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Dong CS, Zhang WL, Wang XY, Wang X, Wang J, Wang M, Fang Y, Liu L. Crystallographic and functional studies of a plant temperature-induced lipocalin. Biochim Biophys Acta Gen Subj 2024; 1868:130540. [PMID: 38103756 DOI: 10.1016/j.bbagen.2023.130540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Arabidopsis thaliana temperature-induced lipocalin (AtTIL) is a prototypical member of plant lipocalins and participates in a variety of cellular processes, particularly stress responses. Bioinformatical and physiological studies have proposed its promiscuous ligand-binding ability, but the molecular basis is yet unclear. Here, we report the 1.9-Å crystal structure of AtTIL in complex with heme. Spectrophotometric absorbance titration with heme yields a dissociation constant of ∼2 micromolar, indicating the relatively weak interaction between AtTIL and heme, which is confirmed by the AtTIL-heme structure. Although binding to retinal or biliverdin is not detected, such possibility can not be precluded as suggested by comparison with other lipocalin structures. These results show that AtTIL is a structural and functional homolog of the bacterial lipocalin Blc.
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Affiliation(s)
- Chen-Song Dong
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Wei-Lun Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Xiao-Ying Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Jia Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Ying Fang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.
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2
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Sen O, Hinks J, Lin Q, Lin Q, Kjelleberg S, Rice SA, Seviour T. Escherichia coli displays a conserved membrane proteomic response to a range of alcohols. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:147. [PMID: 37789404 PMCID: PMC10546733 DOI: 10.1186/s13068-023-02401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Alcohol is a good and environment-friendly fuel that can be microbially produced, capable of eliminating many of the limitations of the present-day fossil fuels. However, the inherent toxic nature of alcohols to the microbial cells leads to end-product inhibition that limits large-scale alcohol production by fermentation. Fundamental knowledge about the stress responses of microorganisms to alcohols would greatly facilitate to improve the microbial alcohol tolerance. The current study elucidates and compares the changes in the membrane proteome of Escherichia coli in response to a range of alcohols. RESULTS Although alcohol toxicity increased exponentially with alcohol chain length (2-6 carbon), similar stress responses were observed in the inner and outer membrane proteome of E. coli in the presence of 2-, 4- and 6-carbon alcohols at the MIC50. This pertains to: (1) increased levels of inner membrane transporters for uptake of energy-producing metabolites, (2) reduced levels of non-essential proteins, associated with anaerobic, carbon starvation and osmotic stress, for energy conservation, (3) increased levels of murein degrading enzymes (MltA, EmtA, MliC and DigH) promoting cell elongation and 4) reduced levels of most outer membrane β-barrel proteins (LptD, FadL, LamB, TolC and BamA). Major outer membrane β-barrel protein OmpC, which is known to contribute to ethanol tolerance and membrane integrity, was notably reduced by alcohol stress. While LPS is important for OmpC trimerisation, LPS release by EDTA did not lower OmpC levels. This suggests that LPS release, which is reported under alcohol stress, does not contribute to the reduced levels of OmpC in the presence of alcohol. CONCLUSIONS Since alcohol primarily targets the integrity of the membrane, maintenance of outer membrane OmpC levels in the presence of alcohol might help in the survival of E. coli to higher alcohol concentrations. The study provides important information about the membrane protein responses of E. coli to a range of alcohols, which can be used to develop targeted strategies for increased microbial alcohol tolerance and hence bioalcohol production.
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Affiliation(s)
- Oishi Sen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Australian Institute for Microbiology and Immunology, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Sydney, Australia
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- WATEC Aarhus University Centre for Water Technology, Universitetsbyen 36, Bldg 1783, 8000, Aarhus, Denmark.
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3
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Bagel A, Lopez C, David-Briand E, Michel V, Douëllou T, Sergentet D. Serotype-dependent adhesion of Shiga toxin-producing Escherichia coli to bovine milk fat globule membrane proteins. Front Microbiol 2022; 13:1010665. [PMID: 36504830 PMCID: PMC9731836 DOI: 10.3389/fmicb.2022.1010665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are food-borne pathogens that can cause severe symptoms for humans. Raw milk products are often incriminated as vehicule for human STEC infection. However, raw milk naturally contains molecules, such as the milk fat globule membrane and associated proteins, that could inhibit pathogen adhesion by acting as mimetic ligands. This study aimed to: (i) evaluate the capability of STEC cells to adhere to bovine milk fat globule membrane proteins (MFGMPs), (ii) highlight STEC surface proteins associated with adhesion and (iii) evaluate the variation between different STEC serotypes. We evaluated the physicochemical interactions between STEC and milk fat globules (MFGs) by analyzing hydrophobic properties and measuring the ζ-potential. We used a plate adhesion assay to assess adhesion between MFGMPs and 15 Escherichia coli strains belonging to three key serotypes (O157:H7, O26:H11, and O103:H2). A relative quantitative proteomic approach was conducted by mass spectrometry to identify STEC surface proteins that may be involved in STEC-MFG adhesion. The majority of E. coli strains showed a hydrophilic profile. The ζ-potential values were between -3.7 and - 2.9 mV for the strains and between -12.2 ± 0.14 mV for MFGs. Our results suggest that non-specific interactions are not strongly involved in STEC-MFG association and that molecular bonds could form between STEC and MFGs. Plate adhesion assays showed a weak adhesion of O157:H7 E. coli strains to MFGMPs. In contrast, O26:H11 and O103:H2 serotypes attached more to MFGMPs. Relative quantitative proteomic analysis showed that the O26:H11 str. 21,765 differentially expressed five outer membrane-associated proteins or lipoproteins compared with the O157:H7 str. EDL933. This analysis also found strain-specific differentially expressed proteins, including four O26:H11 str. 21,765-specific proteins/lipoproteins and eight O103:H2 str. PMK5-specific proteins. For the first time, we demonstrated STEC adhesion to MFGMPs and discovered a serotype effect. Several outer membrane proteins-OmpC and homologous proteins, intimin, Type 1 Fimbriae, and AIDA-I-that may be involved in STEC-MFG adhesion were highlighted. More research on STEC's ability to adhere to MFGMs in diverse biological environments, such as raw milk cheeses and the human gastrointestinal tract, is needed to confirm the anti-adhesion properties of the STEC-MFG complex.
