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Koehler M, Benthin J, Karanth S, Wiesenfarth M, Sebald K, Somoza V. Biophysical investigations using atomic force microscopy can elucidate the link between mouthfeel and flavour perception. NATURE FOOD 2024; 5:281-287. [PMID: 38605131 DOI: 10.1038/s43016-024-00958-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Food texture, along with taste and odour, is an important factor in determining food flavour. However, the physiological properties of oral texture perception require greater examination and definition. Here we explore recent trends and perspectives related to mouthfeel and its relevance in food flavour perception, with an emphasis on the biophysical point of view and methods. We propose that atomic force microscopy, combined with other biophysical techniques and more traditional food science approaches, offers a unique opportunity to study the mechanisms of mouthfeel at cellular and molecular levels. With this knowledge, food composition could be modified to develop healthier products by limiting salt, sugar, fat and calories while maintaining sensory qualities and consumer acceptance.
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Affiliation(s)
- Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.
- TUM Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, Freising, Germany.
| | - Julia Benthin
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Sanjai Karanth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Marina Wiesenfarth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Karin Sebald
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Veronika Somoza
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chair of Nutritional Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
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Cassidy CK, Qin Z, Frosio T, Gosink K, Yang Z, Sansom MSP, Stansfeld PJ, Parkinson JS, Zhang P. Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells. mBio 2023; 14:e0079323. [PMID: 37772839 PMCID: PMC10653900 DOI: 10.1128/mbio.00793-23] [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: 03/28/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and motility. Characterization of the molecular mechanisms underlying chemotaxis is of fundamental interest and requires a high-resolution structural picture of the sensing machinery, the chemosensory array. In this study, we combine cryo-electron tomography and molecular simulation to present the complete structure of the core signaling unit, the basic building block of chemosensory arrays, from Escherichia coli. Our results provide new insight into previously poorly-resolved regions of the complex and offer a structural basis for designing new experiments to test mechanistic hypotheses.
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Affiliation(s)
- C. Keith Cassidy
- Diamond Light Source, Didcot, United Kingdom
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Zhuan Qin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Khoosheh Gosink
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Peijun Zhang
- Diamond Light Source, Didcot, United Kingdom
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
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Pendleton A, Yeo WS, Alqahtani S, DiMaggio DA, Stone CJ, Li Z, Singh VK, Montgomery CP, Bae T, Brinsmade SR. Regulation of the Sae Two-Component System by Branched-Chain Fatty Acids in Staphylococcus aureus. mBio 2022; 13:e0147222. [PMID: 36135382 PMCID: PMC9600363 DOI: 10.1128/mbio.01472-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is a ubiquitous Gram-positive bacterium and an opportunistic human pathogen. S. aureus pathogenesis relies on a complex network of regulatory factors that adjust gene expression. Two important factors in this network are CodY, a repressor protein responsive to nutrient availability, and the SaeRS two-component system (TCS), which responds to neutrophil-produced factors. Our previous work revealed that CodY regulates the secretion of many toxins indirectly via Sae through an unknown mechanism. We report that disruption of codY results in increased levels of phosphorylated SaeR (SaeR~P) and that codY mutant cell membranes contain a higher percentage of branched-chain fatty acids (BCFAs) than do wild-type membranes, prompting us to hypothesize that changes to membrane composition modulate the activity of the SaeS sensor kinase. Disrupting the lpdA gene encoding dihydrolipoyl dehydrogenase, which is critical for BCFA synthesis, significantly reduced the abundance of SaeR, phosphorylated SaeR, and BCFAs in the membrane, resulting in reduced toxin production and attenuated virulence. Lower SaeR levels could be explained in part by reduced stability. Sae activity in the lpdA mutant could be complemented genetically and chemically with exogenous short- or full-length BCFAs. Intriguingly, lack of lpdA also alters the activity of other TCSs, suggesting a specific BCFA requirement managing the basal activity of multiple TCSs. These results reveal a novel method of posttranscriptional virulence regulation via BCFA synthesis, potentially linking CodY activity to multiple virulence regulators in S. aureus. IMPORTANCE Two-component systems (TCSs) are an essential way that bacteria sense and respond to their environment. These systems are usually composed of a membrane-bound histidine kinase that phosphorylates a cytoplasmic response regulator. Because most of the histidine kinases are embedded in the membrane, lipids can allosterically regulate the activity of these sensors. In this study, we reveal that branched-chain fatty acids (BCFAs) are required for the activation of multiple TCSs in Staphylococcus aureus. Using both genetic and biochemical data, we show that the activity of the virulence activator SaeS and the phosphorylation of its response regulator SaeR are reduced in a branched-chain keto-acid dehydrogenase complex mutant and that defects in BCFA synthesis have far-reaching consequences for exotoxin secretion and virulence. Finally, we show that mutation of the global nutritional regulator CodY alters BCFA content in the membrane, revealing a potential mechanism of posttranscriptional regulation of the Sae system by CodY.
