaly
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Zoology Department, Faculty of Science, Al-Azhar University, Assuit 71524, Egypt
| | - Masahiro Miyashita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Correspondence:
| | - Mohammed Abdel-Wahab
- Zoology Department, Faculty of Science, Al-Azhar University, Assuit 71524, Egypt
| | - Yoshiaki Nakagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisashi Miyagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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27
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Hosseini-Giv N, Basas A, Hicks C, El-Omar E, El-Assaad F, Hosseini-Beheshti E. Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer. Front Cell Infect Microbiol 2022; 12:962216. [PMID: 36439225 PMCID: PMC9691856 DOI: 10.3389/fcimb.2022.962216] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/20/2022] [Indexed: 10/03/2023] Open
Abstract
Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.
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Affiliation(s)
- Niloufar Hosseini-Giv
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alyza Basas
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Chloe Hicks
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Emad El-Omar
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Fatima El-Assaad
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- The Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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28
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Morais D, Tanoeiro L, Marques AT, Gonçalves T, Duarte A, Matos APA, Vital JS, Cruz MEM, Carvalheiro MC, Anes E, Vítor JMB, Gaspar MM, Vale FF. Liposomal Delivery of Newly Identified Prophage Lysins in a Pseudomonas aeruginosa Model. Int J Mol Sci 2022; 23:ijms231710143. [PMID: 36077542 PMCID: PMC9456237 DOI: 10.3390/ijms231710143] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium that presents resistance to several antibiotics, thus, representing a major threat to human and animal health. Phage-derived products, namely lysins, or peptidoglycan-hydrolyzing enzymes, can be an effective weapon against antibiotic-resistant bacteria. Whereas in Gram-positive bacteria, lysis from without is facilitated by the exposed peptidoglycan layer, this is not possible in the outer membrane-protected peptidoglycan of Gram-negative bacteria. Here, we suggest the encapsulation of lysins in liposomes as a delivery system against Gram-negative bacteria, using the model of P. aeruginosa. Bioinformatic analysis allowed for the identification of 38 distinct complete prophages within 66 P. aeruginosa genomes (16 of which newly sequenced) and led to the identification of 19 lysins of diverse sequence and function, 5 of which proceeded to wet lab analysis. The four purifiable lysins showed hydrolytic activity against Gram-positive bacterial lawns and, on zymogram assays, constituted of autoclaved P. aeruginosa cells. Additionally, lysins Pa7 and Pa119 combined with an outer membrane permeabilizer showed activity against P. aeruginosa cells. These two lysins were successfully encapsulated in DPPC:DOPE:CHEMS (molar ratio 4:4:2) liposomes with an average encapsulation efficiency of 33.33% and 32.30%, respectively. The application of the encapsulated lysins to the model P. aeruginosa led to a reduction in cell viability and resulted in cell lysis as observed in MTT cell viability assays and electron microscopy. In sum, we report here that prophages may be important sources of new enzybiotics, with prophage lysins showing high diversity and activity. In addition, these enzybiotics following their incorporation in liposomes were able to potentiate their antibacterial effect against the Gram-negative bacteria P. aeruginosa, used as the model.
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Affiliation(s)
- Diana Morais
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Andreia T. Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Tiago Gonçalves
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Advanced Technologies for Drug Delivery, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior Egas Moniz, Quinta da Granja, 2829-511 Monte da Caparica, Portugal
| | - António Pedro Alves Matos
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior Egas Moniz, Quinta da Granja, 2829-511 Monte da Caparica, Portugal
| | - Joana S. Vital
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Maria Eugénia Meirinhos Cruz
- Advanced Technologies for Drug Delivery, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Manuela Colla Carvalheiro
- Advanced Technologies for Drug Delivery, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Jorge M. B. Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Maria Manuela Gaspar
- Advanced Technologies for Drug Delivery, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Correspondence: or (M.M.G.); or (F.F.V.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Correspondence: or (M.M.G.); or (F.F.V.)
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Shekarappa SB, Rimac H, Lee J. In Silico Screening of Quorum Sensing Inhibitor Candidates Obtained by Chemical Similarity Search. Molecules 2022; 27:molecules27154887. [PMID: 35956838 PMCID: PMC9369968 DOI: 10.3390/molecules27154887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022] Open
Abstract
Quorum sensing (QS) is a bacterial communication using signal molecules, by which they sense population density of their own species, leading to group behavior such as biofilm formation and virulence. Autoinducer-2 (AI2) is a QS signal molecule universally used by both gram-positive and gram-negative bacteria. Inhibition of QS mediated by AI2 is important for various practical applications, including prevention of gum-disease caused by biofilm formation of oral bacteria. In this research, molecular docking and molecular dynamics (MD) simulations were performed for molecules that are chemically similar to known AI2 inhibitors that might have a potential to be quorum sensing inhibitors. The molecules that form stable complexes with the AI2 receptor protein were found, suggesting that they could be developed as a novel AI2 inhibitors after further in vitro validation. The result suggests that combination of ligand-based drug design and computational methods such as MD simulation, and experimental verification, may lead to development of novel AI inhibitor, with a broad range of practical applications.
