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Hickman SJ, Miller HL, Bukys A, Kapanidis AN, Berks BC. Aberrant Topologies of Bacterial Membrane Proteins Revealed by High Sensitivity Fluorescence Labelling. J Mol Biol 2024; 436:168368. [PMID: 37977298 DOI: 10.1016/j.jmb.2023.168368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The cytoplasmic membrane compartmentalises the bacterial cell into cytoplasm and periplasm. Proteins located in this membrane have a defined topology that is established during their biogenesis. However, the accuracy of this fundamental biosynthetic process is unknown. We developed compartment-specific fluorescence labelling methods with up to single-molecule sensitivity. Application of these methods to the single and multi-spanning membrane proteins of the Tat protein transport system revealed rare topogenesis errors. This methodology also detected low level soluble protein mislocalization from the cytoplasm to the periplasm. This study shows that it is possible to uncover rare errors in protein localization by leveraging the high sensitivity of fluorescence methods.
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Affiliation(s)
- Samuel J Hickman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
| | - Alfredas Bukys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom; Kavli Institute for Nanoscience Discovery, University of Oxford, Sherrington Road, Oxford OX1 3QU, United Kingdom.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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Bogdanov M. Renovating a double fence with or without notifying the next door and across the street neighbors: why the biogenic cytoplasmic membrane of Gram-negative bacteria display asymmetry? Emerg Top Life Sci 2023; 7:137-150. [PMID: 36960750 PMCID: PMC10725183 DOI: 10.1042/etls20230042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023]
Abstract
The complex two-membrane organization of the envelope of Gram-negative bacteria imposes an unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on the cytoplasm facing leaflet of the cytoplasmic (inner) membrane (IM), across the IM and between the IM and outer membrane (OM). Balanced growth of two membranes and continuous loss of phospholipids in the periplasmic leaflet of the IM as metabolic precursors for envelope components and for translocation to the OM requires a constant supply of phospholipids in the IM cytosolic leaflet. At present we have no explanation as to why the biogenic E. coli IM displays asymmetry. Lipid asymmetry is largely related to highly entropically disfavored, unequal headgroup and acyl group asymmetries which are usually actively maintained by active mechanisms. However, these mechanisms are largely unknown for bacteria. Alternatively, lipid asymmetry in biogenic IM could be metabolically controlled in order to maintain uniform bilayer growth and asymmetric transmembrane arrangement by balancing temporally the net rates of synthesis and flip-flop, inter IM and OM bidirectional flows and bilayer chemical and physical properties as spontaneous response. Does such flippase-less or 'lipid only", 'passive' mechanism of generation and maintenance of lipid asymmetry exists in the IM? The driving force for IM asymmetry can arise from the packing requirements imposed upon the bilayer system during cell division through disproportional distribution of two negatively curved phospholipids, phosphatidylethanolamine and cardiolipin, with consistent reciprocal tendency to increase and decrease lipid order in each membrane leaflet respectively.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, U.S.A
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McCool EN, Lubeckyj RA, Chen D, Sun L. Top-Down Proteomics by Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Characterization of Proteoforms in Complex Samples. Methods Mol Biol 2022; 2531:107-124. [PMID: 35941482 DOI: 10.1007/978-1-0716-2493-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Capillary zone electrophoresis (CZE) is a fundamentally simple and highly efficient separation technique based on differences in electrophoretic mobilities of analytes. CZE-mass spectrometry (MS) has become an important analytical tool in top-down proteomics which aims to delineate proteoforms in cells comprehensively, because of the improvement of capillary coatings, sample stacking methods, and CE-MS interfaces. Here, we present a CZE-MS/MS-based top-down proteomics procedure for the characterization of a standard protein mixture and an Escherichia coli (E. coli) cell lysate using linear polyacrylamide-coated capillaries, a dynamic pH junction sample stacking method, a commercialized electro-kinetically pumped sheath flow CE-MS interface and an Orbitrap mass spectrometer. CZE-MS/MS can identify hundreds of proteoforms routinely from the E. coli sample with a 1% proteoform-level false discovery rate (FDR).