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Affiliation(s)
| | - Won-Sik Yeo
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Shahad Alqahtani
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Carl J. Stone
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Zhaotao Li
- Center for Microbial Pathogenesis, Abigail Wexner Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Vineet K. Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Christopher P. Montgomery
- Center for Microbial Pathogenesis, Abigail Wexner Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
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Abstract
Methylesterase/deamidase CheB is a key component of bacterial chemotaxis systems. It is also a prominent example of a two-component response regulator in which the effector domain is an enzyme. Like other response regulators, CheB is activated by phosphorylation of an aspartyl residue in its regulatory domain, creating an open conformation between its two domains. Studies of CheB in Escherichia coli and related organisms have shown that its enzymatic action is also enhanced by a pentapeptide-binding site for the enzyme at the chemoreceptor carboxyl terminus. Related carboxyl-terminal pentapeptides are found on >25,000 chemoreceptor sequences distributed across 11 bacterial phyla and many bacterial species, in which they presumably play similar roles. Yet, little is known about the interrelationship of CheB phosphorylation, pentapeptide binding, and interactions with its substrate methylesters and amides on the body of the chemoreceptor. We investigated by characterizing the binding kinetics of CheB to Nanodisc-inserted chemoreceptor dimers. The resulting kinetic and thermodynamic constants revealed a synergy between CheB phosphorylation and pentapeptide binding in which a phosphorylation mimic enhanced pentapeptide binding, and the pentapeptide served not only as a high-affinity tether for CheB but also selected the activated conformation of the enzyme. The basis of this selection was revealed by molecular modeling that predicted a pentapeptide-binding site on CheB which existed only in the open, activated enzyme. Recruitment of activated enzyme by selective tethering represents a previously unappreciated strategy for regulating response regulator action, one that may well occur in other two-component systems.
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Gordon JB, Hoffman MC, Troiano JM, Li M, Hazelbauer GL, Schlau-Cohen GS. Concerted Differential Changes of Helical Dynamics and Packing upon Ligand Occupancy in a Bacterial Chemoreceptor. ACS Chem Biol 2021; 16:2472-2480. [PMID: 34647725 PMCID: PMC9990816 DOI: 10.1021/acschembio.1c00576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transmembrane receptors are central components of the chemosensory systems by which motile bacteria detect and respond to chemical gradients. An attractant bound to the receptor periplasmic domain generates conformational signals that regulate a histidine kinase interacting with its cytoplasmic domain. Ligand-induced signaling through the periplasmic and transmembrane domains of the receptor involves a piston-like helical displacement, but the nature of this signaling through the >200 Å four-helix coiled coil of the cytoplasmic domain had not yet been identified. We performed single-molecule Förster resonance energy transfer measurements on Escherichia coli aspartate receptor homodimers inserted into native phospholipid bilayers enclosed in nanodiscs. The receptors were labeled with fluorophores at diagnostic positions near the middle of the cytoplasmic coiled coil. At these positions, we found that the two N-helices of the homodimer were more distant, that is, less tightly packed and more dynamic than the companion C-helix pair, consistent with previous deductions that the C-helices form a stable scaffold and the N-helices are dynamic. Upon ligand binding, the scaffold pair compacted further, while separation and dynamics of the dynamic pair increased. Thus, ligand binding had asymmetric effects on the two helical pairs, shifting mean distances in opposite directions and increasing the dynamics of one pair. We suggest that this reflects a conformational change in which differential alterations to the packing and dynamics of the two helical pairs are coupled. These coupled changes could represent a previously unappreciated mode of conformational signaling that may well occur in other coiled-coil signaling proteins.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Julianne M Troiano
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Mingshan Li
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
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Tookmanian EM, Belin BJ, Sáenz JP, Newman DK. The role of hopanoids in fortifying rhizobia against a changing climate. Environ Microbiol 2021; 23:2906-2918. [PMID: 33989442 DOI: 10.1111/1462-2920.15594] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.
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Affiliation(s)
- Elise M Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Brittany J Belin
- Department of Embryology, The Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - James P Sáenz
- B CUBE Center for Molecular Bioengineering, Tatzberg 41, Technische Universität Dresden, Dresden, 01307, Germany
| | - Dianne K Newman
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
- Division of Geology & Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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Pluhackova K, Horner A. Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity. BMC Biol 2021; 19:4. [PMID: 33441107 PMCID: PMC7807449 DOI: 10.1186/s12915-020-00936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. RESULTS To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. CONCLUSIONS The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.
