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Westensee IN, de Dios Andres P, Brodszkij E, Descours PL, Perez-Rodriguez D, Spinazzola A, Mookerjee RP, Städler B. Engineered Lipids for Intracellular Reactive Oxygen Species Scavenging in Steatotic Hepatocytes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400816. [PMID: 38949047 DOI: 10.1002/smll.202400816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/20/2024] [Indexed: 07/02/2024]
Abstract
Intracellular reactive oxygen species (ROS) in steatotic cells pose a problem due to their potential to cause oxidative stress and cellular damage. Delivering engineered phospholipids to intracellular lipid droplets in steatotic hepatic cells, using the cell's inherent intracellular lipid transport mechanisms are investigated. Initially, it is shown that tail-labeled fluorescent lipids assembled into liposomes are able to be transported to intracellular lipid droplets in steatotic HepG2 cells and HHL-5 cells. Further, an antioxidant, an EUK salen-manganese derivative, which has superoxide dismutase-like and catalase-like activity, is covalently conjugated to the tail of a phospholipid and formulated as liposomes for administration. Steatotic HepG2 cells and HHL-5 cells incubated with these antioxidant liposomes have lower intracellular ROS levels compared to untreated controls and non-covalently formulated antioxidants. This first proof-of-concept study illustrates an alternative strategy to equip native organelles in mammalian cells with engineered enzyme activity.
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Affiliation(s)
- Isabella N Westensee
- Interdisciplinarly Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Paula de Dios Andres
- Interdisciplinarly Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Edit Brodszkij
- Interdisciplinarly Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Pierre-Louis Descours
- Interdisciplinarly Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK
| | - Rajeshwar Prosad Mookerjee
- Institute for Liver and Digestive Health, University College London, Royal Free Campus, Rowland Hill Street, Hampstead, London, NW3 2PF, UK
| | - Brigitte Städler
- Interdisciplinarly Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
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2
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Lehman SS, Verhoeve VI, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates the origins of pathogen effectors. mBio 2024; 15:e0075923. [PMID: 38564675 PMCID: PMC11077975 DOI: 10.1128/mbio.00759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024] Open
Abstract
Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.
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Affiliation(s)
- Stephanie S. Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria I. Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timothy P. Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F. Beckmann
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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3
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van den Noort M, Drougkas P, Paulino C, Poolman B. The substrate-binding domains of the osmoregulatory ABC importer OpuA transiently interact. eLife 2024; 12:RP90996. [PMID: 38695350 PMCID: PMC11065425 DOI: 10.7554/elife.90996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024] Open
Abstract
Bacteria utilize various strategies to prevent internal dehydration during hypertonic stress. A common approach to countering the effects of the stress is to import compatible solutes such as glycine betaine, leading to simultaneous passive water fluxes following the osmotic gradient. OpuA from Lactococcus lactis is a type I ABC-importer that uses two substrate-binding domains (SBDs) to capture extracellular glycine betaine and deliver the substrate to the transmembrane domains for subsequent transport. OpuA senses osmotic stress via changes in the internal ionic strength and is furthermore regulated by the 2nd messenger cyclic-di-AMP. We now show, by means of solution-based single-molecule FRET and analysis with multi-parameter photon-by-photon hidden Markov modeling, that the SBDs transiently interact in an ionic strength-dependent manner. The smFRET data are in accordance with the apparent cooperativity in transport and supported by new cryo-EM data of OpuA. We propose that the physical interactions between SBDs and cooperativity in substrate delivery are part of the transport mechanism.
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Affiliation(s)
- Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Panagiotis Drougkas
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of GroningenGroningenNetherlands
- Biochemistry Center, Heidelberg UniversityHeidelbergGermany
| | - Cristina Paulino
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of GroningenGroningenNetherlands
- Biochemistry Center, Heidelberg UniversityHeidelbergGermany
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of GroningenGroningenNetherlands
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4
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van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K. Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell Rep 2024; 43:114110. [PMID: 38607912 DOI: 10.1016/j.celrep.2024.114110] [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: 09/01/2023] [Revised: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Transmembrane transporter proteins are essential for maintaining cellular homeostasis and, as such, are key drug targets. Many transmembrane transporter proteins are known to undergo large structural rearrangements during their functional cycles. Despite the wealth of detailed structural and functional data available for these systems, our understanding of their dynamics and, consequently, how they function is generally limited. We introduce an innovative approach that enables us to directly measure the dynamics and stability of interdomain interactions of transmembrane proteins using optical tweezers. Focusing on the osmoregulatory ATP-binding cassette transporter OpuA from Lactococcus lactis, we examine the mechanical properties and potential interactions of its substrate-binding domains. Our measurements are performed in lipid nanodiscs, providing a native-mimicking environment for the transmembrane protein. The technique provides high spatial and temporal resolution and allows us to study the functionally relevant motions and interdomain interactions of individual transmembrane transporter proteins in real time in a lipid bilayer.
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Affiliation(s)
- Lyan van der Sleen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Jan A Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Kasia Tych
- Chemical Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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5
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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6
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Con P, Hamar J, Biran J, Kültz D, Cnaani A. Cell-based homologous expression system for in-vitro characterization of environmental effects on transmembrane peptide transport in fish. Curr Res Physiol 2024; 7:100118. [PMID: 38298473 PMCID: PMC10825657 DOI: 10.1016/j.crphys.2024.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
All organisms encounter environmental changes that lead to physiological adjustments that could drive evolutionary adaptations. The ability to adjust performance in order to cope with environmental changes depends on the organism's physiological plasticity. These adjustments can be reflected in behavioral, physiological, and molecular changes, which interact and affect each other. Deciphering the role of molecular adjustments in physiological changes will help to understand how multiple levels of biological organization are synchronized during adaptations. Transmembrane transporters, which facilitate a cell's interaction with its surroundings, are prime targets for molecular studies of the environmental effects on an organism's physiology. Fish are subjected to environmental fluctuations and exhibit different coping mechanisms. To study the molecular adjustments of fish transporters to their external surrounding, suitable experimental systems must be established. The Mozambique tilapia (Oreochromis mossambicus) is an excellent model for environmental stress studies, due to its extreme salinity tolerance. We established a homologous cellular-based expression system and uptake assay that allowed us to study the effects of environmental conditions on transmembrane transport. We applied our expression system to investigate the effects of environmental conditions on the activity of PepT2, a transmembrane transporter critical in the absorption of dietary peptides and drugs. We created a stable, modified fish cell-line, in which we exogenously expressed the tilapia PepT2, and tested the effects of water temperature and salinity on the uptake of a fluorescent di-peptide, β-Ala-Lys-AMCA. While temperature affected only Vmax, medium salinity had a bi-directional effect, with significantly reduced Vmax in hyposaline conditions and significantly increased Km in hypersaline conditions. These assays demonstrate the importance of suitable experimental systems for fish ecophysiology studies. Furthermore, our in-vitro results show how the effect of hypersaline conditions on the transporter activity can explain expression shifts seen in the intestine of saltwater-acclimated fish, emphasizing the importance of complimentary studies in better understanding environmental physiology. This research highlights the advantages of using homologous expression systems to study environmental effects encountered by fish, in a relevant cellular context. The presented tools and methods can be adapted to study other transporters in-vitro.
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Affiliation(s)
- Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jens Hamar
- Department of Animal Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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7
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Elston R, Mulligan C, Thomas GH. Flipping the switch: dynamic modulation of membrane transporter activity in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37948297 DOI: 10.1099/mic.0.001412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The controlled entry and expulsion of small molecules across the bacterial cytoplasmic membrane is essential for efficient cell growth and cellular homeostasis. While much is known about the transcriptional regulation of genes encoding transporters, less is understood about how transporter activity is modulated once the protein is functional in the membrane, a potentially more rapid and dynamic level of control. In this review, we bring together literature from the bacterial transport community exemplifying the extensive and diverse mechanisms that have evolved to rapidly modulate transporter function, predominantly by switching activity off. This includes small molecule feedback, inhibition by interaction with small peptides, regulation through binding larger signal transduction proteins and, finally, the emerging area of controlled proteolysis. Many of these examples have been discovered in the context of metal transport, which has to finely balance active accumulation of elements that are essential for growth but can also quickly become toxic if intracellular homeostasis is not tightly controlled. Consistent with this, these transporters appear to be regulated at multiple levels. Finally, we find common regulatory themes, most often through the fusion of additional regulatory domains to transporters, which suggest the potential for even more widespread regulation of transporter activity in biology.