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Affiliation(s)
| | - Hrvoje Rimac
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia;
| | - Julian Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea;
- Correspondence:
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30
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Zhao Y, Wang XY, Sun Y, Li Z, Liu T, Liu QM, Chen J. Truncated analog Brevinin2-CE-N26V5K: Revelation the Augmentation of Antimicrobial Activity. World J Microbiol Biotechnol 2022; 38:162. [PMID: 35834028 DOI: 10.1007/s11274-022-03333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
Brevinin2-CE (B2CE), a natural peptide containing 37 amino acids, was first isolated from the skin secretions of the Chinese forest frog Rana chensinensis. B2CE shows good antibacterial activity. In this study, a series of B2CE analogs with differences in cationicity, α-helicity, hydrophobicity and amphipathic properties were designed through chain-length deletion and amino acid substitution. The most potent, nontoxic analog, B2CE-N26V5K, was identified by examination of its antibacterial activity, hemolytic activity, and stability under physiological conditions. The increased cationicity, hydrophobicity and more obvious hydrophilic and hydrophobic surface of B2CE-N26-N16WA18KG23K did not improve the antibacterial activity but increased the hemolytic activity of this modified peptide. The helicity might promote antibacterial activity for brevinin-2 peptides, as the 15-aa analogs with lower helicity show decreased potency against different test bacteria (approximately 2- to 72-fold) compared to B2CE-N26V5K. Additionally, the results indicated that the "Rana box" does not affect the antimicrobial activity of brevinin-2 peptides, as B2CE, B2CE-nonDS and B2CE-C31-37 S have similar strong inhibitory effects on both gram-positive and gram-negative bacteria. However, the "Rana box" does affect the hemolytic activity, as the HC50 values of the 3 peptides range from 25 ~ 130 µM. Furthermore, B2CE-N26V5K caused obvious morphological alterations of the bacterial surfaces, as shown by atomic force microscopy. Additionally, B2CE-N26V5K exhibited strong membrane-disrupting activity when examined using the LIVE/DEAD Bac Light Bacterial Viability Kit. Thus, the antibacterial effect of B2CE-N26V5K on gram-negative and gram-positive bacteria may be caused by cell membrane attack. In conclusion, the excellent candidate B2CE-N26V5K was obtained and has application prospects as a novel anti-infective agent.
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Affiliation(s)
- Yi Zhao
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China
| | - Xiao-Yan Wang
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China
| | - Yan Sun
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China.
| | - Zhi Li
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China.
| | - Tao Liu
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China
| | - Qing-Mei Liu
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China
| | - Jingyi Chen
- College of Life Sciences, Shaanxi Normal University, 710119, Xi'an, P. R. China
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Kausar S, Abbas MN, Gul I, Liu R, Li Q, Zhao E, Lv M, Cui H. Molecular Identification of Two DNA Methyltransferase Genes and Their Functional Characterization in the Anti-Bacterial Immunity of Antheraea pernyi. Front Immunol 2022; 13:855888. [PMID: 35651618 PMCID: PMC9149099 DOI: 10.3389/fimmu.2022.855888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/11/2022] [Indexed: 12/29/2022] Open
Abstract
Under different physiological conditions, such as microbial infection, epigenetic mechanisms regulate genes at the transcription level in living organisms. DNA methylation is a type of epigenetic mechanism in which DNA methyltransferases modify the expression of target genes. Here, we identified a full-length sequence of DNMT-1 and DNMT-2 from the Chinese oak silkworm, A. pernyi, which was highly similar to the homologous sequences of Bombyx mori. ApDNMT-1 and ApDNMT-2 have unique domain architectures of insect DNMTs, highlighting their conserved functions in A. pernyi. ApDNMT-1 and ApDNMT-2 were found to be widely expressed in various tissues, with the highest levels of expression in hemocytes, the ovary, testis, and fat bodies. To understand the biological role of these genes in microbial resistance, we challenged the fifth instar larvae of A. pernyi by administrating Gram-positive and Gram-negative bacteria and fungi. The results revealed that transcript levels of ApDNMT-1 and ApDNMT-2 were increased compared to the control group. The inhibition of these genes by a DNMTs inhibitor [5-azacytidine (5-AZA)] significantly reduced bacterial replication and larvae mortality. In addition, 5-AZA treatment modified the expression patterns of antimicrobial peptides (AMPs) in the A. pernyi larvae. Our results suggest that ApDNMT-1 and ApDNMT-2 seem to have a crucial role in innate immunity, mediating antimicrobial peptide responses against bacterial infection in A. pernyi.
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Affiliation(s)
- Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Isma Gul
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Qianqian Li
- Department of Psychology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Muhan Lv
- Department of Gastroenterology, The Affliated Hospital of Southwest Medical University, Luzhao, China
- *Correspondence: Muhan Lv, ; Hongjuan Cui,
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- *Correspondence: Muhan Lv, ; Hongjuan Cui,
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Janowska S, Khylyuk D, Andrzejczuk S, Wujec M. Design, Synthesis, Antibacterial Evaluations and In Silico Studies of Novel Thiosemicarbazides and 1,3,4-Thiadiazoles. Molecules 2022; 27:molecules27103161. [PMID: 35630638 PMCID: PMC9147709 DOI: 10.3390/molecules27103161] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
The emergence of drug-resistant bacterial strains continues to be one of the major challenges of medicine. For this reason, the importance of searching for novel structures of antibacterial drugs chemically different from the currently known antibiotics is still of great importance. In this study, we synthesized the thiosemicarbazide and 1,3,4-thiadiazole derivatives and tested them for antibacterial activity. In in vitro tests, we examined the activity of the synthesized substances against Gram-positive and Gram-negative bacteria strains. While all 1,3,4-thiadiazoles tested lacked significant activity, the antimicrobial response of the thiosemicarbazides was moderate and it was also dependent on the type and position of the substituent on the phenyl ring. The highest activity towards all Gram-positive bacteria strains was shown by all three linear compounds containing the trifluoromethylphenyl group in the structure. The MIC (minimum inhibitory concentration) values were in the range of 3.9–250 µg/mL. Additionally, we try to explain the mechanism of the antibacterial activity of the tested compounds using the molecular docking to DNA gyrase and topoisomerase IV, following previous reports on the molecular basis of the activity of thiosemicarbazides. Docking simulations allow the purposing dual mechanism of the antibacterial activity of the synthesized compounds through inhibition of topoisomerase IV DNA gyrase with the moderate prevalence of the topoisomerase pathway.