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Affiliation(s)
- Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, Basel, 4058, Switzerland.
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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Toyotake Y, Nishiyama M, Yokoyama F, Ogawa T, Kawamoto J, Kurihara T. A Novel Lysophosphatidic Acid Acyltransferase of Escherichia coli Produces Membrane Phospholipids with a cis-vaccenoyl Group and Is Related to Flagellar Formation. Biomolecules 2020; 10:E745. [PMID: 32403425 PMCID: PMC7277886 DOI: 10.3390/biom10050745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/02/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Lysophosphatidic acid acyltransferase (LPAAT) introduces fatty acyl groups into the sn-2 position of membrane phospholipids (PLs). Various bacteria produce multiple LPAATs, whereas it is believed that Escherichia coli produces only one essential LPAAT homolog, PlsC-the deletion of which is lethal. However, we found that E. coli possesses another LPAAT homolog named YihG. Here, we show that overexpression of YihG in E. coli carrying a temperature-sensitive mutation in plsC allowed its growth at non-permissive temperatures. Analysis of the fatty acyl composition of PLs from the yihG-deletion mutant (∆yihG) revealed that endogenous YihG introduces the cis-vaccenoyl group into the sn-2 position of PLs. Loss of YihG did not affect cell growth or morphology, but ∆yihG cells swam well in liquid medium in contrast to wild-type cells. Immunoblot analysis showed that FliC was highly expressed in ∆yihG cells, and this phenotype was suppressed by expression of recombinant YihG in ∆yihG cells. Transmission electron microscopy confirmed that the flagellar structure was observed only in ∆yihG cells. These results suggest that YihG has specific functions related to flagellar formation through modulation of the fatty acyl composition of membrane PLs.
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Affiliation(s)
- Yosuke Toyotake
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Masayoshi Nishiyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Fumiaki Yokoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Takuya Ogawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
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Jia X, Hua J, Liu L, Xu Z, Li Y. Phenotypic characterization of pathogenic Cronobacter spp. strains. Microb Pathog 2018; 121:232-237. [PMID: 29800699 DOI: 10.1016/j.micpath.2018.05.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/15/2018] [Accepted: 05/22/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND Cronobacter species are Gram-negative opportunistic foodborne pathogens that may cause enterocolitis, bacteremia and meningitis in neonates and premature neonates. Lipopolysaccharide (LPS) serves as the major component of the outer membrane of cell, is a potential virulence factor for Cronobacter. METHODS Given the potential importance of this molecule in infection and virulence, SDS-PAGE of LPS, MS and TLC characterization of phospholipids and phenotypic characterization of Cronobacter spp. strains were carried out. RESULT The phospholipids from Cronobacter yielded four major peaks at m/z 719.9, 733.9, 747.9 and 773.9 in the spectrum. All Cronobacter showed O-antigen bands except C. muytjensii ATCC 51329. When Cronobacter defect O-antigen, the outer membrane permeability and cell surface hydrophobicities are increased. All Cronobacter are able to grow under pH 5.0 condition and able to grow under 6% NaCl concentration. C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter. CONCLUSION Invasion of pathogens into a host cell is critical component to an infectious case. And C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter.
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Affiliation(s)
- Xiangyin Jia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jingjing Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Lu Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Zhenbo Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China; Department of Microbial Pathogenesis, University of Maryland, Baltimore, 21201, USA; Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, 510640, China.