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Affiliation(s)
- Rory Elston
- Department of Biology, University of York, York, UK
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8
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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9
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Verhoeve VI, Lehman SS, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates origins of pathogen effectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530123. [PMID: 36909625 PMCID: PMC10002696 DOI: 10.1101/2023.02.26.530123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.
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Affiliation(s)
- Victoria I Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Stephanie S Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Timothy P Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F Beckmann
- Microbiology and Immunology, University of South Alabama, Mobile, AL, USA
| | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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10
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Chen J, Han S, Li S, Wang M, Zhu H, Qiao T, Lin T, Zhu T. Comparative Transcriptomics and Gene Knockout Reveal Virulence Factors of Neofusicoccum parvum in Walnut. Front Microbiol 2022; 13:926620. [PMID: 35910616 PMCID: PMC9335079 DOI: 10.3389/fmicb.2022.926620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 12/11/2022] Open
Abstract
Neofusicoccum parvum can cause stem and branch blight of walnut (Juglans spp.), resulting in great economic losses and ecological damage. A total of two strains of N. parvum were subjected to RNA-sequencing after being fed on different substrates, sterile water (K1/K2), and walnut (T1/T2), and the function of ABC1 was verified by gene knockout. There were 1,834, 338, and 878 differentially expressed genes (DEGs) between the K1 vs. K2, T1 vs. K1, and T2 vs. K2 comparison groups, respectively. The expression changes in thirty DEGs were verified by fluorescent quantitative PCR. These thirty DEGs showed the same expression patterns under both RNA-seq and PCR. In addition, ΔNpABC1 showed weaker virulence due to gene knockout, and the complementary strain NpABC1c showed the same virulence as the wild-type strain. Compared to the wild-type and complemented strains, the relative growth of ΔNpABC1 was significantly decreased when grown with H2O2, NaCl, Congo red, chloramphenicol, MnSO4, and CuSO4. The disease index of walnuts infected by the mutants was significantly lower than those infected by the wild-type and complementary strains. This result indicates that ABC1 gene is required for the stress response and virulence of N. parvum and may be involved in heavy metal resistance.
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Affiliation(s)
- Jie Chen
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shan Han
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shujiang Li
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Ming Wang
- Ecological Institute, Academy of Sichuan Forestry and Grassland Inventory and Planning, Chengdu, China
| | - Hanmingyue Zhu
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tianmin Qiao
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tiantian Lin
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Tianhui Zhu
- Department of Forest Protection, College of Forestry, Sichuan Agricultural University, Chengdu, China
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11
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Mantovanelli L, Gaastra BF, Poolman B. Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell. CURRENT TOPICS IN MEMBRANES 2021; 88:1-54. [PMID: 34862023 DOI: 10.1016/bs.ctm.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.
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Affiliation(s)
- Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands.
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12
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Chen C, Huang K, Li X, Tian H, Yu H, Huang J, Yuan H, Zhao S, Shao L. Effects of CcpA against salt stress in Lactiplantibacillus plantarum as assessed by comparative transcriptional analysis. Appl Microbiol Biotechnol 2021; 105:3691-3704. [PMID: 33852024 DOI: 10.1007/s00253-021-11276-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Lactiplantibacillus plantarum is frequently exposed to salt stress during industrial applications. Catabolite control protein (CcpA) controls the transcription of many genes, but its role in the response to salt stress remains unclear. In this study, we used transcriptome analyses to investigate differences in the logarithmic growth phases of Lactiplantibacillus plantarum ST-III and its ccpA-knockout mutant when grown with or without salt and glycine betaine (GB). The deletion of ccpA significantly affected bacterial growth under different conditions. Among the comparisons, the highest proportion of differentially expressed genes (64%) was observed in the comparison between the wild-type and ccpA mutant grown with NaCl, whereas the lowest proportion (6%) was observed in the comparison between the ccpA mutant strain cultures grown with NaCl alone or with GB together. Transcriptomic analyses showed that CcpA could regulate GB uptake, activate iron uptake, produce acetyl-CoA, and affect fatty acid composition to maintain membrane lipid homeostasis in the adaptation of high-salinity conditions. Conclusively, these results demonstrate the importance of CcpA as a master regulator of these processes in response to salt stress, and provide new insights into the complex regulatory network of lactic acid bacteria. KEY POINTS: • The absence of CcpA significantly affected growth of L. plantarum and its response to salt stress. • CcpA regulates compatible solutes absorption and ions transport to resist salt stress. • CcpA alters fatty acids composition to maintain membrane lipid homeostasis towards salt stress.
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Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Ke Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Xiaohong Li
- Shanghai Customs P. R. China Technical Center For Animal, Plant And Food Inspection And Quarantine, Shanghai, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Juan Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Shanshan Zhao
- College of Agriculture, Hebei University of Engineering, Handan, People's Republic of China
| | - Li Shao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China.
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13
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Tassis K, Vietrov R, de Koning M, de Boer M, Gouridis G, Cordes T. Single-molecule studies of conformational states and dynamics in the ABC importer OpuA. FEBS Lett 2021; 595:717-734. [PMID: 33314056 DOI: 10.1002/1873-3468.14026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/02/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022]
Abstract
The current model of active transport via ABC importers is mostly based on structural, biochemical and genetic data. We here establish single-molecule Förster resonance energy transfer (smFRET) assays to monitor the conformational states and heterogeneity of the osmoregulatory type I ABC importer OpuA from Lactococcus lactis. We present data probing both intradomain distances that elucidate conformational changes within the substrate-binding domain (SBD) OpuAC, and interdomain distances between SBDs or transmembrane domains. Using this methodology, we studied ligand-binding mechanisms, as well as ATP and glycine betaine dependences of conformational changes. Our work expands the scope of smFRET investigations towards a class of so far unstudied ABC importers, and paves the way for a full understanding of their transport cycle in the future.
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Affiliation(s)
- Konstantinos Tassis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Ruslan Vietrov
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Matthijs de Koning
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium.,Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Heraklion-Crete, Greece
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Martinsried, Germany
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14
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Investigations of Dimethylglycine, Glycine Betaine, and Ectoine Uptake by a Betaine-Carnitine-Choline Transporter Family Transporter with Diverse Substrate Specificity in Vibrio Species. J Bacteriol 2020; 202:JB.00314-20. [PMID: 32817090 DOI: 10.1128/jb.00314-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Abstract
Fluctuations in osmolarity are one of the most prevalent stresses to which bacteria must adapt, both hypo- and hyperosmotic conditions. Most bacteria cope with high osmolarity by accumulating compatible solutes (osmolytes) in the cytoplasm to maintain the turgor pressure of the cell. Vibrio parahaemolyticus, a halophile, utilizes at least six compatible solute transporters for the uptake of osmolytes: two ABC family ProU transporters and four betaine-carnitine-choline transporter (BCCT) family transporters. The full range of compatible solutes transported by this species has yet to be determined. Using an osmolyte phenotypic microarray plate for growth analyses, we expanded the known osmolytes used by V. parahaemolyticus to include N,N-dimethylglycine (DMG), among others. Growth pattern analysis of four triple-bccT mutants, possessing only one functional BCCT, indicated that BccT1 (VP1456), BccT2 (VP1723), and BccT3 (VP1905) transported DMG. BccT1 was unusual in that it could take up both compounds with methylated head groups (glycine betaine [GB], choline, and DMG) and cyclic compounds (ectoine and proline). Bioinformatics analysis identified the four coordinating amino acid residues for GB in the BccT1 protein. In silico modeling analysis demonstrated that GB, DMG, and ectoine docked in the same binding pocket in BccT1. Using site-directed mutagenesis, we showed that a strain with all four residues mutated resulted in the loss of uptake of GB, DMG, and ectoine. We showed that three of the four residues were essential for ectoine uptake, whereas only one of the residues was important for GB uptake. Overall, we have demonstrated that DMG is a highly effective compatible solute for Vibrio species and have elucidated the amino acid residues in BccT1 that are important for the coordination of GB, DMG, and ectoine transport.IMPORTANCE Vibrio parahaemolyticus possesses at least six osmolyte transporters, which allow the bacterium to adapt to high-salinity conditions. In this study, we identified several additional osmolytes that were utilized by V. parahaemolyticus We demonstrated that the compound DMG, which is present in the marine environment, was a highly effective osmolyte for Vibrio species. We determined that DMG is transported via BCCT family carriers, which have not been shown previously to take up this compound. BccT1 was a carrier for GB, DMG, and ectoine, and we identified the amino acid residues essential for the coordination of these compounds. The data suggest that for BccT1, GB is more easily accommodated than ectoine in the transporter binding pocket.