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Affiliation(s)
- Elijah N McCool
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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Fagerquist CK, Dodd CE. Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry. PLoS One 2021; 16:e0260650. [PMID: 34843608 PMCID: PMC8629258 DOI: 10.1371/journal.pone.0260650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Fourteen proteins produced by three pathogenic Escherichia coli strains were identified using antibiotic induction, MALDI-TOF-TOF tandem mass spectrometry (MS/MS) and top-down proteomic analysis using software developed in-house. Host proteins as well as plasmid proteins were identified. Mature, intact protein ions were fragmented by post-source decay (PSD), and prominent fragment ions resulted from the aspartic acid effect fragmentation mechanism wherein polypeptide backbone cleavage (PBC) occurs on the C-terminal side of aspartic acid (D), glutamic acid (E) and asparagine (N) residues. These highly specific MS/MS-PSD fragment ions were compared to b- and y-type fragment ions on the C-terminal side of D-, E- and N-residues of in silico protein sequences derived from whole genome sequencing. Nine proteins were found to be post-translationally modified with either removal of an N-terminal methionine or a signal peptide. The protein sequence truncation algorithm of our software correctly identified all full and truncated protein sequences. Truncated sequences were compared to those predicted by SignalP. Nearly complete concurrence was obtained except for one protein where SignalP mis-identified the cleavage site by one residue. Two proteins had intramolecular disulfide bonds that were inferred by the absence of PBC on the C-terminal side of a D-residue located within the disulfide loop. These results demonstrate the utility of MALDI-TOF-TOF for identification of full and truncated bacterial proteins.
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Affiliation(s)
- Clifton K. Fagerquist
- Produce Safety & Microbiology, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, United States of America
| | - Claire E. Dodd
- Produce Safety & Microbiology, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, United States of America
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Liu G, Gu K, Wang F, Jia G, Zhao H, Chen X, Wu C, Zhang R, Tian G, Cai J, Tang J, Wang J. Tryptophan Ameliorates Barrier Integrity and Alleviates the Inflammatory Response to Enterotoxigenic Escherichia coli K88 Through the CaSR/Rac1/PLC-γ1 Signaling Pathway in Porcine Intestinal Epithelial Cells. Front Immunol 2021; 12:748497. [PMID: 34745120 PMCID: PMC8566706 DOI: 10.3389/fimmu.2021.748497] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Background Impaired intestinal barrier integrity plays a crucial role in the development of many diseases such as obesity, inflammatory bowel disease, and type 2 diabetes. Thus, protecting the intestinal barrier from pathological disruption is of great significance. Tryptophan can increase gut barrier integrity, enhance intestinal absorption, and decrease intestinal inflammation. However, the mechanism of tryptophan in decreasing intestinal barrier damage and inflammatory response remains largely unknown. The objective of this study was to test the hypothesis that tryptophan can enhance intestinal epithelial barrier integrity and decrease inflammatory response mediated by the calcium-sensing receptor (CaSR)/Ras-related C3 botulinum toxin substrate 1 (Rac1)/phospholipase Cγ1 (PLC-γ1) signaling pathway. Methods IPEC-J2 cells were treated with or without enterotoxigenic Escherichia coli (ETEC) K88 in the absence or presence of tryptophan, CaSR inhibitor (NPS-2143), wild-type CaSR overexpression (pcDNA3.1-CaSR-WT), Rac1-siRNA, and PLC-γ1-siRNA. Results The results showed that ETEC K88 decreased the protein concentration of occludin, zonula occludens-1 (ZO-1), claudin-1, CaSR, total Rac1, Rho family member 1 of porcine GTP-binding protein (GTP-rac1), phosphorylated phospholipase Cγ1 (p-PLC-γ1), and inositol triphosphate (IP3); suppressed the transepithelial electrical resistance (TEER); and enhanced the permeability of FITC-dextran compared with the control group. Compared with the control group, 0.7 mM tryptophan increased the protein concentration of CaSR, total Rac1, GTP-rac1, p-PLC-γ1, ZO-1, claudin-1, occludin, and IP3; elevated the TEER; and decreased the permeability of FITC-dextran and contents of interleukin-8 (IL-8) and TNF-α. However, 0.7 mM tryptophan+ETEC K88 reversed the effects induced by 0.7 mM tryptophan alone. Rac1-siRNA+tryptophan+ETEC K88 or PLC-γ1-siRNA+tryptophan+ETEC K88 reduced the TEER, increased the permeability of FITC-dextran, and improved the contents of IL-8 and TNF-α compared with tryptophan+ETEC K88. NPS2143+tryptophan+ETEC K88 decreased the TEER and the protein concentration of CaSR, total Rac1, GTP-rac1, p-PLC-γ1, ZO-1, claudin-1, occludin, and IP3; increased the permeability of FITC-dextran; and improved the contents of IL-8 and TNF-α compared with tryptophan+ETEC K88. pcDNA3.1-CaSR-WT+Rac1-siRNA+ETEC K88 and pcDNA3.1-CaSR-WT+PLC-γ1-siRNA+ETEC K88 decreased the TEER and enhanced the permeability in porcine intestine epithelial cells compared with pcDNA3.1-CaSR-WT+ETEC K88. Conclusion Tryptophan can improve intestinal epithelial barrier integrity and decrease inflammatory response through the CaSR/Rac1/PLC-γ1 signaling pathway.