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Affiliation(s)
- Sara Janowska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, 20-093 Lublin, Poland; (S.J.); (D.K.)
| | - Dmytro Khylyuk
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, 20-093 Lublin, Poland; (S.J.); (D.K.)
| | - Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University, 20-093 Lublin, Poland;
| | - Monika Wujec
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, 20-093 Lublin, Poland; (S.J.); (D.K.)
- Correspondence:
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Ge Y, Li Z, Wang X, Luo X, Wang N, He H, Zhang T, Qi W. [The extracellular vesicles from gram-positive bacteria: a review]. Sheng Wu Gong Cheng Xue Bao 2022; 38:1462-1474. [PMID: 35470619 DOI: 10.13345/j.cjb.210515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Extracellular vesicles (EVs), also known as membrane vesicles, are vesicular bodies secreted by eukaryotic cells and bacteria. EVs can carry proteins, DNA, RNA, and various metabolites for the exchange and transmission of substances between cells. They play contents-dependent physiological functions, such as delivering nutrients, participating in immune response, and treating cancers. Currently, most studies focus on the exploration of vesicles secreted by eukaryotic cells and gram-negative bacteria, while few studies focus on gram-positive bacteria. This review summarized the production, content composition, physiological function, and engineering of EVs secreted by gram-positive bacteria, and prospected future perspectives in this area.
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Affiliation(s)
- Yanyan Ge
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zihan Li
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinyue Wang
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuegang Luo
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Hongpeng He
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tongcun Zhang
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wei Qi
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
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Yang M, Liu Y, Liao Y, Tang C, Wen Z, Fazal A, Yang R, Qi J, Hong Z, Li Y, Yang Y. Excess copper promotes catabolic activity of gram-positive bacteria and resistance of gram-negative bacteria but inhibits fungal community in soil. Environ Sci Pollut Res Int 2022; 29:22602-22612. [PMID: 34792767 DOI: 10.1007/s11356-021-17510-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The extensive use of copper fungicides has resulted in significant non-target effects on soil microbial communities. However, the documented effects are often variable and contradictory, depending on the methods used to assess them. In this study, we examined the effects of copper accumulation in surface soils on microbial catabolic activity, active biomass and composition, and sensitive bacterial species. The community-level catabolic profiles (CLCPs) showed that both normal (50 mg CuSO4 kg-1 soil) and high dosages (tenfold rate) of CuSO4 significantly increased the catabolic diversity of gram-positive bacteria, while the high dosage increased the overall catabolic activity of gram-negative bacteria. The phospholipid fatty acid (PLFA) analysis showed that the high dosage reduced the biomass of gram-positive bacteria by 27% but did not affect that of gram-negative bacteria. In comparison, the normal and high dosages decreased the fungal biomass by 34% and 58%, respectively. Furthermore, 16S rRNA-denaturing gradient gel electrophoresis (DGGE) fingerprint revealed that more than two-thirds of identified bands belonged to gram-negative bacteria. Some Cu-resistant gram-negative bacterial genera, such as Actinobacterium, Pseudomonas, and Proteobacterium, were detected in the soil to which the high dosage of CuSO4 had been applied. In conclusion, an excess application of CuSO4 increased the catabolic diversity of gram-positive bacteria and induced resistance in gram-negative bacteria, whereas the active fungal community displayed a dosage-dependent response to CuSO4 and can thus be used as a sensitive indicator of copper contamination.