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15
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Yang S, Lu W, Zhao C, Zhai Y, Wei Y, Liu J, Yu Y, Li Z, Shi J. Leukemia cells remodel marrow adipocytes via TRPV4-dependent lipolysis. Haematologica 2020; 105:2572-2583. [PMID: 33131246 PMCID: PMC7604636 DOI: 10.3324/haematol.2019.225763] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/18/2019] [Indexed: 11/09/2022] Open
Abstract
Remodeling of adipocyte morphology and function plays a critical role in prostate cancer development. We previously reported that leukemia cells secrete growth differentiation factor 15 (GDF15),which remodels the residual bone marrow (BM) adipocytes into small adipocytes and is associated with a poor prognosis in acute myeloid leukemia (AML) patients. However, little is known about how GDF15 drives BM adipocyte remodeling. In this study, we examined the role of the transient receptor potential vanilloid (TRPV) channels in the remodeling of BM adipocytes exposed to GDF15. We found that TRPV4 negatively regulated GDF15-induced remodeling of BM adipocytes. Furthermore, transforming growth factor-β type II receptor (TGFβRII) was identified as the main receptor for GDF15 on BM adipocytes. PI3K inhibitor treatment reduced GDF15-induced pAKT, identifying PI3K/AKT as the downstream stress response pathway. Subsequently, GDF15 reduced the expression of the transcription factor Forkhead box C1 (FOXC1) in BM adipocytes subjected to RNA-seq screening and Western blot analyse. Moreover, it was also confirmed that FOXC1 combined with the TRPV4 promoter by the Chip-qPCR experiments, which suggests that FOXC1 mediates GDF15 regulation of TRPV4. In addition, an AML mouse model exhibited smaller BM adipocytes, whereas the TRPV4 activator 4α-phorbol 12,13-didecanoate (4αPDD) partly rescued this process and increased survival. In conclusion, TRPV4 plays a critical role in BM adipocyte remodeling induced by leukemia cells, suggesting that targeting TRPV4 may constitute a novel strategy for AML therapy.
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Affiliation(s)
- Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
| | - Wei Lu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
| | - Chong Zhao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital
| | - Yuanmei Zhai
- Department of Hematology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine
| | - Yanyu Wei
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
| | - Jiali Liu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital
| | - Yehua Yu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
| | - Zhiqiang Li
- Department of Blood Transfusion, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
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16
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Sikkema HR, van den Noort M, Rheinberger J, de Boer M, Krepel ST, Schuurman-Wolters GK, Paulino C, Poolman B. Gating by ionic strength and safety check by cyclic-di-AMP in the ABC transporter OpuA. SCIENCE ADVANCES 2020; 6:6/47/eabd7697. [PMID: 33208376 PMCID: PMC7673798 DOI: 10.1126/sciadv.abd7697] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
(Micro)organisms are exposed to fluctuating environmental conditions, and adaptation to stress is essential for survival. Increased osmolality (hypertonicity) causes outflow of water and loss of turgor and is dangerous if the cell is not capable of rapidly restoring its volume. The osmoregulatory adenosine triphosphate-binding cassette transporter OpuA restores the cell volume by accumulating large amounts of compatible solute. OpuA is gated by ionic strength and inhibited by the second messenger cyclic-di-AMP, a molecule recently shown to affect many cellular processes. Despite the master regulatory role of cyclic-di-AMP, structural and functional insights into how the second messenger regulates (transport) proteins on the molecular level are lacking. Here, we present high-resolution cryo-electron microscopy structures of OpuA and in vitro activity assays that show how the osmoregulator OpuA is activated by high ionic strength and how cyclic-di-AMP acts as a backstop to prevent unbridled uptake of compatible solutes.
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Affiliation(s)
- Hendrik R Sikkema
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Jan Rheinberger
- Department of Biochemistry, Structural Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Marijn de Boer
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sabrina T Krepel
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Gea K Schuurman-Wolters
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Cristina Paulino
- Department of Biochemistry, Structural Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Bert Poolman
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
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17
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CosR Is a Global Regulator of the Osmotic Stress Response with Widespread Distribution among Bacteria. Appl Environ Microbiol 2020; 86:AEM.00120-20. [PMID: 32169942 DOI: 10.1128/aem.00120-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
Bacteria accumulate small, organic compounds called compatible solutes via uptake from the environment or biosynthesis from available precursors to maintain the turgor pressure of the cell in response to osmotic stress. The halophile Vibrio parahaemolyticus has biosynthesis pathways for the compatible solutes ectoine (encoded by ectABC-asp_ect) and glycine betaine (encoded by betIBA-proXWV), four betaine-carnitine-choline transporters (encoded by bccT1 to bccT4), and a second ProU transporter (encoded by proVWX). All of these systems are osmotically inducible with the exception of bccT2 Previously, it was shown that CosR, a MarR-type regulator, was a direct repressor of ectABC-asp_ect in Vibrio species. In this study, we investigated whether CosR has a broader role in the osmotic stress response. Expression analyses demonstrated that betIBA-proXWV, bccT1, bccT3, bccT4, and proVWX are repressed in low salinity. Examination of an in-frame cosR deletion mutant showed that expression of these systems is derepressed in the mutant at low salinity compared with the wild type. DNA binding assays demonstrated that purified CosR binds directly to the regulatory region of both biosynthesis systems and four transporters. In Escherichia coli green fluorescent protein (GFP) reporter assays, we demonstrated that CosR directly represses transcription of betIBA-proXWV, bccT3, and proVWX Similar to Vibrio harveyi, we showed betIBA-proXWV was directly activated by the quorum-sensing LuxR homolog OpaR, suggesting a conserved mechanism of regulation among Vibrio species. Phylogenetic analysis demonstrated that CosR is ancestral to the Vibrionaceae family, and bioinformatics analysis showed widespread distribution among Gammaproteobacteria in general. Incidentally, in Aliivibrio fischeri, Aliivibrio finisterrensis, Aliivibrio sifiae, and Aliivibrio wodanis, an unrelated MarR-type regulator gene named ectR was clustered with ectABC-asp, which suggests the presence of another novel ectoine biosynthesis regulator. Overall, these data show that CosR is a global regulator of osmotic stress response that is widespread among bacteria.IMPORTANCE Vibrio parahaemolyticus can accumulate compatible solutes via biosynthesis and transport, which allow the cell to survive in high salinity conditions. There is little need for compatible solutes under low salinity conditions, and biosynthesis and transporter systems need to be repressed. However, the mechanism(s) of this repression is not known. In this study, we showed that CosR played a major role in the regulation of multiple compatible solute systems. Phylogenetic analysis showed that CosR is present in all members of the Vibrionaceae family as well as numerous Gammaproteobacteria Collectively, these data establish CosR as a global regulator of the osmotic stress response that is widespread in bacteria, controlling many more systems than previously demonstrated.