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Affiliation(s)
- Arthur Bagel
- Bacterial Opportunistic Pathogens and Environment Research Group, UMR5557 Ecologie Microbienne Lyon, National Center of Scientific Research (CNRS), Université de Lyon, Marcy-l’Etoile, France
| | | | | | | | - Thomas Douëllou
- Bacterial Opportunistic Pathogens and Environment Research Group, UMR5557 Ecologie Microbienne Lyon, National Center of Scientific Research (CNRS), Université de Lyon, Marcy-l’Etoile, France
| | - Delphine Sergentet
- Bacterial Opportunistic Pathogens and Environment Research Group, UMR5557 Ecologie Microbienne Lyon, National Center of Scientific Research (CNRS), Université de Lyon, Marcy-l’Etoile, France,Laboratoire d’Etudes des Microorganismes Alimentaires Pathogènes, VetAgro Sup—Campus Vétérinaire, French National Reference Laboratory for Escherichia coli Including Shiga Toxin-Producing E. coli (NRL-STEC), Université de Lyon, Marcy-l‘Etoile, France,*Correspondence: Delphine Sergentet,
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Palladino G, Caroselli E, Tavella T, D'Amico F, Prada F, Mancuso A, Franzellitti S, Rampelli S, Candela M, Goffredo S, Biagi E. Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO 2 gradient. ISME COMMUNICATIONS 2022; 2:65. [PMID: 37938252 PMCID: PMC9723718 DOI: 10.1038/s43705-022-00152-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 05/13/2023]
Abstract
Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.
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Affiliation(s)
- Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Erik Caroselli
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Teresa Tavella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Fiorella Prada
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Arianna Mancuso
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Silvia Franzellitti
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Sant'Alberto 163, 48123, Ravenna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy.
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
| | - Stefano Goffredo
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
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5
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J. Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput Biol 2021; 17:e1009555. [PMID: 34748541 PMCID: PMC8601599 DOI: 10.1371/journal.pcbi.1009555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed. Computational approaches have recently made significant progress in the protein engineering field evolving from a tool for helping experimentalists to prioritize or short-list mutations for testing to being capable of making fully reliable predictions. However, not all the fields of protein modeling are evolving at a similar pace. That is why evaluating the capabilities of computational tools on different tasks is important to provide other scientists with up-to-date information on the state of the field. Here we tested the performance of Rosetta (one of the leading macromolecule modeling tools) in improving small molecule-binding proteins. We successfully redesigned a fluorogen binding protein DiB1 –a protein that binds a non-fluorescent molecule and enforces its fluorescence in the obtained complex–for improved brightness and better performance in super-resolution imaging. Our results suggest that such tasks can be already achieved without laborious library screenings. However, the flexibility of the proteins might still be underestimated during standard modeling protocols and should be closely evaluated.
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Affiliation(s)
- Nina G. Bozhanova
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joel M. Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brian J. Bender
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Christina B. Mercado
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xuan Zhang
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | - Alexander S. Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- * E-mail:
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7
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Ressurreição M, van Ooij C. Lipid transport proteins in malaria, from Plasmodium parasites to their hosts. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:159047. [PMID: 34461309 DOI: 10.1016/j.bbalip.2021.159047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022]
Abstract
Eukaryotic unicellular pathogens from the genus Plasmodium are the etiological agents of malaria, a disease that persists over a wide range of vertebrate species, including humans. During its dynamic lifecycle, survival in the different hosts depends on the parasite's ability to establish a suitable environmental milieu. To achieve this, specific host processes are exploited to support optimal growth, including extensive modifications to the infected host cell. These modifications include the formation of novel membranous structures, which are induced by the parasite. Consequently, to maintain a finely tuned and dynamic lipid environment, the organisation and distribution of lipids to different cell sites likely requires specialised lipid transfer proteins (LTPs). Indeed, several parasite and host-derived LTPs have been identified and shown to be essential at specific stages. Here we describe the roles of LTPs in parasite development and adaptation to its host including how the latest studies are profiting from the improved genetic, lipidomic and imaging toolkits available to study Plasmodium parasites. Lastly, a list of predicted Plasmodium LTPs is provided to encourage research in this field.
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Affiliation(s)
- Margarida Ressurreição
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
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8
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Burda PC, Crosskey T, Lauk K, Zurborg A, Söhnchen C, Liffner B, Wilcke L, Pietsch E, Strauss J, Jeffries CM, Svergun DI, Wilson DW, Wilmanns M, Gilberger TW. Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum. Cell Rep 2021; 31:107817. [PMID: 32579913 DOI: 10.1016/j.celrep.2020.107817] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/19/2020] [Accepted: 06/03/2020] [Indexed: 02/06/2023] Open
Abstract
Proteins of the lipocalin family are known to bind small hydrophobic ligands and are involved in various physiological processes ranging from lipid transport to oxidative stress responses. The genome of the malaria parasite Plasmodium falciparum contains a single protein PF3D7_0925900 with a lipocalin signature. Using crystallography and small-angle X-ray scattering, we show that the protein has a tetrameric structure of typical lipocalin monomers; hence we name it P. falciparum lipocalin (PfLCN). We show that PfLCN is expressed in the intraerythrocytic stages of the parasite and localizes to the parasitophorous and food vacuoles. Conditional knockdown of PfLCN impairs parasite development, which can be rescued by treatment with the radical scavenger Trolox or by temporal inhibition of hemoglobin digestion. This suggests a key function of PfLCN in counteracting oxidative stress-induced cell damage during multiplication of parasites within erythrocytes.
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Affiliation(s)
- Paul-Christian Burda
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany.
| | - Thomas Crosskey
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
| | - Katharina Lauk
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Aimo Zurborg
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Christoph Söhnchen
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Benjamin Liffner
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Louisa Wilcke
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Emma Pietsch
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Jan Strauss
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany.
| | - Tim-Wolf Gilberger
- Centre for Structural Systems Biology, 22607 Hamburg, Germany; Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; University of Hamburg, 20146 Hamburg, Germany.