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Affiliation(s)
- Minkai Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yehao Liu
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yonghui Liao
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Zhongling Wen
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Aliya Fazal
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Rongwu Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jinliang Qi
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhi Hong
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Yongchun Li
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- State Key Laboratory of Subtropical Silviculture, College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Yonghua Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Aggarwal H, Pathak P, Singh V, Kumar Y, Shankar M, Das B, Jagavelu K, Dikshit M. Vancomycin-Induced Modulation of Gram-Positive Gut Bacteria and Metabolites Remediates Insulin Resistance in iNOS Knockout Mice. Front Cell Infect Microbiol 2022; 11:795333. [PMID: 35127558 PMCID: PMC8807491 DOI: 10.3389/fcimb.2021.795333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/23/2021] [Indexed: 12/27/2022] Open
Abstract
The role of oxidative and nitrosative stress has been implied in both physiology and pathophysiology of metabolic disorders. Inducible nitric oxide synthase (iNOS) has emerged as a crucial regulator of host metabolism and gut microbiota activity. The present study examines the role of the gut microbiome in determining host metabolic functions in the absence of iNOS. Insulin-resistant and dyslipidemic iNOS-/- mice displayed reduced microbial diversity, with a higher relative abundance of Allobaculum and Bifidobacterium, gram-positive bacteria, and altered serum metabolites along with metabolic dysregulation. Vancomycin, which largely depletes gram-positive bacteria, reversed the insulin resistance (IR), dyslipidemia, and related metabolic anomalies in iNOS-/- mice. Such improvements in metabolic markers were accompanied by alterations in the expression of genes involved in fatty acid synthesis in the liver and adipose tissue, lipid uptake in adipose tissue, and lipid efflux in the liver and intestine tissue. The rescue of IR in vancomycin-treated iNOS-/- mice was accompanied with the changes in select serum metabolites such as 10-hydroxydecanoate, indole-3-ethanol, allantoin, hippurate, sebacic acid, aminoadipate, and ophthalmate, along with improvement in phosphatidylethanolamine to phosphatidylcholine (PE/PC) ratio. In the present study, we demonstrate that vancomycin-mediated depletion of gram-positive bacteria in iNOS-/- mice reversed the metabolic perturbations, dyslipidemia, and insulin resistance.
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Affiliation(s)
- Hobby Aggarwal
- Pharmacology Division, Council of Scientific and Industrial Research (CSIR)-Central Drug Research Institute, Lucknow, India
| | - Priya Pathak
- Pharmacology Division, Council of Scientific and Industrial Research (CSIR)-Central Drug Research Institute, Lucknow, India
| | - Vishal Singh
- Department of Nutritional Sciences, The Pennsylvania State University, State College, PA, United States
| | - Yashwant Kumar
- Non-Communicable Diseases Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Manoharan Shankar
- Microbial Physiology Laboratory, Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Kumaravelu Jagavelu
- Pharmacology Division, Council of Scientific and Industrial Research (CSIR)-Central Drug Research Institute, Lucknow, India
| | - Madhu Dikshit
- Pharmacology Division, Council of Scientific and Industrial Research (CSIR)-Central Drug Research Institute, Lucknow, India
- Non-Communicable Diseases Division, Translational Health Science and Technology Institute, Faridabad, India
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Dai W, Li J, Li Q, Cai J, Su J, Stubenrauch C, Wang J. PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. Nucleic Acids Res 2022; 50:D848-D857. [PMID: 34551435 PMCID: PMC8728121 DOI: 10.1093/nar/gkab814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
From industry to food to health, bacteria play an important role in all facets of life. Some of the most important bacteria have been purposely engineered to produce commercial quantities of antibiotics and therapeutics, and non-classical secretion systems are at the forefront of these technologies. Unlike the classical Sec or Tat pathways, non-classically secreted proteins share few common characteristics and use much more diverse secretion pathways for protein transport. Systematically categorizing and investigating the non-classically secreted proteins will enable a deeper understanding of their associated secretion mechanisms and provide a landscape of the Gram-positive secretion pathway distribution. We therefore developed PncsHub (https://pncshub.erc.monash.edu/), the first universal platform for comprehensively annotating and analyzing Gram-positive bacterial non-classically secreted proteins. PncsHub catalogs 4,914 non-classically secreted proteins, which are delicately categorized into 8 subtypes (including the 'unknown' subtype) and annotated with data compiled from up to 26 resources and visualisation tools. It incorporates state-of-the-art predictors to identify new and homologous non-classically secreted proteins and includes three analytical modules to visualise the relationships between known and putative non-classically secreted proteins. As such, PncsHub aims to provide integrated services for investigating, predicting and identifying non-classically secreted proteins to promote hypothesis-driven laboratory-based experiments.
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Affiliation(s)
- Wei Dai
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China
| | - Jiahui Li
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Qi Li
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jiasheng Cai
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jianzhong Su
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China
- School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Christopher Stubenrauch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
- Centre to Impact AMR, Monash University, VIC 3800, Australia
| | - Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
- Centre to Impact AMR, Monash University, VIC 3800, Australia
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Aries ML, Cloninger MJ. NMR Hydrophilic Metabolomic Analysis of Bacterial Resistance Pathways Using Multivalent Antimicrobials with Challenged and Unchallenged Wild Type and Mutated Gram-Positive Bacteria. Int J Mol Sci 2021; 22:ijms222413606. [PMID: 34948402 PMCID: PMC8715671 DOI: 10.3390/ijms222413606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/19/2022] Open
Abstract
Multivalent membrane disruptors are a relatively new antimicrobial scaffold that are difficult for bacteria to develop resistance to and can act on both Gram-positive and Gram-negative bacteria. Proton Nuclear Magnetic Resonance (1H NMR) metabolomics is an important method for studying resistance development in bacteria, since this is both a quantitative and qualitative method to study and identify phenotypes by changes in metabolic pathways. In this project, the metabolic differences between wild type Bacillus cereus (B. cereus) samples and B. cereus that was mutated through 33 growth cycles in a nonlethal dose of a multivalent antimicrobial agent were identified. For additional comparison, samples for analysis of the wild type and mutated strains of B. cereus were prepared in both challenged and unchallenged conditions. A C16-DABCO (1,4-diazabicyclo-2,2,2-octane) and mannose functionalized poly(amidoamine) dendrimer (DABCOMD) were used as the multivalent quaternary ammonium antimicrobial for this hydrophilic metabolic analysis. Overall, the study reported here indicates that B. cereus likely change their peptidoglycan layer to protect themselves from the highly positively charged DABCOMD. This membrane fortification most likely leads to the slow growth curve of the mutated, and especially the challenged mutant samples. The association of these sample types with metabolites associated with energy expenditure is attributed to the increased energy required for the membrane fortifications to occur as well as to the decreased diffusion of nutrients across the mutated membrane.