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18
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Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8–independent protection of respiration on Escherichia coli. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49909-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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19
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Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8-independent protection of respiration on Escherichia coli. J Biol Chem 2019; 295:981-993. [PMID: 31826918 DOI: 10.1074/jbc.ra119.011549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ubiquinone 8 (coenzyme Q8 or Q8) mediates electron transfer within the aerobic respiratory chain, mitigates oxidative stress, and contributes to gene expression in Escherichia coli In addition, Q8 was proposed to confer bacterial osmotolerance by accumulating during growth at high osmotic pressure and altering membrane stability. The osmolyte trehalose and membrane lipid cardiolipin accumulate in E. coli cells cultivated at high osmotic pressure. Here, Q8 deficiency impaired E. coli growth at low osmotic pressure and rendered growth osmotically sensitive. The Q8 deficiency impeded cellular O2 uptake and also inhibited the activities of two proton symporters, the osmosensing transporter ProP and the lactose transporter LacY. Q8 supplementation decreased membrane fluidity in liposomes, but did not affect ProP activity in proteoliposomes, which is respiration-independent. Liposomes and proteoliposomes prepared with E. coli lipids were used for these experiments. Similar oxygen uptake rates were observed for bacteria cultivated at low and high osmotic pressures. In contrast, respiration was dramatically inhibited when bacteria grown at the same low osmotic pressure were shifted to high osmotic pressure. Thus, respiration was restored during prolonged growth of E. coli at high osmotic pressure. Of note, bacteria cultivated at low and high osmotic pressures had similar Q8 concentrations. The protection of respiration was neither diminished by cardiolipin deficiency nor conferred by trehalose overproduction during growth at low osmotic pressure, but rather might be achieved by Q8-independent respiratory chain remodeling. We conclude that osmotolerance is conferred through Q8-independent protection of respiration, not by altering physical properties of the membrane.
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Affiliation(s)
- Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Anita Ayer
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Roland Stocker
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
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20
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Gabba M, Frallicciardi J, van 't Klooster J, Henderson R, Syga Ł, Mans R, van Maris AJA, Poolman B. Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane. Biophys J 2019; 118:422-434. [PMID: 31843263 PMCID: PMC6976801 DOI: 10.1016/j.bpj.2019.11.3384] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022] Open
Abstract
We present a fluorescence-based approach for determination of the permeability of small molecules across the membranes of lipid vesicles and living cells. With properly designed experiments, the method allows us to assess the membrane physical properties both in vitro and in vivo. We find that the permeability of weak acids increases in the order of benzoic > acetic > formic > lactic, both in synthetic lipid vesicles and the plasma membrane of Saccharomyces cerevisiae, but the permeability is much lower in yeast (one to two orders of magnitude). We observe a relation between the molecule permeability and the saturation of the lipid acyl chain (i.e., lipid packing) in the synthetic lipid vesicles. By analyzing wild-type yeast and a manifold knockout strain lacking all putative lactic acid transporters, we conclude that the yeast plasma membrane is impermeable to lactic acid on timescales up to ∼2.5 h.
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Affiliation(s)
- Matteo Gabba
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jacopo Frallicciardi
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Joury van 't Klooster
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Ryan Henderson
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Łukasz Syga
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Robert Mans
- Department of Industrial Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, Delft University of Technology, Delft, the Netherlands; Industrial Biotechnology Division, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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21
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Physicochemical considerations for bottom-up synthetic biology. Emerg Top Life Sci 2019; 3:445-458. [PMID: 33523159 PMCID: PMC7289010 DOI: 10.1042/etls20190017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
The bottom-up construction of synthetic cells from molecular components is arguably one of the most challenging areas of research in the life sciences. We review the impact of confining biological systems in synthetic vesicles. Complex cell-like systems require control of the internal pH, ionic strength, (macro)molecular crowding, redox state and metabolic energy conservation. These physicochemical parameters influence protein activity and need to be maintained within limits to ensure the system remains in steady-state. We present the physicochemical considerations for building synthetic cells with dimensions ranging from the smallest prokaryotes to eukaryotic cells.
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22
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Pols T, Sikkema HR, Gaastra BF, Frallicciardi J, Śmigiel WM, Singh S, Poolman B. A synthetic metabolic network for physicochemical homeostasis. Nat Commun 2019; 10:4239. [PMID: 31534136 PMCID: PMC6751199 DOI: 10.1038/s41467-019-12287-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
One of the grand challenges in chemistry is the construction of functional out-of-equilibrium networks, which are typical of living cells. Building such a system from molecular components requires control over the formation and degradation of the interacting chemicals and homeostasis of the internal physical-chemical conditions. The provision and consumption of ATP lies at the heart of this challenge. Here we report the in vitro construction of a pathway in vesicles for sustained ATP production that is maintained away from equilibrium by control of energy dissipation. We maintain a constant level of ATP with varying load on the system. The pathway enables us to control the transmembrane fluxes of osmolytes and to demonstrate basic physicochemical homeostasis. Our work demonstrates metabolic energy conservation and cell volume regulatory mechanisms in a cell-like system at a level of complexity minimally needed for life.
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Affiliation(s)
- Tjeerd Pols
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Hendrik R Sikkema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jacopo Frallicciardi
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wojciech M Śmigiel
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Shubham Singh
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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23
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Deng Y, Su Y, Liu S, Bei L, Guo Z, Li H, Chen C, Feng J. A novel sRNA srvg17985 identified in Vibrio alginolyticus involving into metabolism and stress response. Microbiol Res 2019; 229:126295. [PMID: 31450184 DOI: 10.1016/j.micres.2019.126295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/28/2022]
Abstract
Vibrio alginolyticus is an opportunistic pathogen that is a threat to the aquaculture industry. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and pathology by modulating gene expression post transcription. However, little information about sRNA-mediated regulation in V. alginolyticus is available. We experimentally verified the existence and characterized the function of sRNA srvg17985 in V. alginolyticus ZJ-T. We identified a 179 nt and growth-phase-dependent transcript with a σ70 promoter and a ρ-independent terminator. The transcript consisted of five stem-loops and was conserved in Vibrio spp. Phenotype microarray assays showed that deletion of srvg17985 led to less use of Gly-Glu as a carbon source but a gain in ability to use l-phenylalanine as a nitrogen source. Srvg17985 regulated the osmotic stress response with stronger tolerance to NaCl but weaker tolerance to urea. In addition, srvg17985 inhibited the deamination of l-serine at pH 9.5 and promoted the hydrolysis of X-beta-d-glucuronide, thus affecting the pH stress response. Bioinformatics by IntaRNA and TargetRNA2 identified 45 common target mRNAs, some of which probably contributed to the observed phenotypes. These results indicated that srvg17985 regulated environmental adaptation. The results provide valuable information for in-depth studies of sRNA-mediated regulation mechanisms of the complex physiological processes of V alginolyticus and provide new targets for antibacterial therapeutics or attenuated vaccines for Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lei Bei
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huo Li
- Jinyang Tropical Haizhen Aquaculture Co., Ltd., Maoming, China
| | - Chang Chen
- Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China.
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24
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Toft-Bertelsen TL, Larsen BR, MacAulay N. Sensing and regulation of cell volume - we know so much and yet understand so little: TRPV4 as a sensor of volume changes but possibly without a volume-regulatory role? Channels (Austin) 2019; 12:100-108. [PMID: 29424275 PMCID: PMC5972811 DOI: 10.1080/19336950.2018.1438009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cellular volume changes lead to initiation of cell volume regulatory events, the molecular identity of which remains unresolved. We here discuss experimental challenges associated with investigation of volume regulation during application of large, non-physiological osmotic gradients. The TRPV4 ion channel responds to volume increase irrespectively of the molecular mechanism underlying cell swelling, and is thus considered a sensor of volume changes. Evidence pointing towards the involvement of TRPV4 in subsequent volume regulatory mechanisms is intriguing, yet far from conclusive. We here present an experimental setting with astrocytic cell swelling in the absence of externally applied osmotic gradients, and the lack of evidence for involvement of TRPV4 in this regulatory volume response. Our aim with these new data and the preceding discussion is to stimulate further experimental effort in this area of research to clarify the role of TRPV4 and other channels and transporters in regulatory volume responses.
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Affiliation(s)
| | - Brian R Larsen
- a Department of Neuroscience , University of Copenhagen , Copenhagen , Denmark
| | - Nanna MacAulay
- a Department of Neuroscience , University of Copenhagen , Copenhagen , Denmark
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25
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Abstract
The cytoplasm of bacterial cells is a highly crowded cellular compartment that possesses considerable osmotic potential. As a result, and owing to the semipermeable nature of the cytoplasmic membrane and the semielastic properties of the cell wall, osmotically driven water influx will generate turgor, a hydrostatic pressure considered critical for growth and viability. Both increases and decreases in the external osmolarity inevitably trigger water fluxes across the cytoplasmic membrane, thus impinging on the degree of cellular hydration, molecular crowding, magnitude of turgor, and cellular integrity. Here, we assess mechanisms that permit the perception of osmotic stress by bacterial cells and provide an overview of the systems that allow them to genetically and physiologically cope with this ubiquitous environmental cue. We highlight recent developments implicating the secondary messenger c-di-AMP in cellular adjustment to osmotic stress and the role of osmotic forces in the life of bacteria-assembled in biofilms.