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
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10
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Flexible Hinges in Bacterial Chemoreceptors. J Bacteriol 2018; 200:JB.00593-17. [PMID: 29229700 DOI: 10.1128/jb.00593-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022] Open
Abstract
Transmembrane bacterial chemoreceptors are extended, rod-shaped homodimers with ligand-binding sites at one end and interaction sites for signaling complex formation and histidine kinase control at the other. There are atomic-resolution structures of chemoreceptor fragments but not of intact, membrane-inserted receptors. Electron tomography of in vivo signaling complex arrays lack distinct densities for chemoreceptor rods away from the well-ordered base plate region, implying structural heterogeneity. We used negative staining, transmission electron microscopy, and image analysis to characterize the molecular shapes of intact homodimers of the Escherichia coli aspartate receptor Tar rendered functional by insertion into nanodisc-provided E. coli lipid bilayers. Single-particle analysis plus tomography of particles in a three-dimensional matrix revealed two bend loci in the chemoreceptor cytoplasmic domain, (i) a short, two-strand gap between the membrane-proximal, four-helix-bundle HAMP (histidine kinases, adenylyl cyclases, methyl-accepting chemoreceptors, and phosphatases) domain and the membrane-distal, four-helix coiled coil and (ii) aligned glycines in the extended, four-helix coiled coil, the position of a bend noted in the previous X-ray structure of a receptor fragment. Our images showed HAMP bends from 0° to ∼13° and glycine bends from 0° to ∼20°, suggesting that the loci are flexible hinges. Variable hinge bending explains indistinct densities for receptor rods outside the base plate region in subvolume averages of chemotaxis arrays. Bending at flexible hinges was not correlated with the chemoreceptor signaling state. However, our analyses showed that chemoreceptor bending avoided what would otherwise be steric clashes between neighboring receptors that would block the formation of core signaling complexes and chemoreceptor arrays.IMPORTANCE This work provides new information about the shape of transmembrane bacterial chemoreceptors, crucial components in the molecular machinery of bacterial chemotaxis. We found that intact, lipid-bilayer-inserted, and thus functional homodimers of the Escherichia coli chemoreceptor Tar exhibited bends at two flexible hinges along their ∼200-Å, rod-like, cytoplasmic domains. One hinge was at the short, two-strand gap between the membrane-proximal, four-helix-bundle HAMP (histidine kinases, adenylyl cyclases, methyl-accepting chemoreceptors, and phosphatases) domain and the membrane-distal, four-helix coiled coil. The other hinge was at aligned glycines in the extended, four-helix coiled coil, where a bend had been identified in the X-ray structure of a chemoreceptor fragment. Our analyses showed that flexible hinge bending avoided structural clashes in chemotaxis core complexes and their arrays.
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11
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Lipid-Mediated Regulation of Embedded Receptor Kinases via Parallel Allosteric Relays. Biophys J 2017; 112:643-654. [PMID: 28256224 DOI: 10.1016/j.bpj.2016.12.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/15/2016] [Accepted: 12/12/2016] [Indexed: 01/29/2023] Open
Abstract
Membrane-anchored receptors are essential cellular signaling elements for stimulus sensing, propagation, and transmission inside cells. However, the contributions of lipid interactions to the function and dynamics of embedded receptor kinases have not been described in detail. In this study, we used amide hydrogen/deuterium exchange mass spectrometry, a sensitive biophysical approach, to probe the dynamics of a membrane-embedded receptor kinase, EnvZ, together with functional assays to describe the role of lipids in receptor kinase function. Our results reveal that lipids play an important role in regulating receptor function through interactions with transmembrane segments, as well as through peripheral interactions with nonembedded domains. Specifically, the lipid membrane allosterically modulates the activity of the embedded kinase by altering the dynamics of a glycine-rich motif that is critical for phosphotransfer from ATP. This allostery in EnvZ is independent of membrane composition and involves direct interactions with transmembrane and periplasmic segments, as well as peripheral interactions with nonembedded domains of the protein. In the absence of the membrane-spanning regions, lipid allostery is propagated entirely through peripheral interactions. Whereas lipid allostery impacts the phosphotransferase function of the kinase, extracellular stimulus recognition is mediated via a four-helix bundle subdomain located in the cytoplasm, which functions as the osmosensing core through osmolality-dependent helical stabilization. Our findings emphasize the functional modularity in a membrane-embedded kinase, separated into membrane association, phosphotransferase function, and stimulus recognition. These components are integrated through long-range communication relays, with lipids playing an essential role in regulation.
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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13
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Samanta D, Widom J, Borbat PP, Freed JH, Crane BR. Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor. J Biol Chem 2016; 291:25809-25814. [PMID: 27803157 DOI: 10.1074/jbc.c116.757492] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
Flagellated bacteria modulate their swimming behavior in response to environmental cues through the CheA/CheY signaling pathway. In addition to responding to external chemicals, bacteria also monitor internal conditions that reflect the availability of oxygen, light, and reducing equivalents, in a process termed "energy taxis." In Escherichia coli, the transmembrane receptor Aer is the primary energy sensor for motility. Genetic and physiological data suggest that Aer monitors the electron transport chain through the redox state of its FAD cofactor. However, direct biochemical data correlating FAD redox chemistry with CheA kinase activity have been lacking. Here, we test this hypothesis via functional reconstitution of Aer into nanodiscs. As purified, Aer contains fully oxidized FAD, which can be chemically reduced to the anionic semiquinone (ASQ). Oxidized Aer activates CheA, whereas ASQ Aer reversibly inhibits CheA. Under these conditions, Aer cannot be further reduced to the hydroquinone, in contrast to the proposed Aer signaling model. Pulse ESR spectroscopy of the ASQ corroborates a potential mechanism for signaling in that the resulting distance between the two flavin-binding PAS (Per-Arnt-Sim) domains implies that they tightly sandwich the signal-transducing HAMP domain in the kinase-off state. Aer appears to follow oligomerization patterns observed for related chemoreceptors, as higher loading of Aer dimers into nanodiscs increases kinase activity. These results provide a new methodological platform to study Aer function along with new mechanistic details into its signal transduction process.