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López Y, Muñoz L, Gargallo-Viola D, Cantón R, Vila J, Zsolt I. Uptake of Ozenoxacin and Other Quinolones in Gram-Positive Bacteria. Int J Mol Sci 2021; 22:13363. [PMID: 34948159 PMCID: PMC8708121 DOI: 10.3390/ijms222413363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/22/2022] Open
Abstract
The big problem of antimicrobial resistance is that it requires great efforts in the design of improved drugs which can quickly reach their target of action. Studies of antibiotic uptake and interaction with their target it is a key factor in this important challenge. We investigated the accumulation of ozenoxacin (OZN), moxifloxacin (MOX), levofloxacin (LVX), and ciprofloxacin (CIP) into the bacterial cells of 5 species, including Staphylococcus aureus (SA4-149), Staphylococcus epidermidis (SEP7602), Streptococcus pyogenes (SPY165), Streptococcus agalactiae (SAG146), and Enterococcus faecium (EF897) previously characterized.The concentration of quinolone uptake was estimated by agar disc-diffusion bioassay. Furthermore, we determined the inhibitory concentrations 50 (IC50) of OZN, MOX, LVX, and CIP against type II topoisomerases from S. aureus.The accumulation of OZN inside the bacterial cell was superior in comparison to MOX, LVX, and CIP in all tested species. The accumulation of OZN inside the bacterial cell was superior in comparison to MOX, LVX, and CIP in all tested species. The rapid penetration of OZN into the cell was reflected during the first minute of exposure with antibiotic values between 190 and 447 ng/mg (dry weight) of bacteria in all strains. Moreover, OZN showed the greatest inhibitory activity among the quinolones tested for both DNA gyrase and topoisomerase IV isolated from S. aureus with IC50 values of 10 and 0.5 mg/L, respectively. OZN intracellular concentration was significantly higher than that of MOX, LVX and CIP. All of these features may explain the higher in vitro activity of OZN compared to the other tested quinolones.
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Affiliation(s)
- Yuly López
- Institute of Global Health of Barcelona, 08036 Barcelona, Spain;
| | - Laura Muñoz
- Institute of Global Health of Barcelona, 08036 Barcelona, Spain;
| | | | - Rafael Cantón
- Department of Clinical Microbiology, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
- CIBER Enfermedades Infecciosas, ISCIII, 28029 Madrid, Spain
| | - Jordi Vila
- Institute of Global Health of Barcelona, 08036 Barcelona, Spain;
- CIBER Enfermedades Infecciosas, ISCIII, 28029 Madrid, Spain
- Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, 08007 Barcelona, Spain
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McMillan HM, Kuehn MJ. The extracellular vesicle generation paradox: a bacterial point of view. EMBO J 2021; 40:e108174. [PMID: 34636061 PMCID: PMC8561641 DOI: 10.15252/embj.2021108174] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
All bacteria produce secreted vesicles that carry out a variety of important biological functions. These extracellular vesicles can improve adaptation and survival by relieving bacterial stress and eliminating toxic compounds, as well as by facilitating membrane remodeling and ameliorating inhospitable environments. However, vesicle production comes with a price. It is energetically costly and, in the case of colonizing pathogens, it elicits host immune responses, which reduce bacterial viability. This raises an interesting paradox regarding why bacteria produce vesicles and begs the question as to whether the benefits of producing vesicles outweigh their costs. In this review, we discuss the various advantages and disadvantages associated with Gram-negative and Gram-positive bacterial vesicle production and offer perspective on the ultimate score. We also highlight questions needed to advance the field in determining the role for vesicles in bacterial survival, interkingdom communication, and virulence.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and MicrobiologyDuke UniversityDurhamNCUSA
| | - Meta J Kuehn
- Department of BiochemistryDuke UniversityDurhamNCUSA
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Otieno W, Liu C, Ji Y. Aloe-Emodin-Mediated Photodynamic Therapy Attenuates Sepsis-Associated Toxins in Selected Gram-Positive Bacteria In Vitro. J Microbiol Biotechnol 2021; 31:1200-1209. [PMID: 34319262 PMCID: PMC9705996 DOI: 10.4014/jmb.2105.05024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Sepsis is an acute inflammatory response that leads to life-threatening complications if not quickly and adequately treated. Cytolysin, hemolysin, and pneumolysin are toxins produced by gram-positive bacteria and are responsible for resistance to antimicrobial drugs, cause virulence and lead to sepsis. This work assessed the effects of aloe-emodin (AE) and photodynamic therapy (PDT) on sepsis-associated gram-positive bacterial toxins. Standard and antibiotic-resistant Enterococcus faecalis, Staphylococcus aureus, and Streptococcus pneumonia bacterial strains were cultured in the dark with varying AE concentrations and later irradiated with 72 J/cm-2 light. Colony and biofilm formation was determined. CCK-8, Griess reagent reaction, and ELISA assays were done on bacteria-infected RAW264.7 cells to determine the cell viability, NO, and IL-1β and IL-6 pro-inflammatory cytokines responses, respectively. Hemolysis and western blot assays were done to determine the effect of treatment on hemolysis activity and sepsis-associated toxins expressions. AE-mediated PDT reduced bacterial survival in a dose-dependent manner with 32 μg/ml of AE almost eliminating their survival. Cell proliferation, NO, IL-1β, and IL-6 cytokines production were also significantly downregulated. Further, the hemolytic activities and expressions of cytolysin, hemolysin, and pneumolysin were significantly reduced following AE-mediated PDT. In conclusion, combined use of AE and light (435 ± 10 nm) inactivates MRSA, S. aureus (ATCC 29213), S. pneumoniae (ATCC 49619), MDR-S. pneumoniae, E. faecalis (ATCC 29212), and VRE (ATCC 51299) in an AE-dose dependent manner. AE and light are also effective in reducing biofilm formations, suppressing pro-inflammatory cytokines, hemolytic activities, and inhibiting the expressions of toxins that cause sepsis.