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Affiliation(s)
- Guangmang Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Ke Gu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Fang Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Gang Jia
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Hua Zhao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Xiaoling Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Caimei Wu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Ruinan Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Gang Tian
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jingyi Cai
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jiayong Tang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
- Key Laboratory of Animal Disease-Resistant Nutrition and Feed, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jing Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Yu D, Wang Z, Cupp-Sutton KA, Guo Y, Kou Q, Smith K, Liu X, Wu S. Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling. J Am Soc Mass Spectrom 2021; 32:1336-1344. [PMID: 33725447 PMCID: PMC8323476 DOI: 10.1021/jasms.0c00464] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Labeling approaches using isobaric chemical tags (e.g., isobaric tagging for relative and absolute quantification, iTRAQ and tandem mass tag, TMT) have been widely applied for the quantification of peptides and proteins in bottom-up MS. However, until recently, successful applications of these approaches to top-down proteomics have been limited because proteins tend to precipitate and "crash" out of solution during TMT labeling of complex samples making the quantification of such samples difficult. In this study, we report a top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples. To reduce the sample complexity and remove large proteins from complex samples, we developed a filter-SEC technique that combines a molecular weight cutoff filtration step with high-performance size exclusion chromatography (SEC) separation. No protein precipitation was observed in filtered samples under the intact protein-level TMT labeling conditions. The proposed top-down TMT MS platform enables high-throughput analysis of intact proteoforms, allowing for the identification and quantification of hundreds of intact proteoforms from Escherichia coli cell lysates. To our knowledge, this represents the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
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Affiliation(s)
- Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Qiang Kou
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Xiaowen Liu
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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Zhao J, Jian R, Wang Y, Yang B, Zhao D, Shen C, Qiao L, Liu B. Mesoporous Silica as Sorbents and Enzymatic Nanoreactors for Microbial Membrane Proteomics. ACS Appl Mater Interfaces 2021; 13:11571-11578. [PMID: 33661597 DOI: 10.1021/acsami.0c19528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The membrane proteins of microbes are at the forefront of host and parasite interactions. Having a general view of the functions of microbial membrane proteins is vital for many biomedical studies on microbiota. Nevertheless, due to the strong hydrophobicity and low concentration of membrane proteins, it is hard to efficiently enrich and digest the proteins for mass spectrometry analysis. Herein, we design an enzymatic nanoreactor for the digestion of membrane proteins using methylated well-ordered hexagonal mesoporous silica (Met-SBA-15). The material can efficiently extract hydrophobic membrane proteins and host the proteolysis in nanopores. The performance of the enzymatic nanoreactor is first demonstrated using standard hydrophobic proteins and then validated using membrane proteins extracted from Escherichia coli (E. coli) or a mixed bacterial sample of eight strains. Using the nanoreactor, 431 membrane proteins are identified from E. coli, accounting for 38.5% of all membrane proteins of the species, which is much more than that by the widely used in-solution digestion protocol. From the mixed bacterial sample of eight strains, 1395 membrane proteins are identified using the nanoreactor. On the contrary, the traditional in-solution proteolysis workflow only leads to the identification of 477 membrane proteins, demonstrating that the Met-SBA-15 can be offered as an excellent tool for microbial membrane proteome research and is expected to be used in human microbiota studies, e.g. host-microbe interactions.
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Affiliation(s)
- Jinzhi Zhao
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Ruijun Jian
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Yuning Wang
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Beibei Yang
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
- Department of Chemistry and Chemical Engineering, Nantong University, Nantong 226000, China
| | - Dan Zhao
- Shanghai Omicsolution Co., Ltd., Shanghai 201100, China
| | - Chengpin Shen
- Shanghai Omicsolution Co., Ltd., Shanghai 201100, China
| | - Liang Qiao
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
| | - Baohong Liu
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China
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Ketter S, Gopinath A, Rogozhnikova O, Trukhin D, Tormyshev VM, Bagryanskaya EG, Joseph B. In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels. Chemistry 2021; 27:2299-2304. [PMID: 33197077 PMCID: PMC7898545 DOI: 10.1002/chem.202004606] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Indexed: 01/03/2023]
Abstract
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
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Affiliation(s)
- Sophie Ketter
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Olga Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Dmitrii Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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Kaur K, Chelangat W, Druzhinin SI, Karuri NW, Müller M, Schönherr H. Quantitative E. coli Enzyme Detection in Reporter Hydrogel-Coated Paper Using a Smartphone Camera. Biosensors (Basel) 2021; 11:25. [PMID: 33477907 PMCID: PMC7833396 DOI: 10.3390/bios11010025] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
There is a growing demand for rapid and sensitive detection approaches for pathogenic bacteria that can be applied by non-specialists in non-laboratory field settings. Here, the detection of the typical E. coli enzyme β-glucuronidase using a chitosan-based sensing hydrogel-coated paper sensor and the detailed analysis of the reaction kinetics, as detected by a smartphone camera, is reported. The chromogenic reporter unit affords an intense blue color in a two-step reaction, which was analyzed using a modified Michaelis-Menten approach. This generalizable approach can be used to determine the limit of detection and comprises an invaluable tool to characterize the performance of lab-in-a-phone type approaches. For the particular system analyzed, the ratio of reaction rate and equilibrium constants of the enzyme-substrate complex are 0.3 and 0.9 pM-1h-1 for β-glucuronidase in phosphate buffered saline and lysogeny broth, respectively. The minimal degree of substrate conversion for detection of the indigo pigment formed during the reaction is 0.15, while the minimal time required for detection in this particular system is ~2 h at an enzyme concentration of 100 nM. Therefore, this approach is applicable for quantitative lab-in-a-phone based point of care detection systems that are based on enzymatic substrate conversion via bacterial enzymes.