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Affiliation(s)
- Dipanjan Samanta
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Joanne Widom
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and
| | - Peter P Borbat
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Jack H Freed
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and.,the National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca, New York 14853
| | - Brian R Crane
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 and
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14
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Duneau JP, Khao J, Sturgis JN. Lipid perturbation by membrane proteins and the lipophobic effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:126-134. [PMID: 27794424 DOI: 10.1016/j.bbamem.2016.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
Abstract
Understanding how membrane proteins interact with their environment is fundamental to the understanding of their structure, function and interactions. We have performed coarse-grained molecular dynamics simulations on a series of membrane proteins in a membrane environment to examine the perturbations of the lipids by the presence of protein. We analyze these perturbations in terms of elastic membrane deformations and local lipid protein interactions. However these two factors are insufficient to describe the variety of effects that we observe and the changes caused by membranes proteins to the structure and dynamics of their lipid environment. Other factors that change the conformation available to lipid molecules are evident and are able to modify lipid structure far from the protein surface, and thus mediate long-range interactions between membrane proteins. We suggest that these multiple modifications to lipid behavior are responsible, at the molecular level, for the lipophobic effect we have proposed to account for our observations of membrane protein organization.
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Affiliation(s)
- Jean-Pierre Duneau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
| | - Jonathan Khao
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France
| | - James N Sturgis
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
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15
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Bartelli NL, Hazelbauer GL. Bacterial Chemoreceptor Dynamics: Helical Stability in the Cytoplasmic Domain Varies with Functional Segment and Adaptational Modification. J Mol Biol 2016; 428:3789-804. [PMID: 27318193 PMCID: PMC5193150 DOI: 10.1016/j.jmb.2016.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/28/2022]
Abstract
Dynamics are thought to be important features of structure and signaling in the cytoplasmic domain of bacterial chemoreceptors. However, little is known about which structural features are dynamic. For this largely helical domain, comprising a four-helix bundle and an extended four-helix coiled coil, functionally important structural dynamics likely involves helical mobility and stability. To investigate, we used continuous wave EPR spectroscopy and site-specific spin labels that directly probed, in essentially physiological conditions, the mobility of helical backbones in the cytoplasmic domain of intact chemoreceptor Tar homodimers inserted into lipid bilayers of Nanodiscs. We observed differences among functional regions, between companion helices in helical hairpins of the coiled coil and between receptor conformational states generated by adaptational modification. Increased adaptational modification decreased helical dynamics while preserving dynamics differences among functional regions and between companion helices. In contrast, receptor ligand occupancy did not have a discernable effect on dynamics to which our approach was sensitive, implying that the two sensory inputs alter different chemoreceptor features. Spectral fitting indicated that differences in helical dynamics we observed for ensemble spin-label mobility reflected differences in proportions of a minority receptor population in which the otherwise helical backbone was essentially disordered. We suggest that our measurements provided site-specific snapshots of equilibria between a majority state of well-ordered helix and a minority state of locally disordered polypeptide backbone. Thus, the proportion of polypeptide chain that is locally and presumably transiently disordered is a structural feature of cytoplasmic domain dynamics that varies with functional region and modification-induced signaling state.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA
| | - Gerald L Hazelbauer
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
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16
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Bartelli NL, Hazelbauer GL. Differential backbone dynamics of companion helices in the extended helical coiled-coil domain of a bacterial chemoreceptor. Protein Sci 2015; 24:1764-76. [PMID: 26257396 DOI: 10.1002/pro.2767] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 12/25/2022]
Abstract
Cytoplasmic domains of transmembrane bacterial chemoreceptors are largely extended four-helix coiled coils. Previous observations suggested the domain was structurally dynamic. We probed directly backbone dynamics of this domain of the transmembrane chemoreceptor Tar from Escherichia coli using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. Spin labels were positioned on solvent-exposed helical faces because EPR spectra for such positions reflect primarily polypeptide backbone movements. We acquired spectra for spin-labeled, intact receptor homodimers solubilized in detergent or inserted into native E. coli lipid bilayers in Nanodiscs, characterizing 16 positions distributed throughout the cytoplasmic domain and on both helices of its helical hairpins, one amino terminal to the membrane-distal tight turn (N-helix), and the other carboxyl terminal (C-helix). Detergent solubilization increased backbone dynamics for much of the domain, suggesting that loss of receptor activities upon solubilization reflects wide-spread destabilization. For receptors in either condition, we observed an unanticipated difference between the N- and C-helices. For bilayer-inserted receptors, EPR spectra from sites in the membrane-distal protein-interaction region and throughout the C-helix were typical of well-structured helices. In contrast, for approximately two-thirds of the N-helix, from its origin as the AS-2 helix of the membrane-proximal HAMP domain to the beginning of the membrane-distal protein-interaction region, spectra had a significantly mobile component, estimated by spectral deconvolution to average approximately 15%. Differential helical dynamics suggests a four-helix bundle organization with a pair of core scaffold helices and two more dynamic partner helices. This newly observed feature of chemoreceptor structure could be involved in receptor function.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Biochemistry, University of Missouri Columbia, 117 Schweitzer Hall, Missouri, 65211
| | - Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri Columbia, 117 Schweitzer Hall, Missouri, 65211
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17
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Keller R, Ariöz C, Hansmeier N, Stenberg-Bruzell F, Burstedt M, Vikström D, Kelly A, Wieslander Å, Daley DO, Hunke S. The Escherichia coli Envelope Stress Sensor CpxA Responds to Changes in Lipid Bilayer Properties. Biochemistry 2015; 54:3670-6. [PMID: 25993101 DOI: 10.1021/acs.biochem.5b00242] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Cpx stress response system is induced by various environmental and cellular stimuli. It is also activated in Escherichia coli strains lacking the major phospholipid, phosphatidylethanolamine (PE). However, it is not known whether CpxA directly senses changes in the lipid bilayer or the presence of misfolded proteins due to the lack of PE in their membranes. To address this question, we used an in vitro reconstitution system and vesicles with different lipid compositions to track modulations in the activity of CpxA in different lipid bilayers. Moreover, the Cpx response was validated in vivo by monitoring expression of a PcpxP-gfp reporter in lipid-engineered strains of E. coli. Our combined data indicate that CpxA responds specifically to different lipid compositions.
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Affiliation(s)
- Rebecca Keller
- †Department of Pharmacy and Biochemistry, Johannes Gutenberg-University, D-55128 Mainz, Germany
| | - Candan Ariöz
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Nicole Hansmeier
- §Department of Microbiology, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Filippa Stenberg-Bruzell
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Malin Burstedt
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - David Vikström
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Amelie Kelly
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Åke Wieslander
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Daniel O Daley
- ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Sabine Hunke
- ∥Molecular Microbiology, University of Osnabrück, D-49076 Osnabrück, Germany
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18
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Parkinson JS, Hazelbauer GL, Falke JJ. Signaling and sensory adaptation in Escherichia coli chemoreceptors: 2015 update. Trends Microbiol 2015; 23:257-66. [PMID: 25834953 DOI: 10.1016/j.tim.2015.03.003] [Citation(s) in RCA: 253] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 11/25/2022]
Abstract
Motile Escherichia coli cells track gradients of attractant and repellent chemicals in their environment with transmembrane chemoreceptor proteins. These receptors operate in cooperative arrays to produce large changes in the activity of a signaling kinase, CheA, in response to small changes in chemoeffector concentration. Recent research has provided a much deeper understanding of the structure and function of core receptor signaling complexes and the architecture of higher-order receptor arrays, which, in turn, has led to new insights into the molecular signaling mechanisms of chemoreceptor networks. Current evidence supports a new view of receptor signaling in which stimulus information travels within receptor molecules through shifts in the dynamic properties of adjoining structural elements rather than through a few discrete conformational states.
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Affiliation(s)
- John S Parkinson
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| | - Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri Columbia, Columbia, MO 65211, USA
| | - Joseph J Falke
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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19
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Zhao Y, Zhong Z, Low ZX, Yao Z. A multifunctional multi-walled carbon nanotubes/ceramic membrane composite filter for air purification. RSC Adv 2015. [DOI: 10.1039/c5ra18200j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carbon nanotubes (CNTs) are very small diameter fibers that have the potential to be integrated into filters to further increase particle capture efficiency.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering
- National Engineering Research Center for Special Separation Membrane
- Nanjing Tech University
- Nanjing 210009
- China
| | - Zhaoxiang Zhong
- State Key Laboratory of Materials-Oriented Chemical Engineering
- National Engineering Research Center for Special Separation Membrane
- Nanjing Tech University
- Nanjing 210009
- China
| | - Ze-Xian Low
- Centre for Advanced Separations Engineering and Membranes@Bath
- Department of Chemical Engineering
- University of Bath
- Bath BA2 7AY
- UK
| | - Zhong Yao
- State Key Laboratory of Materials-Oriented Chemical Engineering
- National Engineering Research Center for Special Separation Membrane
- Nanjing Tech University
- Nanjing 210009
- China
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20
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Wang Y, Wang J, Li Y, Wang B, Tao G, Wang X. Structure characterization of phospholipids and lipid A of Pseudomonas putida KT2442. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:739-746. [PMID: 26579930 DOI: 10.1255/ejms.1390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Pseudomonas putida KT2442 is an important bacterium for producing various types of polyhydroxyalkanoate polymers. Phospholipids and lipid A in membranes of P. putida play important roles in stress responses, but detailed structural information of these lipids is not known. In this study, phospholipids and lipid A were isolated from P. putida KT2442, and their structures were analyzed using thin layer chromatography, high performance liquid chromatography, and electrospray ionization/mass spectrometry. Major phospholipids in P. putida KT2442 were phosphatidylethanolamine (79.9%), phosphatidylglycero1 (12.7%), and cardiolipin (7.4%), with C16:1 and/or C18:1 acyl chains. Four lipid A species were found in P. putida KT2442: two are hexa-acylated, and the other two are penta-acylated. Compared with lipid A of P. aeruginosa, P. putida lipid A has less hydroxylation on the secondary acyl chains and less modification. Therefore, P. putida lipid A could be used as a base structure to investigate lipid A modification of P. aeruginosa for understanding its pathogenesis.