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Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology; and Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany;
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26
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Culham DE, Marom D, Boutin R, Garner J, Ozturk TN, Sahtout N, Tempelhagen L, Lamoureux G, Wood JM. Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. Biophys J 2018; 115:2152-2166. [PMID: 30448037 PMCID: PMC6289098 DOI: 10.1016/j.bpj.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/23/2022] Open
Abstract
ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.g., ProPEc, from Escherichia coli). Group B orthologs lack that feature (e.g., ProPXc, from Xanthomonas campestris). ProPXc was expressed and characterized in E. coli to further elucidate the role of the coiled coil in osmosensing. The activity of ProPXc was a sigmoid function of the osmolality in cells and proteoliposomes. ProPEc and ProPXc attained similar activities at the same expression level in E. coli. ProPEc transports proline and glycine betaine with comparable high affinities at low osmolality. In contrast, proline weakly inhibited high-affinity glycine-betaine uptake via ProPXc. The KM for proline uptake via ProPEc increases dramatically with the osmolality. The KM for glycine-betaine uptake via ProPXc did not. Thus, ProPXc is an osmosensing transporter, and the C-terminal coiled coil is not essential for osmosensing. The role of CTD-membrane interaction in osmosensing was examined further. As for ProPEc, the ProPXc CTD co-sedimented with liposomes comprising E. coli phospholipid. Molecular dynamics simulations illustrated association of the monomeric ProPEc CTD with the membrane surface. Comparison with the available NMR structure for the homodimeric coiled coil formed by the ProPEc-CTD suggested that membrane association and homodimeric coiled-coil formation by that peptide are mutually exclusive. The membrane fluidity in liposomes comprising E. coli phospholipid decreased with increasing osmolality in the range relevant for ProP activation. These data support the proposal that ProP activates as cellular dehydration increases cytoplasmic cation concentration, releasing the CTD from the membrane surface. For group A orthologs, this also favors α-helical coiled-coil formation that stabilizes the transporter in an active form.
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Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David Marom
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rebecca Boutin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jennifer Garner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada; Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada
| | - Tugba Nur Ozturk
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada
| | - Naheda Sahtout
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Guillaume Lamoureux
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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Glycine betaine transport conditions of Lactobacillus delbrueckii subsp. bulgaricus in salt induced hyperosmotic stress. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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Pham HT, Nhiep NTH, Vu TNM, Huynh TN, Zhu Y, Huynh ALD, Chakrabortti A, Marcellin E, Lo R, Howard CB, Bansal N, Woodward JJ, Liang ZX, Turner MS. Enhanced uptake of potassium or glycine betaine or export of cyclic-di-AMP restores osmoresistance in a high cyclic-di-AMP Lactococcus lactis mutant. PLoS Genet 2018; 14:e1007574. [PMID: 30074984 PMCID: PMC6108528 DOI: 10.1371/journal.pgen.1007574] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/24/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022] Open
Abstract
The broadly conserved bacterial signalling molecule cyclic-di-adenosine monophosphate (c-di-AMP) controls osmoresistance via its regulation of potassium (K+) and compatible solute uptake. High levels of c-di-AMP resulting from inactivation of c-di-AMP phosphodiesterase activity leads to poor growth of bacteria under high osmotic conditions. To better understand how bacteria can adjust in response to excessive c-di-AMP levels and to identify signals that feed into the c-di-AMP network, we characterised genes identified in a screen for osmoresistant suppressor mutants of the high c-di-AMP Lactococcus ΔgdpP strain. Mutations were identified which increased the uptake of osmoprotectants, including gain-of-function mutations in a Kup family K+ importer (KupB) and inactivation of the glycine betaine transporter transcriptional repressor BusR. The KupB mutations increased the intracellular K+ level while BusR inactivation increased the glycine betaine level. In addition, BusR was found to directly bind c-di-AMP and repress expression of the glycine betaine transporter in response to elevated c-di-AMP. Interestingly, overactive KupB activity or loss of BusR triggered c-di-AMP accumulation, suggesting turgor pressure changes act as a signal for this second messenger. In another group of suppressors, overexpression of an operon encoding an EmrB family multidrug resistance protein allowed cells to lower their intracellular level of c-di-AMP through active export. Lastly evidence is provided that c-di-AMP levels in several bacteria are rapidly responsive to environmental osmolarity changes. Taken together, this work provides evidence for a model in which high c-di-AMP containing cells are dehydrated due to lower K+ and compatible solute levels and that this osmoregulation system is able to sense and respond to cellular water stress.
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Affiliation(s)
- Huong Thi Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- The University of Danang, University of Science and Technology, Da Nang, Vietnam
| | - Nguyen Thi Hanh Nhiep
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Thu Ngoc Minh Vu
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - TuAnh Ngoc Huynh
- Department of Microbiology, University of Washington, Seattle, WA, United States of America
| | - Yan Zhu
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Anh Le Diep Huynh
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Raquel Lo
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Nidhi Bansal
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Joshua J. Woodward
- Department of Microbiology, University of Washington, Seattle, WA, United States of America
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mark S. Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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29
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Abstract
Niosomes are used in studies for drug delivery or gene transfer. However, their physical properties and features relative to liposomes are not well documented. To characterize and more rationally optimize niosome formulations, the properties of these vesicle systems are compared to those of liposomes composed of phosphatidylcholine and phosphatidylethanolamine lipids plus cholesterol. Niosomes are highly stable and only slightly more leaky than liposomes as assayed by calcein leakage; the permeability for ions (KCl) is higher than that of liposomes. Contrary to liposomes, the size of niosomes decreases substantially upon freezing in liquid nitrogen and subsequent thawing, as shown by cryo-EM and dynamic light scattering. The packing of niosomal membranes was determined by laurdan fluorescence and is slightly lower than that of liposomes. We did not succeed in the functional reconstitution of the L-arginine/L-ornithine antiporter ArcD2 in niosomes, which we attribute to the non-ionic nature of the surfactants. The antimicrobial peptides alamethicin and melittin act similarly on niosomes and liposomes composed of unsaturated components, whereas both niosomes and liposomes are unaffected when saturated amphiphiles are used. In conclusion, in terms of stability and permeability for drug-size molecules niosomes are comparable to liposomes and they may offer an excellent, inexpensive alternative for delivery purposes.