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Affiliation(s)
- Kawaljit Kaur
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany; (K.K.); (W.C.); (M.M.)
| | - Winny Chelangat
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany; (K.K.); (W.C.); (M.M.)
- Mechatronics Engineering Department, Dedan Kimathi University of Technology, Nyeri-Mweiga Road, Nyeri 10143, Kenya
| | - Sergey I. Druzhinin
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany; (K.K.); (W.C.); (M.M.)
| | - Nancy Wangechi Karuri
- Chemical Engineering Department, Dedan Kimathi University of Technology, Nyeri-Mweiga Road, Nyeri 10143, Kenya;
| | - Mareike Müller
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany; (K.K.); (W.C.); (M.M.)
| | - Holger Schönherr
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany; (K.K.); (W.C.); (M.M.)
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10
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Starke R, Schäpe SS, Jehmlich N, von Bergen M. Protein stable isotope probing with H 2 18 O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12. Rapid Commun Mass Spectrom 2021; 35:e8941. [PMID: 32885498 DOI: 10.1002/rcm.8941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Tracing isotopically labeled water into proteins allows for the detection of species-specific metabolic activity in complex communities. However, a stress response may alter the newly synthesized proteins. METHODS We traced 18-oxygen from heavy water into proteins of Escherichia coli K12 grown from permissive to retardant temperatures. All samples were analyzed using UPLC/Orbitrap Q-Exactive-MS/MS operating in positive electrospray ionization mode. RESULTS We found that warmer temperatures resulted in significantly (P-value < 0.05) higher incorporation of 18-oxygen as seen by both substrate utilization as relative isotope abundance (RIA) and growth as labeling ratio (LR). However, the absolute number of peptides with incorporation of 18-oxygen showed no significant correlation to temperature, potentially caused by the synthesis of different proteins at low temperatures, namely, proteins related to cold stress response. CONCLUSIONS Our results unveil the species-specific cold stress response of E. coli K12 that could be misinterpreted as general growth; this is why the quantity as RIA and LR but also the quality as absolute number of peptides with incorporation (relative abundance, RA) and their function must be considered to fully understand the activity of microbial communities.
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Affiliation(s)
- Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
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11
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Taverna D, Gaspari M. A critical comparison of three MS-based approaches for quantitative proteomics analysis. J Mass Spectrom 2021; 56:e4669. [PMID: 33128495 DOI: 10.1002/jms.4669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/07/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
MS-based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data-dependent methods for protein relative quantification (label-free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole-Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label-based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold-changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field.
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Affiliation(s)
- Domenico Taverna
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
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12
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Xu T, Shen X, Yang Z, Chen D, Lubeckyj RA, McCool EN, Sun L. Automated Capillary Isoelectric Focusing-Tandem Mass Spectrometry for Qualitative and Quantitative Top-Down Proteomics. Anal Chem 2020; 92:15890-15898. [PMID: 33263984 PMCID: PMC8564864 DOI: 10.1021/acs.analchem.0c03266] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Top-down proteomics (TDP) aims to delineate proteomes in a proteoform-specific manner, which is vital for accurately understanding protein function in cellular processes. It requires high-capacity separation of proteoforms before mass spectrometry (MS) and tandem MS (MS/MS). Capillary isoelectric focusing (cIEF)-MS has been recognized as a useful tool for TDP in the 1990s because cIEF is capable of high-resolution separation of proteoforms. Previous cIEF-MS studies concentrated on measuring the protein's mass without MS/MS, impeding the confident proteoform identification in complex samples and the accurate localization of post-translational modifications on proteoforms. Herein, for the first time, we present automated cIEF-MS/MS-based TDP for large-scale delineation of proteoforms in complex proteomes. Single-shot cIEF-MS/MS identified 711 proteoforms from an Escherichia coli (E. coli) proteome consuming only nanograms of proteins. Coupling two-dimensional size-exclusion chromatography (SEC)-cIEF to ESI-MS/MS enabled the identification of nearly 2000 proteoforms from the E. coli proteome. Label-free quantitative TDP of zebrafish male and female brains using SEC-cIEF-MS/MS quantified thousands of proteoforms and revealed sex-dependent proteoform profiles in brains. Particularly, we discovered several proteolytic proteoforms of pro-opiomelanocortin and prodynorphin with significantly higher abundance in male zebrafish brains as potential endogenous hormone proteoforms. Multilevel quantitative proteomics (TDP and bottom-up proteomics) of the brains revealed that the majority of proteoforms having statistically significant difference in abundance between genders showed no abundance difference at the protein group level. This work represents the first multilevel quantitative proteomics study of sexual dimorphism of the brain.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824, United States