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Affiliation(s)
- Yuqian Wang
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, Chinaof Biotechnology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
| | - Ye Li
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, Chinaotechnology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
| | - Biwen Wang
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, Chinaotechnology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
| | - Guanjun Tao
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, Chinaotechnology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, Chinaechnology, State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 21422, China.
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21
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Haselwandter CA, Wingreen NS. The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. PLoS Comput Biol 2014; 10:e1003932. [PMID: 25503274 PMCID: PMC4263354 DOI: 10.1371/journal.pcbi.1003932] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 09/22/2014] [Indexed: 01/04/2023] Open
Abstract
In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of “gateway” states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers. The chemotaxis system allows bacteria to respond to minute changes in chemical concentration, and serves as a paradigm for biological signal processing and the self-assembly of large protein lattices in living cells. The sensitivity of the chemotaxis system relies crucially on cooperative interactions among chemoreceptor trimers, which are organized into intricate honeycomb lattices. Chemoreceptors are membrane proteins and, hence, are expected to deform the surrounding lipid bilayer, leading to membrane-mediated interactions between chemoreceptor trimers. Using a biophysical model of bilayer-chemoreceptor interactions we show that the membrane-mediated interactions induced by chemoreceptor trimers provide a mechanism for the observed self-assembly of chemoreceptor lattices. We find that the directionality of membrane-mediated interactions between trimers complements protein-protein interactions in the stabilization of the observed honeycomb architecture of chemoreceptor lattices. Our results suggest that the symmetry of membrane protein complexes such as chemoreceptor trimers is reflected in the anisotropy of membrane-mediated interactions, yielding a general mechanism for the self-assembly of ordered protein lattices in cell membranes.
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Affiliation(s)
- Christoph A. Haselwandter
- Departments of Physics & Astronomy and Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (CAH); (NSW)
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (CAH); (NSW)
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22
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Abstract
Bacterial chemotaxis is mediated by signaling complexes that sense chemical gradients and direct bacteria to favorable environments by controlling a histidine kinase as a function of chemoreceptor ligand occupancy. Core signaling complexes contain two trimers of transmembrane chemoreceptor dimers, each trimer binding a coupling protein CheW and a protomer of the kinase dimer. Core complexes assemble into hexagons, and these form hexagonal arrays. The notable cooperativity and amplification in bacterial chemotaxis is thought to reflect allosteric interactions in cores, hexagons, and arrays, but little is known about this presumed allostery. We investigated allostery in core complexes assembled with two chemoreceptor species, each recognizing a different ligand. Chemoreceptors were inserted in Nanodiscs, which rendered them water soluble and allowed isolation of individual complexes. Neighboring dimers in receptor trimers influenced one another's operational ligand affinity, indicating allosteric coupling. However, this coupling did not include the key function of kinase inhibition. Our data indicated that only one receptor dimer could inhibit kinase as a function of ligand occupancy. This selective allosteric coupling corresponded with previously identified structural asymmetry: only one dimer in a trimer contacts kinase and only one CheW. We suggest one of these dimers couples ligand occupancy to kinase inhibition. Additionally, we found that kinase protomers are allosterically coupled, conveying inhibition across the dimer interface. Because kinase dimers connect core complex hexagons, allosteric communication across dimer interfaces provides a pathway for receptor-generated kinase inhibition in one hexagon to spread to another, providing a crucial step for the extensive amplification characteristic of chemotactic signaling.