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9
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Bozhanova NG, Calcutt MW, Beavers WN, Brown BP, Skaar EP, Meiler J. Lipocalin Blc is a potential heme-binding protein. FEBS Lett 2020; 595:206-219. [PMID: 33210733 PMCID: PMC8177097 DOI: 10.1002/1873-3468.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022]
Abstract
Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin P Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Discovery, Medical School, Leipzig University, Germany
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10
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Muslinkina L, Gavrikov AS, Bozhanova NG, Mishin AS, Baranov MS, Meiler J, Pletneva NV, Pletnev VZ, Pletnev S. Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy. ACS Chem Biol 2020; 15:2456-2465. [PMID: 32809793 DOI: 10.1021/acschembio.0c00440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-resolution fluorescent imaging in living cells remains technically challenging, largely due to the photodecomposition of fluorescent tags. The recently suggested protein-PAINT is the only super-resolution technique available for prolonged imaging of proteins in living cells. It is realized with complexes of fluorogen-activating proteins, expressed as fusions, and solvatochromic synthetic dyes. Once photobleached, the dye in the complex is replaced with a fresh fluorogen available in the sample. With suitable kinetics, this replacement creates fluorescence blinking required for attaining super-resolution and overcomes photobleaching associated with the loss of an irreplaceable fluorophore. Here we report on the rational design of two protein-PAINT tags based on the 1.58 Å crystal structure of the DiB1:M739 complex, an improved green-emitting DiB3/F74V:M739 and a new orange-emitting DiB3/F53L:M739. They outperform previously reported DiB-based tags to become best in class biomarkers for protein-PAINT. The new tags advance protein-PAINT from the proof-of-concept to a reliable tool suitable for prolonged super-resolution imaging of intracellular proteins in fixed and living cells and two-color PAINT-like nanoscopy with a single fluorogen.
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Affiliation(s)
- Liya Muslinkina
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
| | - Alexey S. Gavrikov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Nina G. Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Alexander S. Mishin
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Mikhail S. Baranov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Nadya V. Pletneva
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergei Pletnev
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
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11
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Bozhanova NG, Gavrikov AS, Mishin AS, Meiler J. DiB-splits: nature-guided design of a novel fluorescent labeling split system. Sci Rep 2020; 10:11049. [PMID: 32632329 PMCID: PMC7338535 DOI: 10.1038/s41598-020-67095-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
Fluorogen-activating proteins (FAPs) are innovative fluorescent probes combining advantages of genetically-encoded proteins such as green fluorescent protein and externally added fluorogens that allow for highly tunable and on demand fluorescent signaling. Previously, a panel of green- and red-emitting FAPs has been created from bacterial lipocalin Blc (named DiBs). Here we present a rational design as well as functional and structural characterization of the first self-assembling FAP split system, DiB-splits. This new system decreases the size of the FAP label to ~8-12 kDa while preserving DiBs' unique properties: strong increase in fluorescence intensity of the chromophore upon binding, binding affinities to the chromophore in nanomolar to low micromolar range, and high photostability of the protein-ligand complex. These properties allow for use of DiB-splits for wide-field, confocal, and super-resolution fluorescence microscopy. DiB-splits also represent an attractive starting point for further design of a protein-protein interaction detection system as well as novel FAP-based sensors.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany.
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12
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Fluorescent Tags in Biology: Three-Dimensional Structure. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Lu J, Wang Y, Zhang S, Bond P, Yuan Z, Guo J. Triclosan at environmental concentrations can enhance the spread of extracellular antibiotic resistance genes through transformation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136621. [PMID: 32019018 DOI: 10.1016/j.scitotenv.2020.136621] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 05/23/2023]
Abstract
The dissemination of antibiotic resistance mediated by horizontal transfer of antibiotic resistance genes (ARGs) is exacerbating the global antibiotic crisis. Currently, little is known about whether non-antibiotic, anti-microbial (NAAM) chemicals are associated with the dissemination of ARGs in the environment. In this study, we aimed to evaluate whether a ubiquitous NAAM chemical, triclosan (TCS), is able to promote the transformation of plasmid-borne antibiotic resistance genes (ARGs). By using the plasmid pUC19 carrying ampicillin resistance genes as the extracellular ARG and a model microorganism Escherichia coli DH5ɑ as the recipient, we found that TCS at environmentally detected concentrations (0.2 μg/L to 20 μg/L) significantly enhanced the transformation of plasmid-borne ARGs into E. coli DH5ɑ for up to 1.4-fold. The combination of phenotypic experiments, genome-wide RNA sequencing and proteomic analyses revealed that TCS exposure stimulated the reactive oxygen species (ROS) production for 1.3- to 1.5-fold, induced bacterial membrane damage and up-regulated the translation of outer membrane porin. Moreover, general secretion system Sec (1.4-fold), twin arginine translocation system Tat (1.2-fold) and type IV pilus secretion systems (2.5-fold) were enhanced by TCS, which might contribute to the DNA searching/capture by pilus. Together, TCS might increase the transformation frequency of ARGs into E. coli DH5ɑ by ROS over-production, damaging cell membrane barrier, mediating the pilus capture of plasmid and the translocation of plasmid via cell membrane channels. This study reports that TCS could accelerate the transformation of extracellular ARGs to competent bacteria at environmentally relevant concentrations. The findings advance our understanding of the fate of ARGs in ecosystems and call for risk assessments of NAAM chemicals on disseminating antibiotic resistance.
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Affiliation(s)
- Ji Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Yue Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Shuai Zhang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Philip Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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14
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Zook J, Shekhar M, Hansen D, Conrad C, Grant T, Gupta C, White T, Barty A, Basu S, Zhao Y, Zatsepin N, Ishchenko A, Batyuk A, Gati C, Li C, Galli L, Coe J, Hunter M, Liang M, Weierstall U, Nelson G, James D, Stauch B, Craciunescu F, Thifault D, Liu W, Cherezov V, Singharoy A, Fromme P. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure 2020; 28:540-547.e3. [PMID: 32142641 DOI: 10.1016/j.str.2020.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/23/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
Francisella tularensis is the causative agent for the potentially fatal disease tularemia. The lipoprotein Flpp3 has been identified as a virulence determinant of tularemia with no sequence homology outside the Francisella genus. We report a room temperature structure of Flpp3 determined by serial femtosecond crystallography that exists in a significantly different conformation than previously described by the NMR-determined structure. Furthermore, we investigated the conformational space and energy barriers between these two structures by molecular dynamics umbrella sampling and identified three low-energy intermediate states, transitions between which readily occur at room temperature. We have also begun to investigate organic compounds in silico that may act as inhibitors to Flpp3. This work paves the road to developing targeted therapeutics against tularemia and aides in our understanding of the disease mechanisms of tularemia.