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13
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Talaat KR, Porter CK, Jaep KM, Duplessis CA, Gutierrez RL, Maciel M, Adjoodani B, Feijoo B, Chakraborty S, Brubaker J, Trop SA, Riddle MS, Joseph SS, Bourgeois AL, Prouty MG. Refinement of the CS6-expressing enterotoxigenic Escherichia coli strain B7A human challenge model: A randomized trial. PLoS One 2020; 15:e0239888. [PMID: 33264302 PMCID: PMC7710093 DOI: 10.1371/journal.pone.0239888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 09/01/2020] [Indexed: 12/29/2022] Open
Abstract
Background Human challenge models for enterotoxigenic Escherichia coli (ETEC) facilitate vaccine down-selection. The B7A (O148:H28 CS6+LT+ST+) strain is important for vaccine development. We sought to refine the B7A model by identifying a dose and fasting regimen consistently inducing moderate-severe diarrhea. Methods An initial cohort of 28 subjects was randomized (1:1:1:1) to receive B7A following an overnight fast at doses of 108 or 109 colony forming units (cfu) or a 90-minute fast at doses of 109 or 1010 cfu. A second cohort included naïve and rechallenged subjects who had moderate-severe diarrhea and were given the target regimen. Immune responses to important ETEC antigens were assessed. Results Among subjects receiving 108 cfu of B7A, overnight fast, or 109 cfu, 90-minute fast, 42.9% (3/7) had moderate-severe diarrhea. Higher attack rates (71.4%; 5/7) occurred in subjects receiving 109 cfu, overnight fast, or 1010 cfu, 90-minute fast. Upon rechallenge with 109 cfu of B7A, overnight fast, 5/11 (45.5%) had moderate-severe diarrhea; the attack rate among concurrently challenge naïve subjects was 57.9% (11/19). Anti-CS6, O148 LPS and LT responses were modest across all groups. Conclusions An overnight fast enabled a reduction in the B7A inoculum dose; however, the attack rate was inconsistent and protection upon rechallenge was minimal.
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Affiliation(s)
- Kawsar R. Talaat
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- * E-mail:
| | - Chad K. Porter
- Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Kayla M. Jaep
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | | | | | - Milton Maciel
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Brittany Adjoodani
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Brittany Feijoo
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Jessica Brubaker
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Stefanie A. Trop
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Mark S. Riddle
- Naval Medical Research Center, Silver Spring, MD, United States of America
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | | | - A. Louis Bourgeois
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- PATH, Washington, DC, United States of America
| | - Michael G. Prouty
- Naval Medical Research Center, Silver Spring, MD, United States of America
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14
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Midha MK, Kusebauch U, Shteynberg D, Kapil C, Bader SL, Reddy PJ, Campbell DS, Baliga NS, Moritz RL. A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS. Sci Data 2020; 7:389. [PMID: 33184295 PMCID: PMC7665006 DOI: 10.1038/s41597-020-00724-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).
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Affiliation(s)
- Mukul K Midha
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - David Shteynberg
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Samuel L Bader
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | | | - David S Campbell
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
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15
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Dobbs JM, Jenkins ML, Burke JE. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. J Am Soc Mass Spectrom 2020; 31:2202-2209. [PMID: 32869988 DOI: 10.1021/jasms.0c00283] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filtering of nonspecifically binding contaminant proteins from affinity purification mass spectrometry (AP-MS) data is a well-established strategy to improve statistical confidence in identified proteins. The CRAPome (contaminant repository for affinity purification) describes the contaminating background content present in many purification strategies. However, full contaminant lists for nickel-nitrilotriacetic acid (NiNTA) and glutathione S-transferase (GST) affinity matrices are lacking. Similarly, no Spodoptera frugiperda (Sf9) contaminants are available, and only the FLAG-purified contaminants are described for Escherichia coli. For MS experiments that use recombinant protein, such as structural mass spectrometry experiments (hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking, and radical foot-printing), failing to include these contaminants in the search database during the initial tandem MS (MS/MS) identification stage can result in complications in peptide identification. We have created contaminant FASTA databases for Sf9 and E. coli NiNTA or GST purification strategies and show that the use of these databases can effectively improve HDX-MS protein coverage, fragment count, and confidence in peptide identification. This approach provides a robust strategy toward the design of contaminant databases for any purification approach that will expand the complexity of systems able to be interrogated by HDX-MS.