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Affiliation(s)
- Woodvine Otieno
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710061, P.R. China
| | - Chengcheng Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710061, P.R. China
| | - Yanhong Ji
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710061, P.R. China
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Medapati MR, Bhagirath AY, Singh N, Schroth RJ, Bhullar RP, Duan K, Chelikani P. Bitter Taste Receptor T2R14 Modulates Gram-Positive Bacterial Internalization and Survival in Gingival Epithelial Cells. Int J Mol Sci 2021; 22:ijms22189920. [PMID: 34576085 PMCID: PMC8469602 DOI: 10.3390/ijms22189920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 01/01/2023] Open
Abstract
Bitter-taste receptors (T2Rs) have emerged as key players in host–pathogen interactions and important modulators of oral innate immunity. Previously, we reported that T2R14 is expressed in gingival epithelial cells (GECs) and interacts with competence stimulating peptides (CSPs) secreted by the cariogenic Streptococcus mutans. The underlying mechanisms of the innate immune responses and physiological effects of T2R14 on Gram-positive bacteria are not well characterized. In this study, we examined the role of T2R14 in internalization and growth inhibitory effects on Gram-positive bacteria, namely Staphylococcus aureus and S. mutans. We utilized CRISPR-Cas9 T2R14 knockdown (KD) GECs as the study model to address these key physiological mechanisms. Our data reveal that the internalization of S. aureus is significantly decreased, while the internalization of S. mutans remains unaffected upon knockdown of T2R14 in GECs. Surprisingly, GECs primed with S. mutans CSP-1 resulted in an inhibition of growth for S. aureus, but not for S. mutans. The GECs infected with S. aureus induced T2R14-dependent human β-defensin-2 (hBD-2) secretion; however, S. mutans–infected GECs did not induce hBD-2 secretion, but induced T2R14 dependent IL-8 secretion. Interestingly, our results show that T2R14 KD affects the cytoskeletal reorganization in GECs, thereby inhibiting S. aureus internalization. Our study highlights the distinct mechanisms and a direct role of T2R14 in influencing physiological responses to Gram-positive bacteria in the oral cavity.
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Affiliation(s)
- Manoj Reddy Medapati
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
| | - Anjali Yadav Bhagirath
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
- Children’s Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Nisha Singh
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
| | - Robert J. Schroth
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
- Children’s Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
- Department of Preventive Dental Sciences, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada
| | - Rajinder P. Bhullar
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
| | - Kangmin Duan
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
- Children’s Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Prashen Chelikani
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, Rady Faculty of Health Sciences, Dr. Gerald Niznick College of Dentistry, University of Manitoba, 780 Bannatyne Avenue, Winnipeg, MB R3E 0W2, Canada; (M.R.M.); (A.Y.B.); (N.S.); (R.J.S.); (R.P.B.); (K.D.)
- Children’s Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
- Correspondence: ; Tel.: +1-204-789-3539; Fax: +1-204-789-3913
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Dalal N, Jalandra R, Bayal N, Yadav AK, Sharma M, Makharia GK, Kumar P, Singh R, Solanki PR, Kumar A. Gut microbiota-derived metabolites in CRC progression and causation. J Cancer Res Clin Oncol 2021; 147:3141-3155. [PMID: 34273006 DOI: 10.1007/s00432-021-03729-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/04/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities. PURPOSE In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development. CONCLUSION Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Nitin Bayal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Amit K Yadav
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, 110029, India
| | - Pramod Kumar
- Sri Aurobindo College, Delhi University, New Delhi, 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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Avican K, Aldahdooh J, Togninalli M, Mahmud AKMF, Tang J, Borgwardt KM, Rhen M, Fällman M. RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection. Nat Commun 2021; 12:3282. [PMID: 34078900 PMCID: PMC8172932 DOI: 10.1038/s41467-021-23588-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific 'universal stress responders', that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).