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Affiliation(s)
- James Zook
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Mrinal Shekhar
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Center for the Development of TherapeuticsThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Debra Hansen
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie Conrad
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Thomas Grant
- Hauptman Woodward Institute, Jacobs School of Medicine and Biomedical Science, SUNY, Buffalo, NY 14260, USA
| | - Chitrak Gupta
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas White
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Anton Barty
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble, Grenoble Cedex 9 38042, France
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Alex Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Cornelius Gati
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Lorenzo Galli
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Meng Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Garret Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | | | - Felicia Craciunescu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Darren Thifault
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Abhishek Singharoy
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Petra Fromme
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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15
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Zhang J, Gao C, Yu XM, Lun HY, Du ZJ. Chryseobacterium lacus sp. nov. Isolated From the Surface Water of Two Lakes With Light-Induced Carotenoid Production. Front Microbiol 2020; 11:251. [PMID: 32194523 PMCID: PMC7064467 DOI: 10.3389/fmicb.2020.00251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
Two Gram-stain-negative, rod-shaped, gliding, catalase-positive, and facultative anaerobic strains, YLOS41T and XH07, were isolated from surface water of Yilong Lake and West Lake of Dali in Yunnan Province, respectively. Both strains were yellow-colored under light conditions and white-colored under dark conditions. The results of physiological and chemotaxonomic characterization, sequencing and phylogenetic analysis, and draft genome sequence comparison demonstrated that the two strains represented a single novel species within the genus Chryseobacterium, for which the name Chryseobacterium lacus sp. nov. is proposed. The type strain is YLOS41T (= KCTC 62352T = MCCC 1H00300T), and the second strain is XH07 (= KCTC 62993). During the cultivation process, we found that the colony color of the two strains changed from white to yellow with illumination. The study investigated the effects of light irradiation on the strain YLOS41T. Results showed that light irradiation did not affect the growth of cells but significantly increased carotenoid synthesis, which caused the change of colony color. In-depth metabolic analysis was conducted by transcriptome. The predominant changes were found for genes involved in carotenoid synthesis as protection from light damage. Based on the genome and transcriptome, we proved that strain YLOS41T possessed a complete synthetic pathway of carotenoid and speculated that the production was zeaxanthin. This was the first report of Chryseobacterium species with light-induced carotenoid synthesis. This study enhances our present knowledge on how Chryseobacterium species isolated from surface water responds to light damage.
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Affiliation(s)
- Jing Zhang
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cheng Gao
- Marine College, Shandong University, Weihai, China
| | - Xue-Mei Yu
- Marine College, Shandong University, Weihai, China
| | - He-Yuan Lun
- Marine College, Shandong University, Weihai, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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16
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Zou D, Pei J, Lan J, Sang H, Chen H, Yuan H, Wu D, Zhang Y, Wang Y, Wang D, Zou Y, Chen D, Ren J, Gao X, Lin Z. A SNP of bacterial blc disturbs gut lysophospholipid homeostasis and induces inflammation through epithelial barrier disruption. EBioMedicine 2020; 52:102652. [PMID: 32058942 PMCID: PMC7026729 DOI: 10.1016/j.ebiom.2020.102652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
Background Alteration of commensal bacterial composition is associated with many inflammatory diseases. However, few studies have pinpointed the specific bacterial genes that may suppress host immune responses against microbes and maintain homeostasis in the host intestine. Methods High-throughput screening was performed in Caenorhabditis elegans with a single gene knockout ut screening was performed in Caenorhabditis elegans with a single gene knockout Escherichia coli (E. coli) library and identified the immune suppression gene blc. The coding sequences of blc among different kinds of E. coli strains were aligned to identify the single nucleotide polymorphisms (SNPs). Physiological and biochemical experiments were performed in C. elegans and mice to explore the function of the blc variant. Findings By screening 3983 E. coli mutants, we discovered that 9 bacterial genes, when deleted, activate innate immunity in the host C. elegans. Among these 9 genes, the gene encoding blc showed a distinctive SNP in many clinically pathogenic bacteria. We found that bacteria with this SNP, which converts Blc G84 to Blc E84, are highly enriched in the faeces of patients with inflammatory bowel disease (IBD). Exposure to BlcE84-encoding bacteria resulted in epithelial barrier disruption and immune activation in both worms and mice. Detailed analysis indicated that infection with BlcE84-encoding bacteria causes a significant decrease in LPE levels in the intestine and subsequently disrupts gut epithelial integrity in mice. Consistently, the levels of LPE in patients with IBD are significantly lower than those in healthy people. Finally, supplementation with LPE, which activates LPA1/PLCβ/PKC signaling, reversed the defects induced by BlcE84-encoding bacteria. Interpretation Our results identified a novel bacterial gene, blc, in E. coli that regulates host gut integrity and immunity. Fund The Ministry of Science and Technology of China; the National Natural Science Foundation of China; and the Natural Science Foundation of Jiangsu Province.
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Affiliation(s)
- Dayuan Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Jingwen Pei
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Jianfeng Lan
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Hong Sang
- Department of Dermatology, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Hongjuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Haoliang Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Di Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Yuanyuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Yufang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Dingyu Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Yujie Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Jianan Ren
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China.
| | - Zhaoyu Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China.
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17
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di Masi A, Trezza V, Leboffe L, Ascenzi P. Human plasma lipocalins and serum albumin: Plasma alternative carriers? J Control Release 2016; 228:191-205. [PMID: 26951925 DOI: 10.1016/j.jconrel.2016.02.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/14/2023]
Abstract
Lipocalins are an evolutionarily conserved family of proteins that bind and transport a variety of exogenous and endogenous ligands. Lipocalins share a conserved eight anti-parallel β-sheet structure. Among the different lipocalins identified in humans, α-1-acid glycoprotein (AGP), apolipoprotein D (apoD), apolipoprotein M (apoM), α1-microglobulin (α1-m) and retinol-binding protein (RBP) are plasma proteins. In particular, AGP is the most important transporter for basic and neutral drugs, apoD, apoM, and RBP mainly bind endogenous molecules such as progesterone, pregnenolone, bilirubin, sphingosine-1-phosphate, and retinol, while α1-m binds the heme. Human serum albumin (HSA) is a monomeric all-α protein that binds endogenous and exogenous molecules like fatty acids, heme, and acidic drugs. Changes in the plasmatic levels of lipocalins and HSA are responsible for the onset of pathological conditions associated with an altered drug transport and delivery. This, however, does not necessary result in potential adverse effects in patients because many drugs can bind both HSA and lipocalins, and therefore mutual compensatory binding mechanisms can be hypothesized. Here, molecular and clinical aspects of ligand transport by plasma lipocalins and HSA are reviewed, with special attention to their role as alterative carriers in health and disease.