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Affiliation(s)
- Joseph M Dobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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16
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Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Çapuni R, Han X, de Astigarraga E, Diercks T, Fucini P, Connell SR. Backbone and sidechain NMR assignments for the ribosome maturation factor RbfA from Escherichia coli. Biomol NMR Assign 2020; 14:317-321. [PMID: 32671633 DOI: 10.1007/s12104-020-09969-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
RbfA (ribosome binding factor A; 15.2 kDa) is a protein involved in ribosome biogenesis and has been shown to be important for growth at low temperatures and to act as a suppressor for a cold-sensitive mutation (C23U) in the ribosomal RNA of the small 30S ribosomal subunit. The 3D structure of isolated RbfA has been determined from several organisms showing that RbfA has type-II KH-domain fold topology similar to the KH domain of another assembly factor, Era, whose overexpression can compensate for the deletion of rbfA, suppressing both the cold sensitivity and abnormal accumulation of 17S rRNA in rbfA knockout stains. Interestingly, a RbfAΔ25 variant used in previous NMR studies, truncated at the C-terminal domain to remove 25 unstructured residues causing aggregation at room temperature, was biologically active in the sense that it could complement a knock-out of wildtype RbfA, although it did not act as a suppressor for a 16S cold-sensitive mutation (C23U), nor did it interact stably with the 30S subunit. To complement this work, we report the 1H, 13C, and 15 N backbone and sidechain NMR resonance assignments of full length RbfA from Escherichia coli measured under physiological conditions (pH 7.6). This construct contains seven additional C-terminal residues from the cloning (i.e. one alanine and six residues from the HRV 3C cleavage site) and no aggregation issues were observed over a 1-week period at 293 K. The assignment data has been deposited in the BMRB data bank under Accession No. 27857.
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Affiliation(s)
- Andreas Schedlbauer
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Idoia Iturrioz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Borja Ochoa-Lizarralde
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Xu Han
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Elisa de Astigarraga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain.
- Basque Foundation for Science, IKERBASQUE, 48011, Bilbao, Spain.
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain.
- Basque Foundation for Science, IKERBASQUE, 48011, Bilbao, Spain.
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17
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Yang Y, Ke Z, Wang Z, Li Y, Li Y, Wang Y, Liu B. 1H, 13C and 15 N NMR assignments of solubility tag protein Msyb of Escherichia coli. Biomol NMR Assign 2020; 14:251-254. [PMID: 32504338 DOI: 10.1007/s12104-020-09955-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Biochemical and structural characterizations of a protein are the prerequisite for the further understanding of its biological role and potential applications. The expression of recombinant protein is almost unavoidable to produce the amount of the protein required for these studies, especially at the industrial level. Escherichia coli is the single most used system for recombinant protein expression and the first choice for a trial expression. Besides the inherited defects of its prokaryotic origin, the E. coli system has problems like low protein solubility and formation of inclusion bodies. To improve the solubility while assisting correct folding of the target protein, fusing a tag protein prior to its N-terminus is one of the common approaches. GST, MBP, Trx and SUMO proteins are among the most used tags by providing different advantages during recombinant protein expression. Msyb, a small and acidic protein native to E. coli, is another example that could improve the solubility of the target protein. While the biophysical and biochemical properties of these common tag proteins have been studied to a great extent, Msyb protein remains largely uncharacterized. Here, using solution-state NMR, our near-complete resonance assignment of Msyb provides a basis for future structure determination which would help to expand its usage as a common tag protein.
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Affiliation(s)
- Yanan Yang
- BioBank, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Zunhui Ke
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Zhihao Wang
- BioBank, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Yanqing Li
- BioBank, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Yan Li
- Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yawen Wang
- BioBank, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China
| | - Bing Liu
- BioBank, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, 710061, China.
- Instrument Analysis Centre, of Xi'an Jiaotong University, Shaanxi, China.
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18
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Yang DH, Liu S, Cao L, Zheng YD, Huang JF, Ge R, He QY, Sun X. Quantitative secretome analysis of polymyxin B resistance in Escherichia coli. Biochem Biophys Res Commun 2020; 530:307-313. [PMID: 32828304 DOI: 10.1016/j.bbrc.2020.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 02/02/2023]
Abstract
Bacterial resistance has become a serious threat to human health. In particular, the gradual development of resistance to polymyxins, the last line of defense for human infections, is a major issue. Secreted proteins contribute to the interactions between bacteria and the environment. In this study, we compared the secretomes of polymyxin B-sensitive and -resistant Escherichia coli strains by data-independent acquisition mass spectrometry. In total, 87 differentially expressed secreted proteins were identified in polymyxin B-resistant E. coli compared to the sensitive strain. A GO enrichment analysis indicated that the differentially expressed proteins were involved in biological processes, including bacterial-type flagellum-dependent cell motility, ion transport, carbohydrate derivative biosynthetic process, cellular response to stimulus, organelle organization, and cell wall organization or biogenesis. The differentially expressed secreted proteins in polymyxin B-resistant bacteria were enriched for multiple pathways, suggesting that the resistance phenotype depends on complex regulatory mechanisms. A potential biomarker or drug target (YebV) was found in polymyxin B-resistant E. coli. This work clarifies the secretome changes associated with the acquisition of polymyxin resistance and may contribute to drug development.