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23
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Briegel A, Ladinsky MS, Oikonomou C, Jones CW, Harris MJ, Fowler DJ, Chang YW, Thompson LK, Armitage JP, Jensen GJ. Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling. eLife 2014; 3:e02151. [PMID: 24668172 PMCID: PMC3964821 DOI: 10.7554/elife.02151] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm. Although the cytoplasmic cluster is essential for normal chemotaxis in some organisms, its structure and function remain unknown. Here we use electron cryotomography to image the cytoplasmic chemoreceptor cluster in Rhodobacter sphaeroides and Vibrio cholerae. We show that just like transmembrane arrays, cytoplasmic clusters contain trimers-of-receptor-dimers organized in 12-nm hexagonal arrays. In contrast to transmembrane arrays, however, cytoplasmic clusters comprise two CheA/CheW baseplates sandwiching two opposed receptor arrays. We further show that cytoplasmic fragments of normally transmembrane E. coli chemoreceptors form similar sandwiched structures in the presence of molecular crowding agents. Together these results suggest that the 12-nm hexagonal architecture is fundamentally important and that sandwiching and crowding can replace the stabilizing effect of the membrane. DOI:http://dx.doi.org/10.7554/eLife.02151.001 Many bacteria swim through water by rotating tiny hair-like structures called flagella. In E. coli, if all the flagella on the surface of a bacterium rotate in a counterclockwise fashion, then it will swim in a particular direction, but if the flagella all rotate in an clockwise fashion, then the bacterium will stop swimming and start to tumble. Bacteria use a combination of swimming and tumbling in order to move towards or away from certain chemicals. For example, a bacterium is able to move towards a source of nutrients because it is constantly evaluating its environment and will swim forward for longer periods of time when it recognizes the concentration of the nutrient is increasing. And if it senses that the nutrient concentration is decreasing, it will tumble in an effort to move in a different direction. Many bacteria, such as E. coli, rely on proteins in their cell membrane called chemoreceptors to sense specific chemicals and then send signals that tell the flagella how to rotate. These transmembrane receptors and their role in chemotaxis—that is, movement towards or away from specific chemicals in the environment—have been widely studied. However, other bacteria also have chemoreceptors in the cytoplasm inside the bacterial cell, and much less is known about these. Now, Briegel et al. have examined the cytoplasmic chemoreceptors of two unrelated bacteria, R. sphaeroides and V. cholera, and found that the cytoplasmic chemoreceptors arrange themselves in hexagonal arrays, similar to the way that transmembrane chemoreceptors are arranged. However, the cytoplasmic chemoreceptors arrange themselves in a two-layer sandwich-like structure, whereas the transmembrane chemoreceptors are arranged in just one layer. The next step is to understand how chemical binding causes these arrays to send their signals to the motor. A complete understanding of this signaling system may ultimately allow scientists to re-engineer it to draw bacteria to targets of medical or environmental interest, such as cancer cells or contaminated soils. DOI:http://dx.doi.org/10.7554/eLife.02151.002
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Affiliation(s)
- Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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24
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Briegel A, Wong ML, Hodges HL, Oikonomou CM, Piasta KN, Harris MJ, Fowler DJ, Thompson LK, Falke JJ, Kiessling LL, Jensen GJ. New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography. Biochemistry 2014; 53:1575-85. [PMID: 24580139 PMCID: PMC3985956 DOI: 10.1021/bi5000614] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial chemoreceptors cluster in highly ordered, cooperative, extended arrays with a conserved architecture, but the principles that govern array assembly remain unclear. Here we show images of cellular arrays as well as selected chemoreceptor complexes reconstituted in vitro that reveal new principles of array structure and assembly. First, in every case, receptors clustered in a trimers-of-dimers configuration, suggesting this is a highly favored fundamental building block. Second, these trimers-of-receptor dimers exhibited great versatility in the kinds of contacts they formed with each other and with other components of the signaling pathway, although only one architectural type occurred in native arrays. Third, the membrane, while it likely accelerates the formation of arrays, was neither necessary nor sufficient for lattice formation. Molecular crowding substituted for the stabilizing effect of the membrane and allowed cytoplasmic receptor fragments to form sandwiched lattices that strongly resemble the cytoplasmic chemoreceptor arrays found in some bacterial species. Finally, the effective determinant of array structure seemed to be CheA and CheW, which formed a "superlattice" of alternating CheA-filled and CheA-empty rings that linked receptor trimers-of-dimer units into their native hexagonal lattice. While concomitant overexpression of receptors, CheA, and CheW yielded arrays with native spacing, the CheA occupancy was lower and less ordered, suggesting that temporal and spatial coordination of gene expression driven by a single transcription factor may be vital for full order, or that array overgrowth may trigger a disassembly process. The results described here provide new insights into the assembly intermediates and assembly mechanism of this massive macromolecular complex.
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Affiliation(s)
- Ariane Briegel
- Division of Biology, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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