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Affiliation(s)
- Alessandra di Masi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy; Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy.
| | - Viviana Trezza
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Loris Leboffe
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy; Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy
| | - Paolo Ascenzi
- Istituto Nazionale di Biostrutture e Biosistemi, Via delle Medaglie d'Oro 305, I-00136 Roma, Italy; Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy
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18
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Sharma D, Ashaduzzaman M, Golabi M, Shriwastav A, Bisetty K, Tiwari A. Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses. ACS APPLIED MATERIALS & INTERFACES 2015; 7:23848-23856. [PMID: 26439810 DOI: 10.1021/acsami.5b06617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80-125 nm, surface area 20.27 m(2)/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antibacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antibacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electron spectroscopy (SEM) observation showed that the ZnO NHs ruptured the cell wall of bacteria and internalized into the cell. The molecular docking studies were carried out using binding proteins present in the gram negative bacteria (lipopolysaccharide and lipocalin Blc) and gram positive bacteria (Staphylococcal Protein A, SpA). It was envisaged that the proteins present in the bacterial cell wall were found to interact and adsorb on the surface of SIZnO NHs thereby blocking the active sites of the proteins used for cell wall synthesis. The binding affinity and interaction energies were higher in the case of binding proteins present in gram negative bacteria as compared to that of gram positive bacteria. In addition, a kinetic mathematical model (KMM) was developed in MATLAB to predict the internalization in the bacterial cellular uptake of the ZnO NHs for better understanding of their controlled toxicity. The results obtained from KMM exhibited a good agreement with the experimental data. Exploration of mechanistic interactions, as well as the formation of bioconjugate of proteins and ZnO NHs would play a key role to interpret more complex biological systems in nature.
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Affiliation(s)
- Deepali Sharma
- Department of Chemistry, Durban University of Technology , Durban 4000, South Africa
| | - Md Ashaduzzaman
- Biosensors and Bioelectronics Centre, IFM, Linköping University , Linköping 58183, Sweden
| | - Mohsen Golabi
- Biosensors and Bioelectronics Centre, IFM, Linköping University , Linköping 58183, Sweden
| | - Amritanshu Shriwastav
- Department of Civil Engineering, Indian Institute of Technology Kanpur , Kanpur 208016, Uttar Pradesh, India
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology , Durban 4000, South Africa
| | - Ashutosh Tiwari
- Biosensors and Bioelectronics Centre, IFM, Linköping University , Linköping 58183, Sweden
- Tekidag AB , UCS, Teknikringen 4A, Mjärdevi Science Park, Linköping 58330, Sweden
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19
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Franchini AG, Ihssen J, Egli T. Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth. PLoS One 2015. [PMID: 26204448 PMCID: PMC4512719 DOI: 10.1371/journal.pone.0133793] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya), were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σD with σS. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow, carbon-limited growth, whereas RpoS is primarily involved in the regulation of stress response systems necessary for the survival of this bacterium under hunger conditions.
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Affiliation(s)
- Alessandro G. Franchini
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
- * E-mail:
| | - Julian Ihssen
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
| | - Thomas Egli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
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20
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Abstract
Human meibomian gland secretions (MGS, or meibum) are formed from a complex mixture of lipids of different classes such as wax esters, cholesteryl esters, (O-acyl)-ω-hydroxy fatty acids (OAHFA) and their esters, acylglycerols, diacylated diols, free fatty acids, cholesterol, and a smaller amount of other polar and nonpolar lipids, whose chemical nature and the very presence in MGS have been a matter of intense debates. The purpose of this review is to discuss recent results that were obtained using different experimental techniques, estimate limitations of their usability, and discuss their biochemical, biophysical, and physiological implications. To create a lipid map of MGS and tears, the results obtained in the author's laboratory were integrated with available information on chemical composition of MGS and tears. The most informative approaches that are available today to researchers, such as HPLC-MS, GC-MS, and proton NMR, are discussed in details. A map of the meibomian lipidome (as it is seen in reverse phase liquid chromatography/mass spectrometry experiments) is presented. Directions of future efforts in the area are outlined.
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Affiliation(s)
- Igor A Butovich
- Department of Ophthalmology and the Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390-9057, USA.
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Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. Antimicrob Agents Chemother 2013; 57:3752-62. [PMID: 23716056 DOI: 10.1128/aac.02096-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance is often associated with metabolic costs. To investigate the metabolic consequences of antibiotic resistance, the genomic and transcriptomic profiles of an amoxicillin-resistant Escherichia coli strain and the wild type it was derived from were compared. A total of 125 amino acid substitutions and 7 mutations that were located <1,000 bp upstream of differentially expressed genes were found in resistant cells. However, broad induction and suppression of genes were observed when comparing the expression profiles of resistant and wild-type cells. Expression of genes involved in cell wall maintenance, DNA metabolic processes, cellular stress response, and respiration was most affected in resistant cells regardless of the absence or presence of amoxicillin. The SOS response was downregulated in resistant cells. The physiological effect of the acquisition of amoxicillin resistance in cells grown in chemostat cultures consisted of an initial increase in glucose consumption that was followed by an adaptation process. Furthermore, no difference in maintenance energy was observed between resistant and sensitive cells. In accordance with the transcriptomic profile, exposure of resistant cells to amoxicillin resulted in reduced salt and pH tolerance. Taken together, the results demonstrate that the acquisition of antibiotic resistance in E. coli is accompanied by specifically reorganized metabolic networks in order to circumvent metabolic costs. The overall effect of the acquisition of resistance consists not so much of an extra energy requirement, but more a reduced ecological range.
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Bukhari SA, Caetano-Anollés G. Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PLoS Comput Biol 2013; 9:e1003009. [PMID: 23555236 PMCID: PMC3610613 DOI: 10.1371/journal.pcbi.1003009] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/13/2013] [Indexed: 12/22/2022] Open
Abstract
The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable.