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Affiliation(s)
- Dong-Hong Yang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Shiqin Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Linlin Cao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yun-Dan Zheng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jian-Fang Huang
- Guangdong Province Key Laboratory of Molecule Immunology and Antibody Engineering, Jinan University, Guangzhou, 510632, China
| | - Ruiguang Ge
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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19
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Lin Z, Ren Y, Shi Z, Zhang K, Yang H, Liu S, Hao P. Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation. Rapid Commun Mass Spectrom 2020; 34:e8733. [PMID: 32031715 DOI: 10.1002/rcm.8733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
UNLABELLED High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation. METHODS In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry. RESULTS Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol. CONCLUSIONS The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.
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Affiliation(s)
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhaomei Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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20
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Shi H, Fan J, Zhao Y, Hu X, Zhang X, Tang Z. Visible light driven CuBi 2O 4/Bi 2MoO 6 p-n heterojunction with enhanced photocatalytic inactivation of E. coli and mechanism insight. J Hazard Mater 2020; 381:121006. [PMID: 31442686 DOI: 10.1016/j.jhazmat.2019.121006] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 05/21/2023]
Abstract
Here, a novel CuBi2O4/Bi2MoO6 (CBO/BMO) p-n heterojunction was fabricated and exhibited markedly improved photocatalytic inactivation capacity of E. coli cells under visible light excitation (λ > 420 nm) compared with pure CuBi2O4 and Bi2MoO6. The CBO/BMO-0.5 hybrid displayed the highest photoinactivation ability which could completely inactivate the E. coli cellswithin 4 h. The mechanism of photocatalytic disinfection towards E. coli of CBO/BMO heterojunctions was attributed to the disruption of cell-membrane, leakage and damage of cellular content including total protein and DNA as verified with SEM, fluorescence-base dead/live stain, sodium dodecyl sulfate polyacrylamide gel electropheresis (SDS-PAGE) and agarose gel electrophoresis (AGE). Additionally, the scavenge experiments showed that the reactive species h+, e- and •O2-play the predominant role in the photocatalytic system of CBO/BMO hybrids. The improved photocatalytic activity of CBO/BMO composites was mainly attributed to the promotion of spatial separation and migration rate of photoproduced electron-hole pairs, enhancement of visible light absorption and more generation of reactive species (•O2-) on the interface of catalyst and water which was demonstrated by nitroblue tetrazolium (NBT) and EPR. Our work indicated that construction of CuBi2O4/Bi2MoO6 p-n heterostructure photocatalyst is a promising environmental friendly alternative method to deal with the biohazards of pathogenic microorganisms.
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Affiliation(s)
- Huanxian Shi
- School of Chemical Engineering, Northwest University, Xi'an, 710069, PR China
| | - Jun Fan
- College of Food Science and Engineering, Northwest University, Xi'an 710069, PR China.
| | - Yanyan Zhao
- School of Chemical Engineering, Northwest University, Xi'an, 710069, PR China
| | - Xiaoyun Hu
- School of Physics, Northwest University, Xi'an, 710069, PR China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Zhishu Tang
- Shaanxi University of Chinese Medicine/Shaanxi collaborative Innovation Center of Idustrialization of Tradition Chinese Medicine Resources, Xianyang 712083, PR China.
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21
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Gnuchikh E, Baranova A, Schukina V, Khaliullin I, Zavilgelsky G, Manukhov I. Kinetics of the thermal inactivation and the refolding of bacterial luciferases in Bacillus subtilis and in Escherichia coli differ. PLoS One 2019; 14:e0226576. [PMID: 31869349 PMCID: PMC6927610 DOI: 10.1371/journal.pone.0226576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/28/2019] [Indexed: 11/19/2022] Open
Abstract
Here we present a study of the thermal inactivation and the refolding of the proteins in Gram positive Bacillus subtilis. To enable use of bacterial luciferases as the models for protein thermal inactivation and refolding in B. subtilis cells, we developed a variety of bright luminescent B. subtilis strains which express luxAB genes encoding luciferases of differing thermolability. The kinetics of the thermal inactivation and the refolding of luciferases from Photorhabdus luminescens and Photobacterium leiognathi were compared in Gram negative and Gram positive bacteria. In B. subtilis cells, these luciferases are substantially more thermostable than in Escherichia coli. Thermal inactivation of the thermostable luciferase P. luminescens in B. subtilis at 48.5°С behaves as a first-order reaction. In E.coli, the first order rate constant (Kt) of the thermal inactivation of luciferase in E. coli exceeds that observed in B. subtilis cells 2.9 times. Incubation time dependence curves for the thermal inactivation of the thermolabile luciferase of P. leiognathi luciferase in the cells of E. coli and B. subtilis may be described by first and third order kinetics, respectively. Here we shown that the levels and the rates of refolding of thermally inactivated luciferases in B. subtilis cells are substantially lower that that observed in E. coli. In dnaK-negative strains of B. subtilis, both the rates of thermal inactivation and the efficiency of refolding are similar to that observed in wild-type strains. These experiments point that the role that DnaKJE plays in thermostability of luciferases may be limited to bacterial species resembling E. coli.