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Affiliation(s)
- Kemal Avican
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| | - Jehad Aldahdooh
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matteo Togninalli
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - A K M Firoj Mahmud
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jing Tang
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Karsten M Borgwardt
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Mikael Rhen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden
| | - Maria Fällman
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
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Handayani I, Saad H, Ratnakomala S, Lisdiyanti P, Kusharyoto W, Krause J, Kulik A, Wohlleben W, Aziz S, Gross H, Gavriilidou A, Ziemert N, Mast Y. Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. Mar Drugs 2021; 19:316. [PMID: 34071728 PMCID: PMC8227522 DOI: 10.3390/md19060316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
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Affiliation(s)
- Ira Handayani
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
- Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Shanti Ratnakomala
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia;
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Wien Kusharyoto
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor KM.46, Cibinong, West Java 16911, Indonesia; (P.L.); (W.K.)
| | - Janina Krause
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Andreas Kulik
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
| | - Saefuddin Aziz
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany; (H.S.); (S.A.); (H.G.)
| | - Athina Gavriilidou
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
| | - Nadine Ziemert
- Applied Natural Products Genome Mining, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (A.G.); (N.Z.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Yvonne Mast
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen (IMIT), Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (I.H.); (J.K.); (A.K.); (W.W.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Department of Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Department of Microbiology, Technical University of Braunschweig, 38124 Braunschweig, Germany
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Wagstaff BA, Zorzoli A, Dorfmueller HC. NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature. Biochem J 2021; 478:685-701. [PMID: 33599745 DOI: 10.1042/bcj20200505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022]
Abstract
Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.
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Affiliation(s)
- Ben A Wagstaff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, U.K
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Azul Zorzoli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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Linciano P, Cavalloro V, Martino E, Kirchmair J, Listro R, Rossi D, Collina S. Tackling Antimicrobial Resistance with Small Molecules Targeting LsrK: Challenges and Opportunities. J Med Chem 2020; 63:15243-15257. [PMID: 33152241 PMCID: PMC8016206 DOI: 10.1021/acs.jmedchem.0c01282] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is a growing threat with severe health and economic consequences. The available antibiotics are losing efficacy, and the hunt for alternative strategies is a priority. Quorum sensing (QS) controls biofilm and virulence factors production. Thus, the quenching of QS to prevent pathogenicity and to increase bacterial susceptibility to antibiotics is an appealing therapeutic strategy. The phosphorylation of autoinducer-2 (a mediator in QS) by LsrK is a crucial step in triggering the QS cascade. Thus, LsrK represents a valuable target in fighting AMR. Few LsrK inhibitors have been reported so far, allowing ample room for further exploration. This perspective aims to provide a comprehensive analysis of the current knowledge about the structural and biological properties of LsrK and the state-of-the-art technology for LsrK inhibitor design. We elaborate on the challenges in developing novel LsrK inhibitors and point out promising avenues for further research.
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Affiliation(s)
- Pasquale Linciano
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Valeria Cavalloro
- Department
of Earth and Environmental Science, University
of Pavia, Via Sant’Epifanio 14, 27100 Pavia, Italy
| | - Emanuela Martino
- Department
of Earth and Environmental Science, University
of Pavia, Via Sant’Epifanio 14, 27100 Pavia, Italy
| | - Johannes Kirchmair
- Department
of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Roberta Listro
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Simona Collina
- Department
of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy
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Sorensen M, Chandler CE, Gardner FM, Ramadan S, Khot PD, Leung LM, Farrance CE, Goodlett DR, Ernst RK, Nilsson E. Rapid microbial identification and colistin resistance detection via MALDI-TOF MS using a novel on-target extraction of membrane lipids. Sci Rep 2020; 10:21536. [PMID: 33299017 PMCID: PMC7725828 DOI: 10.1038/s41598-020-78401-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 12/18/2022] Open
Abstract
Rapid infection diagnosis is critical to improving patient treatment and outcome. Recent studies have shown microbial lipids to be sensitive and selective biomarkers for identifying bacterial and fungal species and antimicrobial resistance. Practical procedures for microbial lipid biomarker analysis will therefore improve patient outcomes and antimicrobial stewardship. However, current lipid extraction methods require significant hands-on time and are thus not suited for direct adoption as a clinical assay for microbial identification. Here, we have developed a method for lipid extraction directly on the surface of stainless-steel matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) plates, termed fast lipid analysis technique or FLAT, which facilitates the identification of bacterial and fungal species using a sub-60-minute workflow. Additionally, our method detects lipid A modifications in Gram-negative bacteria that are associated with antimicrobial resistance, including to colistin.
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Affiliation(s)
| | - Courtney E Chandler
- Pataigin, LLC, Seattle, WA, USA
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
- Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Francesca M Gardner
- Pataigin, LLC, Seattle, WA, USA
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
| | | | | | - Lisa M Leung
- Maryland Department of Health and Mental Hygiene, Baltimore, MD, 21205, USA
- U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | - David R Goodlett
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdańsk, Poland
| | - Robert K Ernst
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA.