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Affiliation(s)
- Syed Abbas Bukhari
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
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Soma Y, Inokuma K, Tanaka T, Ogino C, Kondo A, Okamoto M, Hanai T. Direct isopropanol production from cellobiose by engineered Escherichia coli using a synthetic pathway and a cell surface display system. J Biosci Bioeng 2012; 114:80-5. [PMID: 22561882 DOI: 10.1016/j.jbiosc.2012.02.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 02/20/2012] [Accepted: 02/22/2012] [Indexed: 11/18/2022]
Abstract
Efficient bio-production from lignocellulosic biomass is required for the purpose of developing an inexpensive, practical bio-refinery process. As one approach to address this problem, we genetically engineered Escherichia coli to produce isopropanol directly from cellobiose via the cellobiose degradation by Beta-Glucosidase (BGL) on the cell surface. First, we investigated the cellobiose consumption of two E. coli strains with the BGL protein from Thermobifida fusca YX (Tfu0937) fused to the anchor protein Blc (Tfu0937/Blc) using different fusion sites. Next, we introduced the synthetic pathway for isopropanol production into those strains and compared their isopropanol production in the presence of glucose. Based on the results of these assays, TA212/pTA411, which was introduced Tfu-Blc fused protein expression system and the synthetic pathway for isopropanol production, was selected for the directly isopropanol production from cellobiose. TA212/pTA411 produced 69.0±11.6mM isopropanol at 21h of fermentation, whereas TA212/pTA147, which did not introduced the BGL/anchor fused protein but was introduced the synthetic pathway for isopropanol production, showed no cellobiose consumption and no isopropanol production during fermentation. To our knowledge, this is the first report of the production of a bio-product from cellobiose using E. coli.
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Affiliation(s)
- Yuki Soma
- Laboratory for Bioinformatics, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Mukherjee J, Karunakaran E, Biggs CA. Using a multi-faceted approach to determine the changes in bacterial cell surface properties influenced by a biofilm lifestyle. BIOFOULING 2012; 28:1-14. [PMID: 22150164 DOI: 10.1080/08927014.2011.639067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biofilm formation is a developmental process in which initial reversible adhesion is governed by physico-chemical forces, whilst irreversible adhesion is mediated by biological changes within a cell, such as the production of extracellular polymeric substances. Using two bacteria, E. coli MG1655 and B. cereus ATCC 10987, this study establishes that the surface of the bacterial cell also undergoes specific modifications, which result in biofilm formation and maintenance. Using various surface characterisation techniques and proteomics, an increase in the surface exposed proteins on E. coli cells during biofilm formation was demonstrated, along with an increase in hydrophobicity and a decrease in surface charge. For B. cereus, an increase in the surface polysaccharides during biofilm formation was found as well as a decrease in hydrophobicity and surface charge. This work therefore shows that surface modifications during biofilm formation occur and understanding these specific changes may lead to the formulation of effective biofilm control strategies in the future.
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Affiliation(s)
- Joy Mukherjee
- Department of Chemical and Biological Engineering, The ChELSI Institute, The University of Sheffield, Sheffield S1 3JD, UK
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Abstract
In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in Escherichia coli depends on the σS (RpoS) subunit of RNA polymerase. σS is closely related to the vegetative sigma factor σ70 (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σS is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σS levels, which mainly rely on the rapid inhibition of σS proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σS directly or indirectly activates more than 500 genes. Additional signal input is integrated by σS cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σS. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σS is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σS to specific environmental niches.
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Ozbalci Ç, Unsal Ç, Kazan D, Sariyar-Akbulut B. Proteomic response of Escherichia coli to the alkaloid extract of Papaver polychaetum. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0118-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Jobichen C, Fernandis AZ, Velazquez-Campoy A, Leung KY, Mok YK, Wenk MR, Sivaraman J. Identification and characterization of the lipid-binding property of GrlR, a locus of enterocyte effacement regulator. Biochem J 2009; 420:191-9. [PMID: 19228114 PMCID: PMC3672471 DOI: 10.1042/bj20081588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lipocalins are a broad family of proteins identified initially in eukaryotes and more recently in Gram-negative bacteria. The functions of lipocalin or lipid-binding proteins are often elusive and very diverse. Recently, we have determined the structure of GrlR (global regulator of LEE repressor), which plays a key role in the regulation of LEE (locus of enterocyte effacement) proteins. GrlR adopts a lipocalin-like fold that is composed of an eight-stranded beta-barrel followed by an alpha-helix at the C-terminus. GrlR has a highly hydrophobic cavity region and could be a potential transporter of lipophilic molecules. To verify this hypothesis, we carried out structure-based analysis of GrlR, determined the structure of the lipid-GrlR complex and measured the binding of lipid to recombinant GrlR by ITC (isothermal titration calorimetry). In addition, we identified phosphatidylglycerol and phosphatidylethanolamine as the endogenously bound lipid species of GrlR using electrospray-ionization MS. Furthermore, we have shown that the lipid-binding property of GrlR is similar to that of its closest lipocalin structural homologue, beta-lactoglobulin. Our studies demonstrate the hitherto unknown lipid-binding property of GrlR.
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Affiliation(s)
- Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Aaron Zefrin Fernandis
- Yong Loo Lin School of Medicine, Department of Biochemistry, Centre for Life Sciences, National University of Singapore, Singapore 117456
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), and Fundacion Aragon I+D (ARAID-BIFI), University of Zaragoza, Zaragoza 50009, Spain
| | - Ka Yin Leung
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- Faculty of Natural and Applied Sciences, Department of Biology, Trinity Western University, Langley, B.C., Canada V2Y 1Y1
| | - Yu-Keung Mok
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Markus R Wenk
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- Yong Loo Lin School of Medicine, Department of Biochemistry, Centre for Life Sciences, National University of Singapore, Singapore 117456
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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Adam B, Charloteaux B, Beaufays J, Vanhamme L, Godfroid E, Brasseur R, Lins L. Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling. BMC STRUCTURAL BIOLOGY 2008; 8:1. [PMID: 18190694 PMCID: PMC2254393 DOI: 10.1186/1472-6807-8-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 01/11/2008] [Indexed: 11/23/2022]
Abstract
Background Lipocalins are widely distributed in nature and are found in bacteria, plants, arthropoda and vertebra. In hematophagous arthropods, they are implicated in the successful accomplishment of the blood meal, interfering with platelet aggregation, blood coagulation and inflammation and in the transmission of disease parasites such as Trypanosoma cruzi and Borrelia burgdorferi. The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions. Results It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein. Conclusion By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.