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30
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Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I. Helical jackknives control the gates of the double-pore K + uptake system KtrAB. eLife 2017; 6. [PMID: 28504641 PMCID: PMC5449183 DOI: 10.7554/elife.24303] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/14/2017] [Indexed: 12/27/2022] Open
Abstract
Ion channel gating is essential for cellular homeostasis and is tightly controlled. In some eukaryotic and most bacterial ligand-gated K+ channels, RCK domains regulate ion fluxes. Until now, a single regulatory mechanism has been proposed for all RCK-regulated channels, involving signal transduction from the RCK domain to the gating area. Here, we present an inactive ADP-bound structure of KtrAB from Vibrio alginolyticus, determined by cryo-electron microscopy, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulatory mechanism for ligand-induced action at a distance. Exchange of activating ATP to inactivating ADP triggers short helical segments in the K+-translocating KtrB dimer to organize into two long helices that penetrate deeply into the regulatory RCK domains, thus connecting nucleotide-binding sites and ion gates. As KtrAB and its homolog TrkAH have been implicated as bacterial pathogenicity factors, the discovery of this functionally relevant inactive conformation may advance structure-guided drug development. DOI:http://dx.doi.org/10.7554/eLife.24303.001
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Affiliation(s)
- Marina Diskowski
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Natalie Bärland
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany.,Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Jan Hoffmann
- Institute for Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | - Nina Morgner
- Institute for Physical and Theoretical Chemistry, Goethe-University, Frankfurt, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe-University, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
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31
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Toft-Bertelsen TL, Križaj D, MacAulay N. When size matters: transient receptor potential vanilloid 4 channel as a volume-sensor rather than an osmo-sensor. J Physiol 2017; 595:3287-3302. [PMID: 28295351 DOI: 10.1113/jp274135] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/07/2017] [Indexed: 12/11/2022] Open
Abstract
KEY POINTS Mammalian cells are frequently exposed to stressors causing volume changes. The transient receptor potential vanilloid 4 (TRPV4) channel translates osmotic stress into ion flux. The molecular mechanism coupling osmolarity to TRPV4 activation remains elusive. TRPV4 responds to isosmolar cell swelling and osmolarity translated via different aquaporins. TRPV4 functions as a volume-sensing ion channel irrespective of the origin of the cell swelling. ABSTRACT Transient receptor potential channel 4 of the vanilloid subfamily (TRPV4) is activated by a diverse range of molecular cues, such as heat, lipid metabolites and synthetic agonists, in addition to hyposmotic challenges. As a non-selective cation channel permeable to Ca2+ , it transduces physical stress in the form of osmotic cell swelling into intracellular Ca2+ -dependent signalling events. Its contribution to cell volume regulation might include interactions with aquaporin (AQP) water channel isoforms, although the proposed requirement for a TRPV4-AQP4 macromolecular complex remains to be resolved. To characterize the elusive mechanics of TRPV4 volume-sensing, we expressed the channel in Xenopus laevis oocytes together with AQP4. Co-expression with AQP4 facilitated the cell swelling induced by osmotic challenges and thereby activated TRPV4-mediated transmembrane currents. Similar TRPV4 activation was induced by co-expression of a cognate channel, AQP1. The level of osmotically-induced TRPV4 activation, although proportional to the degree of cell swelling, was dependent on the rate of volume changes. Importantly, isosmotic cell swelling obtained by parallel activation of the co-expressed water-translocating Na+ /K+ /2Cl- cotransporter promoted TRPV4 activation despite the absence of the substantial osmotic gradients frequently employed for activation. Upon simultaneous application of an osmotic gradient and the selective TRPV4 agonist GSK1016790A, enhanced TRPV4 activation was observed only with subsaturating stimuli, indicating that the agonist promotes channel opening similar to that of volume-dependent activation. We propose that, contrary to the established paradigm, TRPV4 is activated by increased cell volume irrespective of the molecular mechanism underlying cell swelling. Thus, the channel functions as a volume-sensor, rather than as an osmo-sensor.
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Affiliation(s)
- Trine L Toft-Bertelsen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - David Križaj
- Department of Ophthalmology & Visual Sciences, Moran Eye Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Nanna MacAulay
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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32
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Erne PM, Štacko P, van Dijken DJ, Chen J, Stuart MCA, Feringa BL. End-capping of amphiphilic nanotubes with phospholipid vesicles: impact of the phospholipid on the cap formation and vesicle loading under osmotic conditions. Chem Commun (Camb) 2016; 52:11697-11700. [PMID: 27709184 DOI: 10.1039/c6cc05101d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Soft amphiphilic nanotubes are capped with vesicles comprised of either overall neutral, zwitterionic phospholipids, or those that carry a net charge. The phase transition temperature of the zwitterionic phospholipids plays a crucial role in the phase separation that leads to the end-capped nanotubes. The cationic vesicle caps can be loaded into the nanotubes via osmosis whereas the anionic vesicle caps are stable under hyper-osmotic conditions. Furthermore, no additional salt needs to be added for the cationic vesicle caps to induce the loading of the vesicles into the nanotubes due to the presence of counterions.
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Affiliation(s)
- Petra M Erne
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Peter Štacko
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Derk Jan van Dijken
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Jiawen Chen
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Abstract
Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.
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34
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Culham DE, Shkel IA, Record MT, Wood JM. Contributions of Coulombic and Hofmeister Effects to the Osmotic Activation of Escherichia coli Transporter ProP. Biochemistry 2016; 55:1301-13. [PMID: 26871755 DOI: 10.1021/acs.biochem.5b01169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Osmosensing transporters mediate osmolyte accumulation to forestall cellular dehydration as the extracellular osmolality increases. ProP is a bacterial osmolyte-H(+) symporter, a major facilitator superfamily member, and a paradigm for osmosensing. ProP activity is a sigmoid function of the osmolality. It is determined by the osmolality, not the magnitude or direction of the osmotic shift, in cells and salt-loaded proteoliposomes. The activation threshold varies directly with the proportion of anionic phospholipid in cells and proteoliposomes. The osmosensory mechanism was probed by varying the salt composition and concentration outside and inside proteoliposomes. Data analysis was based on the hypothesis that the fraction of maximal transporter activity at a particular luminal salt concentration reflects the proportion of ProP molecules in an active conformation. ProP attained the same activity at the same osmolality when diverse, membrane-impermeant salts were added to the external medium. Contributions of Coulombic and/or Hofmeister salt effects to ProP activation were examined by varying the luminal salt cation (K(+) and Na(+)) and anion (chloride, phosphate, and sulfate) composition and then systematically increasing the luminal salt concentration by increasing the external osmolality. ProP activity increased with the sixth power of the univalent cation concentration, independent of the type of anion. This indicates that salt activation of ProP is a Coulombic, cation effect resulting from salt cation accumulation and not site-specific cation binding. Possible origins of this Coulombic effect include folding or assembly of anionic cytoplasmic ProP domains, an increase in local membrane surface charge density, and/or the juxtaposition of anionic protein and membrane surfaces during activation.
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Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - Irina A Shkel
- Departments of Biochemistry and Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Departments of Biochemistry and Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
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35
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Su J, Yao Z, de la Cruz MO. Vesicle Geometries Enabled by Dynamically Trapped States. ACS NANO 2016; 10:2287-2294. [PMID: 26795199 DOI: 10.1021/acsnano.5b06991] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Understanding and controlling vesicle shapes is a fundamental challenge in biophysics and materials design. In this paper, we design dynamic protocols for enlarging the shape space of both fluid and crystalline vesicles beyond the equilibrium zone. By removing water from within the vesicle at different rates, we numerically produced a series of dynamically trapped stable vesicle shapes for both fluid and crystalline vesicles in a highly controllable fashion. In crystalline vesicles that are continuously dehydrated, simulations show the initial appearance of small flat areas over the surface of the vesicles that ultimately merge to form fewer flat faces. In this way, the vesicles transform from a fullerene-like shape into various faceted polyhedrons. We perform analytical elasticity analysis to show that these salient features are attributable to the crystalline nature of the vesicle. The potential to use dynamic protocols, such as those used in this study, to engineer vesicle shape transformations is helpful for exploiting the richness of vesicle geometries for desired applications.
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Affiliation(s)
- Jiaye Su
- Department of Applied Physics, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
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36
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Erne PM, van Bezouwen LS, Štacko P, van Dijken DJ, Chen J, Stuart MCA, Boekema EJ, Feringa BL. Loading of Vesicles into Soft Amphiphilic Nanotubes using Osmosis. Angew Chem Int Ed Engl 2015; 54:15122-7. [PMID: 26503858 DOI: 10.1002/anie.201506493] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/17/2015] [Indexed: 11/12/2022]
Abstract
The facile assembly of higher-order nanoarchitectures from simple building blocks is demonstrated by the loading of vesicles into soft amphiphilic nanotubes using osmosis. The nanotubes are constructed from rigid interdigitated bilayers which are capped with vesicles comprising phospholipid-based flexible bilayers. When a hyperosmotic gradient is applied to these vesicle-capped nanotubes, the closed system loses water and the more flexible vesicle bilayer is pulled inwards. This leads to inclusion of vesicles inside the nanotubes without affecting the tube structure, showing controlled reorganization of the self-assembled multicomponent system upon a simple osmotic stimulus.
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Affiliation(s)
- Petra M Erne
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands)
| | - Laura S van Bezouwen
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands)
| | - Peter Štacko
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands)
| | - Derk Jan van Dijken
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands)
| | - Jiawen Chen
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands)
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands).,Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands)
| | - Egbert J Boekema
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands)
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The Netherlands).