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Wang C, Wu J, Xu L, Zou Q. NonClasGP-Pred: robust and efficient prediction of non-classically secreted proteins by integrating subset-specific optimal models of imbalanced data. Microb Genom 2020; 6:mgen000483. [PMID: 33245691 PMCID: PMC8116686 DOI: 10.1099/mgen.0.000483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
Non-classically secreted proteins (NCSPs) are proteins that are located in the extracellular environment, although there is a lack of known signal peptides or secretion motifs. They usually perform different biological functions in intracellular and extracellular environments, and several of their biological functions are linked to bacterial virulence and cell defence. Accurate protein localization is essential for all living organisms, however, the performance of existing methods developed for NCSP identification has been unsatisfactory and in particular suffer from data deficiency and possible overfitting problems. Further improvement is desirable, especially to address the lack of informative features and mining subset-specific features in imbalanced datasets. In the present study, a new computational predictor was developed for NCSP prediction of gram-positive bacteria. First, to address the possible prediction bias caused by the data imbalance problem, ten balanced subdatasets were generated for ensemble model construction. Then, the F-score algorithm combined with sequential forward search was used to strengthen the feature representation ability for each of the training subdatasets. Third, the subset-specific optimal feature combination process was adopted to characterize the original data from different aspects, and all subdataset-based models were integrated into a unified model, NonClasGP-Pred, which achieved an excellent performance with an accuracy of 93.23 %, a sensitivity of 100 %, a specificity of 89.01 %, a Matthew's correlation coefficient of 87.68 % and an area under the curve value of 0.9975 for ten-fold cross-validation. Based on assessment on the independent test dataset, the proposed model outperformed state-of-the-art available toolkits. For availability and implementation, see: http://lab.malab.cn/~wangchao/softwares/NonClasGP/.
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Affiliation(s)
- Chao Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, PR China
| | - Jin Wu
- School of Management, Shenzhen Polytechnic, Shenzhen, PR China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, PR China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, PR China
- Hainan Key Laboratory for Computational Science and Application, Hainan Normal University, Haikou, PR China
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Sułek A, Pucelik B, Kobielusz M, Barzowska A, Dąbrowski JM. Photodynamic Inactivation of Bacteria with Porphyrin Derivatives: Effect of Charge, Lipophilicity, ROS Generation, and Cellular Uptake on Their Biological Activity In Vitro. Int J Mol Sci 2020; 21:ijms21228716. [PMID: 33218103 PMCID: PMC7698881 DOI: 10.3390/ijms21228716] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Resistance of microorganisms to antibiotics has led to research on various therapeutic strategies with different mechanisms of action, including photodynamic inactivation (PDI). In this work, we evaluated a cationic, neutral, and anionic meso-tetraphenylporphyrin derivative’s ability to inactivate the Gram-negative and Gram-positive bacteria in a planktonic suspension under blue light irradiation. The spectroscopic, physicochemical, redox properties, as well as reactive oxygen species (ROS) generation capacity by a set of photosensitizers varying in lipophilicity were investigated. The theoretical calculations were performed to explain the distribution of the molecular charges in the evaluated compounds. Moreover, logP partition coefficients, cellular uptake, and phototoxicity of the photosensitizers towards bacteria were determined. The role of a specific microbial efflux pump inhibitor, verapamil hydrochloride, in PDI was also studied. The results showed that E. coli exhibited higher resistance to PDI than S. aureus (3–5 logs) with low light doses (1–10 J/cm2). In turn, the prolongation of irradiation (up to 100 J/cm2) remarkably improved the inactivation of pathogens (up to 7 logs) and revealed the importance of photosensitizer photostability. The PDI potentiation occurs after the addition of KI (more than 3 logs extra killing). Verapamil increased the uptake of photosensitizers (especially in E. coli) due to efflux pump inhibition. This effect suggests that PDI is mediated by ROS, the electrostatic charge interaction, and the efflux of photosensitizers (PSs) regulated by multidrug-resistance (MDR) systems. Thus, MDR inhibition combined with PDI gives opportunities to treat more resistant bacteria.
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Affiliation(s)
- Adam Sułek
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland; (A.S.); (M.K.)
| | - Barbara Pucelik
- Małopolska Center of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (B.P.); (A.B.)
| | - Marcin Kobielusz
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland; (A.S.); (M.K.)
| | - Agata Barzowska
- Małopolska Center of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (B.P.); (A.B.)
| | - Janusz M. Dąbrowski
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland; (A.S.); (M.K.)
- Correspondence: ; Tel.: +48-12-686-2488; Fax: +48-12-686-2750
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50
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Jeckelmann JM, Erni B. The mannose phosphotransferase system (Man-PTS) - Mannose transporter and receptor for bacteriocins and bacteriophages. Biochim Biophys Acta Biomembr 2020; 1862:183412. [PMID: 32710850 DOI: 10.1016/j.bbamem.2020.183412] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
Mannose transporters constitute a superfamily (Man-PTS) of the Phosphoenolpyruvate Carbohydrate Phosphotransferase System (PTS). The membrane complexes are homotrimers of protomers consisting of two subunits, IIC and IID. The two subunits without recognizable sequence similarity assume the same fold, and in the protomer are structurally related by a two fold pseudosymmetry axis parallel to membrane-plane (Liu et al. (2019) Cell Research 29 680). Two reentrant loops and two transmembrane helices of each subunit together form the N-terminal transport domain. Two three-helix bundles, one of each subunit, form the scaffold domain. The protomer is stabilized by a helix swap between these bundles. The two C-terminal helices of IIC mediate the interprotomer contacts. PTS occur in bacteria and archaea but not in eukaryotes. Man-PTS are abundant in Gram-positive bacteria living on carbohydrate rich mucosal surfaces. A subgroup of IICIID complexes serve as receptors for class IIa bacteriocins and as channel for the penetration of bacteriophage lambda DNA across the inner membrane. Some Man-PTS are associated with host-pathogen and -symbiont processes.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
| | - Bernhard Erni
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
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