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Affiliation(s)
- Benoit Adam
- Centre de Biophysique Moléculaire et Numérique, Faculté Universitaire des Sciences Agronomiques de Gembloux, Gembloux, Belgium.
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Vanini MMT, Spisni A, Sforça ML, Pertinhez TA, Benedetti CE. The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction. Proteins 2008; 71:2051-64. [DOI: 10.1002/prot.21886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Eichinger A, Nasreen A, Kim HJ, Skerra A. Structural Insight into the Dual Ligand Specificity and Mode of High Density Lipoprotein Association of Apolipoprotein D. J Biol Chem 2007; 282:31068-75. [PMID: 17699160 DOI: 10.1074/jbc.m703552200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human apolipoprotein D (ApoD) occurs in plasma associated with high density lipoprotein. Apart from the involvement in lipid metabolism, its binding activity for progesterone and arachidonic acid plays a role in cancer development and neurological diseases. The crystal structures of free ApoD and its complex with progesterone were determined at 1.8A resolution and reveal a lipocalin fold. The narrow, mainly uncharged pocket within the typical beta-barrel accommodates progesterone with its acetyl side chain oriented toward the bottom. The cavity adopts essentially the same shape in the absence of progesterone and allows complexation of arachidonic acid as another cognate ligand. Three of the four extended loops at the open end of the beta-barrel expose hydrophobic side chains, which is an unusual feature for lipocalins and probably effects association with the high density lipoprotein particle by mediating insertion into the lipid phase. This mechanism is in line with an unpaired Cys residue in the same surface region that can form a disulfide cross-link with apolipoprotein A-II.
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Affiliation(s)
- Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
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31
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Grzyb J, Latowski D, Strzałka K. Lipocalins - a family portrait. JOURNAL OF PLANT PHYSIOLOGY 2006; 163:895-915. [PMID: 16504339 DOI: 10.1016/j.jplph.2005.12.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 12/12/2005] [Indexed: 05/06/2023]
Abstract
Lipocalins are a widely distributed group of proteins whose common feature is the presence of six-or eight-stranded beta-barrel in their tertiary structure and highly conservative motifs short conserved region, (SCR) in their amino acid sequences. The presence of three SCRs is typical for kernel lipocalins, while outlier lipocalins have only one or two such regions. Owing to their ability to bind and transport small, hydrophobic molecules, lipocalins participate in the distribution of such substances. However, the physiological significance of lipocalins is not limited to transfer processes. They play an important role in the regulation of immunological and developmental processes, and are also involved in the reactions of organisms to various stress factors and in the pathways of signal transduction. Of special interest is the enzymatic activity found in a few members of the lipocalin family, as well as the interaction with natural membranes, both directly with lipids and through membrane-localized protein receptors.
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Affiliation(s)
- Joanna Grzyb
- Department of Plant Physiology and Biochemistry, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
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Campanacci V, Bishop RE, Blangy S, Tegoni M, Cambillau C. The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids. FEBS Lett 2006; 580:4877-83. [PMID: 16920109 PMCID: PMC5007124 DOI: 10.1016/j.febslet.2006.07.086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 07/26/2006] [Accepted: 07/28/2006] [Indexed: 11/16/2022]
Abstract
Lipocalins, a widespread multifunctional family of small proteins (15-25kDa) have been first described in eukaryotes and more recently in Gram-negative bacteria. Bacterial lipocalins belonging to class I are outer membrane lipoproteins, among which Blc from E. coli is the better studied. Blc is expressed under conditions of starvation and high osmolarity, conditions known to exert stress on the cell envelope. The structure of Blc that we have previously solved (V. Campanacci, D. Nurizzo, S. Spinelli, C. Valencia, M. Tegoni, C. Cambillau, FEBS Lett. 562 (2004) 183-188.) suggested its possible role in binding fatty acids or phospholipids. Both physiological and structural data on Blc, therefore, point to a role in storage or transport of lipids necessary for membrane maintenance. In order to further document this hypothesis for Blc function, we have performed binding studies using fluorescence quenching experiments. Our results indicate that dimeric Blc binds fatty acids and phospholipids in a micromolar K(d) range. The crystal structure of Blc with vaccenic acid, an unsaturated C18 fatty acid, reveals that the binding site spans across the Blc dimer, opposite to its membrane anchored face. An exposed unfilled pocket seemingly suited to bind a polar group attached to the fatty acid prompted us to investigate lyso-phospholipids, which were found to bind in a nanomolar K(d) range. We discuss these findings in terms of a potential role for Blc in the metabolism of lysophospholipids generated in the bacterial outer membrane.
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Affiliation(s)
- Valérie Campanacci
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre 4H19, 1200 Main Street West, Hamilton, Ont., Canada L8N 3Z5
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Mariella Tegoni
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
- Corresponding author. Fax: +33 491 266 720. (C. Cambillau)
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Zsila F, Matsunaga H, Bikádi Z, Haginaka J. Multiple ligand-binding properties of the lipocalin member chicken α1-acid glycoprotein studied by circular dichroism and electronic absorption spectroscopy: The essential role of the conserved tryptophan residue. Biochim Biophys Acta Gen Subj 2006; 1760:1248-73. [PMID: 16813999 DOI: 10.1016/j.bbagen.2006.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 04/19/2006] [Accepted: 04/25/2006] [Indexed: 11/28/2022]
Abstract
Multiple ligand-binding properties of the 30-kDa chicken alpha(1)-acid glycoprotein (cAGP), a member of the lipocalin protein family, were investigated for the first time by using circular dichroism (CD) and UV/Vis absorption spectroscopy methods. By measuring induced CD (ICD) spectra, high-affinity binding (K(a) approximately 10(5)-10(6) M(-1)) of several drugs, dyes and natural compounds to cAGP was demonstrated including antimalarial agents (quinacrine, primaquine), phenotiazines (chlorpromazine, methylene blue), propranolol, non-steroidal antiinflammatory drugs (ketoprofen, diclofenac), tamoxifen, diazepam, tacrine, dicoumarol, cationic dyes (auramine O, thioflavine T, ethidium bromide), benzo[a]pyrene, L-thyroxine, bile pigments (bilirubin, biliverdin), alkaloids (piperine, aristolochic acid), saturated and unsaturated fatty acids. Analysis of the extrinsic CD spectra with the study of the covalently modified protein and CD displacement experiments revealed that a single Trp26 residue of cAGP conserved in the whole lipocalin family is part of the binding site, and it is essentially involved in the ligand-binding process via pi-pi stacking interaction resulting in the appearance of strong induced CD bands due to the non-degenerate intermolecular exciton coupling between the pi-pi* transitions of the stacked indole ring-ligand chromophore. The finding that cAGP is able to accommodate a broad spectrum of ligands belonging to different chemical classes suggests that its core beta-barrel cavity is unusually wide containing overlapping sub-sites. Significance of these new data in understanding of the ligand-binding properties of other lipocalins, especially that of human AGP, and potential practical applications are briefly discussed. Overall, cAGP serves as a simple, ultimate model to extend our knowledge on ligand-binding properties of lipocalins and to study the role of tryptophan residues in molecular recognition processes.