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Erne PM, van Bezouwen LS, Štacko P, van Dijken DJ, Chen J, Stuart MCA, Boekema EJ, Feringa BL. Loading of Vesicles into Soft Amphiphilic Nanotubes using Osmosis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Zhong D, Blount P. Electrostatics at the membrane define MscL channel mechanosensitivity and kinetics. FASEB J 2014; 28:5234-41. [PMID: 25223610 DOI: 10.1096/fj.14-259309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The bacterial mechanosensitive channel of large conductance (MscL) serves as a biological emergency release valve, preventing the occurrence of cell lysis caused by acute osmotic stress. Its tractable nature allows it to serve as a paradigm for how a protein can directly sense membrane tension. Although much is known of the importance of the hydrophobicity of specific residues in channel gating, it has remained unclear whether electrostatics at the membrane plays any role. We studied MscL chimeras derived from functionally distinct orthologues: Escherichia coli and Staphylococcus aureus. Dissection of one set led to an observation that changing the charge of a single residue, K101, of E. coli (Ec)-MscL, effects a channel phenotype: when mutated to a negative residue, the channel is less mechanosensitive and has longer open dwell times. Assuming electrostatic interactions, we determined whether they are due to protein-protein or protein-lipid interactions by performing site-directed mutagenesis elsewhere in the protein and reconstituting channels into defined lipids, with and without negative head groups. We found that although both interactions appear to play some role, the primary determinant of the channel phenotype seems to be protein-lipid electrostatics. The data suggest a model for the role of electrostatic interactions in the dynamics of MscL gating.
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Affiliation(s)
- Dalian Zhong
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China; and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Paul Blount
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Koshy C, Ziegler C. Structural insights into functional lipid-protein interactions in secondary transporters. Biochim Biophys Acta Gen Subj 2014; 1850:476-87. [PMID: 24859688 DOI: 10.1016/j.bbagen.2014.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Structural evidences with functional corroborations have revealed distinct features of lipid-protein interactions especially in channels and receptors. Many membrane embedded transporters are also known to require specific lipids for their functions and for some of them cellular and biochemical data suggest tight regulation by the lipid bilayer. However, molecular details on lipid-protein interactions in transporters are sparse since lipids are either depleted from the detergent solubilized transporters in three-dimensional crystals or not readily resolved in crystal structures. Nevertheless the steady increase in the progress of transporter structure determination contributed more examples of structures with resolved lipids. SCOPE OF REVIEW This review gives an overview on transporter structures in complex with lipids reported to date and discusses commonly encountered difficulties in the identification of functionally significant lipid-protein interactions based on those structures and functional in vitro data. Recent structures provided molecular details into regulation mechanism of transporters by specific lipids. The review highlights common findings and conserved patterns for distantly related transporter families to draw a more general picture on the regulatory role of lipid-protein interactions. MAJOR CONCLUSIONS Several common themes of the manner in which lipids directly influence membrane-mediated folding, oligomerization and structure stability can be found. Especially for LeuT-like fold transporters similarities in structurally resolved lipid-protein interactions suggest a common way in which transporter conformations are affected by lipids even in evolutionarily distinct transporters. Lipids appear to play an additional role as joints mechanically reinforcing the inverted repeat topology, which is a major determinant in the alternating access mechanism of secondary transporters. GENERAL SIGNIFICANCE This review brings together and adds to the repertoire of knowledge on lipid-protein interactions of functional significance presented in structures of membrane transporters. Knowledge of specific lipid-binding sites and modes of lipid influence on these proteins not only accomplishes the molecular description of transport cycle further, but also sheds light into localization dependent differences of transporter function. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Caroline Koshy
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Max-Planck Institute of Biophysics, Computational Structural Biology Group, Frankfurt am Main, Germany
| | - Christine Ziegler
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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40
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Maximov S, Ott V, Belkoura L, Krämer R. Stimulus analysis of BetP activation under in vivo conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1288-95. [DOI: 10.1016/j.bbamem.2013.12.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/18/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
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41
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A lipid-mediated conformational switch modulates the thermosensing activity of DesK. Proc Natl Acad Sci U S A 2014; 111:3579-84. [PMID: 24522108 DOI: 10.1073/pnas.1317147111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The thermosensor DesK is a multipass transmembrane histidine-kinase that allows the bacterium Bacillus subtilis to adjust the levels of unsaturated fatty acids required to optimize membrane lipid fluidity. The cytoplasmic catalytic domain of DesK behaves like a kinase at low temperature and like a phosphatase at high temperature. Temperature sensing involves a built-in instability caused by a group of hydrophilic residues located near the N terminus of the first transmembrane (TM) segment. These residues are buried in the lipid phase at low temperature and partially "buoy" to the aqueous phase at higher temperature with the thinning of the membrane, promoting the required conformational change. Nevertheless, the core question remains poorly understood: How is the information sensed by the transmembrane region converted into a rearrangement in the cytoplasmic catalytic domain to control DesK activity? Here, we identify a "linker region" (KSRKERERLEEK) that connects the TM sensor domain with the cytoplasmic catalytic domain involved in signal transmission. The linker adopts two conformational states in response to temperature-dependent membrane thickness changes: (i) random coiled and bound to the phospholipid head groups at the water-membrane interface, promoting the phosphatase state or (ii) unbound and forming a continuous helix spanning a region from the membrane to the cytoplasm, promoting the kinase state. Our results uphold the view that the linker is endowed with a helix/random coil conformational duality that enables it to behave like a transmission switch, with helix disruption decreasing the kinase/phosphatase activity ratio, as required to modulate the DesK output response.
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42
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Structural evidence for functional lipid interactions in the betaine transporter BetP. EMBO J 2013; 32:3096-105. [PMID: 24141878 DOI: 10.1038/emboj.2013.226] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/11/2013] [Indexed: 11/09/2022] Open
Abstract
Bilayer lipids contribute to the stability of membrane transporters and are crucially involved in their proper functioning. However, the molecular knowledge of how surrounding lipids affect membrane transport is surprisingly limited and despite its general importance is rarely considered in the molecular description of a transport mechanism. One reason is that only few atomic resolution structures of channels or transporters reveal a functional interaction with lipids, which are difficult to detect in X-ray structures per se. Overcoming these difficulties, we report here on a new structure of the osmotic stress-regulated betaine transporter BetP in complex with anionic lipids. This lipid-associated BetP structure is important in the molecular understanding of osmoregulation due to the strong dependence of activity regulation in BetP on the presence of negatively charged lipids. We detected eight resolved palmitoyl-oleoyl phosphatidyl glycerol (PG) lipids mimicking parts of the membrane leaflets and interacting with key residues in transport and regulation. The lipid-protein interactions observed here in structural detail in BetP provide molecular insights into the role of lipids in osmoregulated secondary transport.
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Karasawa A, Swier LJYM, Stuart MCA, Brouwers J, Helms B, Poolman B. Physicochemical factors controlling the activity and energy coupling of an ionic strength-gated ATP-binding cassette (ABC) transporter. J Biol Chem 2013; 288:29862-71. [PMID: 23979139 DOI: 10.1074/jbc.m113.499327] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cells control their volume through the accumulation of compatible solutes. The bacterial ATP-binding cassette transporter OpuA couples compatible solute uptake to ATP hydrolysis. Here, we study the gating mechanism and energy coupling of OpuA reconstituted in lipid nanodiscs. We show that anionic lipids are essential both for the gating and the energy coupling. The tight coupling between substrate binding on extracellular domains and ATP hydrolysis by cytoplasmic nucleotide-binding domains allows the study of transmembrane signaling in nanodiscs. From the tight coupling between processes at opposite sides of the membrane, we infer that the ATPase activity of OpuA in nanodiscs reflects solute translocation. Intriguingly, the substrate-dependent, ionic strength-gated ATPase activity of OpuA in nanodiscs is at least an order of magnitude higher than in lipid vesicles (i.e. with identical membrane lipid composition, ionic strength, and nucleotide and substrate concentrations). Even with the chemical components the same, the lateral pressure (profile) of the nanodiscs will differ from that of the vesicles. We thus propose that membrane tension limits translocation in vesicular systems. Increased macromolecular crowding does not activate OpuA but acts synergistically with ionic strength, presumably by favoring gating interactions of like-charged surfaces via excluded volume effects.