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Affiliation(s)
- Ferenc Zsila
- Department of Molecular Pharmacology, Institute of Biomolecular Chemistry, Chemical Research Center, Budapest, P.O. Box 17, H-1525, Hungary.
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Paci E, Greene LH, Jones RM, Smith LJ. Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach. FEBS J 2005; 272:4826-38. [PMID: 16156801 DOI: 10.1111/j.1742-4658.2005.04898.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic conditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state. Simulation conformers, with a radius of gyration at least 1.1 A greater than that of the native state, contain on average 37%beta-sheet secondary structure. In these conformers the central regions of the two orthogonal beta-sheets that make up the beta-barrel in the native protein are highly persistent. However, there are sizable fluctuations for residues in the outer regions of the beta-sheets, and large variations in side chain packing even in the protein core. Significant conformational changes are seen in the simulation conformers for residues 85-104 (beta-strands E and F and the E-F loop). These changes give an opening of the retinol-binding site. Comparisons with experimental data suggest that the unfolding in this region may provide a mechanism by which the complex of retinol-binding protein and transthyretin dissociates, and retinol is released at the cell surface.
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Affiliation(s)
- Emanuele Paci
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of Leeds, UK.
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Malakhova ML, Malinina L, Pike HM, Kanack AT, Patel DJ, Brown RE. Point mutational analysis of the liganding site in human glycolipid transfer protein. Functionality of the complex. J Biol Chem 2005; 280:26312-20. [PMID: 15901739 PMCID: PMC1393170 DOI: 10.1074/jbc.m500481200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian glycolipid transfer proteins (GLTPs) facilitate the selective transfer of glycolipids between lipid vesicles in vitro. Recent structural determinations of the apo- and glycolipid-liganded forms of human GLTP have provided the first insights into the molecular architecture of the protein and its glycolipid binding site (Malinina, L., Malakhova, M. L., Brown, R. E., and Patel, D. J. (2004) Nature 430, 1048-1053). In the present study, we have evaluated the functional consequences of point mutation of the glycolipid liganding site of human GLTP within the context of a carrier-based mechanism of glycolipid intermembrane transfer. Different approaches were developed to rapidly and efficiently assess the uptake and release of glycolipid by GLTP. They included the use of glass-immobilized, glycolipid films to load GLTP with glycolipid and separation of GLTP/glycolipid complexes from vesicles containing glycolipid (galactosylceramide or lactosylceramide) or from monosialoganglioside dispersions by employing nickel-nitrilotriacetic acid-based affinity or gel filtration strategies. Point mutants of the sugar headgroup recognition center (Trp-96, Asp-48, Asn-52) and of the ceramide-accommodating hydrophobic tunnel (Phe-148, Phe-183, Leu-136) were analyzed for their ability to acquire and release glycolipid ligand. Two manifestations of point mutation within the liganding site were apparent: (i) impaired formation of the GLTP/glycolipid complex; (ii) impaired acquisition and release of bound glycolipid by GLTP. The results are consistent with a carrier-based mode of GLTP action to accomplish the intermembrane transfer of glycolipid. Also noteworthy was the inefficient release of glycolipid by wtGLTP into phosphatidylcholine acceptor vesicles, raising the possibility of a function other than intermembrane glycolipid transfer in vivo.
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Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, Privé GG. A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin. EMBO J 2004; 23:2931-41. [PMID: 15272304 PMCID: PMC514935 DOI: 10.1038/sj.emboj.7600320] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 06/18/2004] [Indexed: 11/08/2022] Open
Abstract
The ability of enzymes to distinguish between fatty acyl groups can involve molecular measuring devices termed hydrocarbon rulers, but the molecular basis for acyl-chain recognition in any membrane-bound enzyme remains to be defined. PagP is an outer membrane acyltransferase that helps pathogenic bacteria to evade the host immune response by transferring a palmitate chain from a phospholipid to lipid A (endotoxin). PagP can distinguish lipid acyl chains that differ by a single methylene unit, indicating that the enzyme possesses a remarkably precise hydrocarbon ruler. We present the 1.9 A crystal structure of PagP, an eight-stranded beta-barrel with an unexpected interior hydrophobic pocket that is occupied by a single detergent molecule. The buried detergent is oriented normal to the presumed plane of the membrane, whereas the PagP beta-barrel axis is tilted by approximately 25 degrees. Acyl group specificity is modulated by mutation of Gly88 lining the bottom of the hydrophobic pocket, thus confirming the hydrocarbon ruler mechanism for palmitate recognition. A striking structural similarity between PagP and the lipocalins suggests an evolutionary link between these proteins.
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Affiliation(s)
- Victoria E Ahn
- Department of Medical Biophysics, University of Toronto, Canada
| | - Eileen I Lo
- Department of Biochemistry, University of Toronto, Canada
| | - Christian K Engel
- Division of Molecular and Structural Biology, Ontario Cancer Institute, Canada
| | - Lu Chen
- Division of Molecular and Structural Biology, Ontario Cancer Institute, Canada
| | - Peter M Hwang
- Department of Biochemistry, University of Toronto, Canada
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Canada
- Department of Chemistry, University of Toronto, Canada
| | - Russell E Bishop
- Department of Biochemistry, University of Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
- 6213 Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8. E-mail:
| | - Gilbert G Privé
- Department of Medical Biophysics, University of Toronto, Canada
- Department of Biochemistry, University of Toronto, Canada
- Division of Molecular and Structural Biology, Ontario Cancer Institute, Canada
- Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9. Tel.: +1 416 946 2971; Fax: +1 416 946 6529; E-mail:
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