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Affiliation(s)
- Akira Karasawa
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre
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44
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Gul N, Poolman B. Functional reconstitution and osmoregulatory properties of the ProU ABC transporter from Escherichia coli. Mol Membr Biol 2012; 30:138-48. [PMID: 23249124 DOI: 10.3109/09687688.2012.754060] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The ATP-binding cassette (ABC) transporter ProU from Escherichia coli translocates a wide range of compatible solutes and contributes to the regulation of cell volume, which is particularly important when the osmolality of the environment fluctuates. We have purified the components of ProU, i.e., the substrate-binding protein ProX, the nucleotide-binding protein ProV and the transmembrane protein ProW, and reconstituted the full transporter complex in liposomes. We engineered a lipid anchor to ProX for surface tethering of this protein to ProVW-containing proteoliposomes. We show that glycine betaine binds to ProX with high-affinity and is transported via ProXVW in an ATP-dependent manner. The activity ProU is salt and anionic lipid-dependent and mimics the ionic strength-gating of transport of the homologous OpuA system.
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Affiliation(s)
- Nadia Gul
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands
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45
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Choi HJ, Yoon YJ, Kwon YK, Lee YJ, Chae S, Hwang D, Hwang GS, Kwon TH. Patterns of gene and metabolite define the effects of extracellular osmolality on kidney collecting duct. J Proteome Res 2012; 11:3816-28. [PMID: 22686594 DOI: 10.1021/pr300309d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To investigate the effects of changes in extracellular osmolality on the function of kidney collecting duct cells, particularly on water and sodium reabsorption in the conditions of diuresis and antidiuresis, we generated transcriptome and metabolome profiles of primary cultured inner medullary collecting duct (IMCD) cells. They were grown in hyperosmolar culture medium (640 mOsm) for 4 days and then exposed to either reduced (300 mOsm) or same osmolality for 1 or 2 days more. Integrated analysis of the transcriptome and metabolome revealed that decreased extracellular osmolality was associated with decreased levels of organic osmolytes, glucose, intermediates of citric acid cycle, and branched-chain amino acids (BCAA) in IMCD cells, along with significantly decreased gene expression and protein abundance of P-type transporters (ATP1B1), ABC transporters (ABCC5 and ABCG1), and insulin signaling pathways (IRS2). Quantitative real-time RT-PCR and semiquantitative immunoblotting confirmed the changes of transcript levels of differentially expressed genes and protein levels. Taken together, integrated analysis of omics data demonstrated that water and sodium reabsorption could be reduced by decreased extracellular osmolality per se, through decreased levels of ABC transporters and IRS2, which play a potential role in the transport of organic osmolytes, BCAA, glucose, and trafficking of epithelial sodium channel.
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Affiliation(s)
- Hyo-Jung Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Taegu, Korea
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46
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Culham DE, Meinecke M, Wood JM. Impacts of the osmolality and the lumenal ionic strength on osmosensory transporter ProP in proteoliposomes. J Biol Chem 2012; 287:27813-22. [PMID: 22740696 DOI: 10.1074/jbc.m112.387936] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
H(+) symporter ProP serves as a paradigm for the study of osmosensing. ProP attains the same activity at the same osmolality when the medium outside cells or proteoliposomes is supplemented with diverse, membrane-impermeant solutes. The osmosensory mechanism of ProP has been probed by varying the solvent within membrane vesicles and proteoliposomes. ProP activation was not ion specific, did not require K(+), and could be elicited by large, uncharged solutes polyethylene glycols (PEGS). We hypothesized that ProP is an ionic strength sensor and lumenal macromolecules activate ProP by altering ion activities. The attainable range of lumenal ionic strength was expanded by lowering the phosphate concentration within proteoliposomes. ProP activity at high osmolality, but not the osmolality, yielding half-maximal activity (Π(1/2)/RT), decreased with the lumenal phosphate concentration. This was attributed to acidification of the proteoliposome lumen due to H(+)-proline symport. The ionic strength yielding half-maximal ProP activity was more anion-dependent than Π(1/2)/RT for proteoliposomes loaded with citrate, sulfate, phosphate, chloride, or iodide. The anion effects followed the Hofmeister series. Lumenal bovine serum albumin (BSA) lowered the lumenal ionic strength at which ProP became active. Osmolality measurements documented the non-idealities of solutions including potassium phosphate and other solutes. The impacts of PEGS and BSA on ion activities did not account for their impacts on ProP activity. The effects of the tested solutes on ProP appear to be non-coulombic in nature. They may arise from effects of preferential interactions and macromolecular crowding on the membrane or on ProP.
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Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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47
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Erkens GB, Majsnerowska M, ter Beek J, Slotboom DJ. Energy coupling factor-type ABC transporters for vitamin uptake in prokaryotes. Biochemistry 2012; 51:4390-6. [PMID: 22574898 DOI: 10.1021/bi300504v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Energy coupling factor (ECF) transporters are a subgroup of ATP-binding cassette (ABC) transporters involved in the uptake of vitamins and micronutrients in prokaryotes. In contrast to classical ABC importers, ECF transporters do not make use of water-soluble substrate binding proteins or domains but instead employ integral membrane proteins for substrate binding (named S-components). S-components form active translocation complexes with the ECF module, an assembly of two nucleotide-binding domains (NBDs, or EcfA) and a second transmembrane protein. In some cases, the ECF module is dedicated to a single S-component, but in many cases, the ECF module can interact with several different S-components that are unrelated in sequence and bind diverse substrates. The modular organization with exchangeable S-components on a single ECF module allows the transport of chemically different substrates via a common route. The recent determination of the crystal structures of the S-components that recognize thiamin and riboflavin has provided a first clue about the mechanism of S-component exchange. This review describes recent advances and the current views of the mechanism of transport by ECF transporters.
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Affiliation(s)
- Guus B Erkens
- University of Groningen, Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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48
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Abstract
To thrive, cells must control their own physical and chemical properties. This process is known as cellular homeostasis. The dilute solutions traditionally favored by experimenters do not simulate the cytoplasm, where macromolecular crowding and preferential interactions among constituents may dominate critical processes. Solutions that do simulate cytoplasmic conditions are now being characterized. Corresponding cytoplasmic properties can be varied systematically by imposing osmotic stress. This osmotic stress approach is revealing how cytoplasmic properties modulate protein folding and protein?nucleic acid interactions. Results suggest that cytoplasmic homeostasis may require adjustments to multiple, interwoven cytoplasmic properties. Osmosensory transporters with diverse structures and bioenergetic mechanisms activate in response to osmotic stress as other proteins inactivate. These transporters are serving as paradigms for the study of in vivo protein-solvent interactions. Experimenters have proposed three different osmosensory mechanisms. Distinct mechanisms may exist, or these proposals may reflect different perceptions of a single, unifying mechanism.
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Affiliation(s)
- Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, N1G 2W1, Canada.
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A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. J Bacteriol 2011; 194:376-94. [PMID: 22056929 DOI: 10.1128/jb.06244-11] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ~35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity.
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50
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Karasawa A, Erkens GB, Berntsson RPA, Otten R, Schuurman-Wolters GK, Mulder FAA, Poolman B. Cystathionine β-synthase (CBS) domains 1 and 2 fulfill different roles in ionic strength sensing of the ATP-binding cassette (ABC) transporter OpuA. J Biol Chem 2011; 286:37280-91. [PMID: 21878634 PMCID: PMC3199475 DOI: 10.1074/jbc.m111.284059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/26/2011] [Indexed: 01/05/2023] Open
Abstract
The cystathionine β-synthase module of OpuA in conjunction with an anionic membrane surface acts as a sensor of internal ionic strength, which allows the protein to respond to osmotic stress. We now show by chemical modification and cross-linking studies that CBS2-CBS2 interface residues are critical for transport activity and/or ionic regulation of transport, whereas CBS1 serves no functional role. We establish that Cys residues in CBS1, CBS2, and the nucleotide-binding domain are more accessible for cross-linking at high than low ionic strength, indicating that these domains undergo conformational changes when transiting between the active and inactive state. Structural analyses suggest that the cystathionine β-synthase module is largely unstructured. Moreover, we could substitute CBS1 by a linker and preserve ionic regulation of transport. These data suggest that CBS1 serves as a linker and the structured CBS2-CBS2 interface forms a hinge point for ionic strength-dependent rearrangements that are transmitted to the nucleotide-binding domain and thereby affect translocation activity.
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Affiliation(s)
- Akira Karasawa
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Guus B. Erkens
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ronnie P.-A. Berntsson
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Renee Otten
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Gea K. Schuurman-Wolters
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Frans A. A. Mulder
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- From the Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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