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Affiliation(s)
- Eugeny Gnuchikh
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- National Research Center, Kurchatov Institute, GOSNIIGENETIKA, Moscow, Russia
| | - Ancha Baranova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- School of Systems Biology, George Mason University, Fairfax, VA, United States of America
- Research Centre for Medical Genetics, Moscow, Russia
| | - Vera Schukina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ilyas Khaliullin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Gennady Zavilgelsky
- National Research Center, Kurchatov Institute, GOSNIIGENETIKA, Moscow, Russia
| | - Ilya Manukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- National Research Center, Kurchatov Institute, GOSNIIGENETIKA, Moscow, Russia
- * E-mail:
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22
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McCool EN, Lodge JM, Basharat AR, Liu X, Coon JJ, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics. J Am Soc Mass Spectrom 2019; 30:2470-2479. [PMID: 31073891 PMCID: PMC6527361 DOI: 10.1007/s13361-019-02206-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 05/21/2023]
Abstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as an efficient approach for top-down proteomics recently for its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based dissociation methods often cannot provide extensive fragmentation of proteoforms for thorough characterization. Activated ion electron transfer dissociation (AI-ETD), that combines infrared photoactivation concurrent with ETD, has shown better performance for proteoform fragmentation than higher energy-collisional dissociation (HCD) and standard ETD. Here, we present the first application of CZE-AI-ETD on an Orbitrap Fusion Lumos mass spectrometer for large-scale top-down proteomics of Escherichia coli (E. coli) cells. CZE-AI-ETD outperformed CZE-ETD regarding proteoform and protein identifications (IDs). CZE-AI-ETD reached comparable proteoform and protein IDs with CZE-HCD. CZE-AI-ETD tended to generate better expectation values (E values) of proteoforms than CZE-HCD and CZE-ETD, indicating a higher quality of MS/MS spectra from AI-ETD respecting the number of sequence-informative fragment ions generated. CZE-AI-ETD showed great reproducibility regarding the proteoform and protein IDs with relative standard deviations less than 4% and 2% (n = 3). Coupling size exclusion chromatography (SEC) to CZE-AI-ETD identified 3028 proteoforms and 387 proteins from E. coli cells with 1% spectrum level and 5% proteoform-level false discovery rates. The data represents the largest top-down proteomics dataset using the AI-ETD method so far. Single-shot CZE-AI-ETD of one SEC fraction identified 957 proteoforms and 253 proteins. N-terminal truncations, signal peptide cleavage, N-terminal methionine removal, and various post-translational modifications including protein N-terminal acetylation, methylation, S-thiolation, disulfide bonds, and lysine succinylation were detected.
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Affiliation(s)
- Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Jean M Lodge
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN, 46202, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
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23
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Kuhlmann FM, Martin J, Hazen TH, Vickers TJ, Pashos M, Okhuysen PC, Gómez-Duarte OG, Cebelinski E, Boxrud D, del Canto F, Vidal R, Qadri F, Mitreva M, Rasko DA, Fleckenstein JM. Conservation and global distribution of non-canonical antigens in Enterotoxigenic Escherichia coli. PLoS Negl Trop Dis 2019; 13:e0007825. [PMID: 31756188 PMCID: PMC6897418 DOI: 10.1371/journal.pntd.0007825] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/06/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Enterotoxigenic Escherichia coli (ETEC) cause significant diarrheal morbidity and mortality in children of resource-limited regions, warranting development of effective vaccine strategies. Genetic diversity of the ETEC pathovar has impeded development of broadly protective vaccines centered on the classical canonical antigens, the colonization factors and heat-labile toxin. Two non-canonical ETEC antigens, the EtpA adhesin, and the EatA mucinase are immunogenic in humans and protective in animal models. To foster rational vaccine design that complements existing strategies, we examined the distribution and molecular conservation of these antigens in a diverse population of ETEC isolates. METHODS Geographically diverse ETEC isolates (n = 1159) were interrogated by PCR, immunoblotting, and/or whole genome sequencing (n = 46) to examine antigen conservation. The most divergent proteins were purified and their core functions assessed in vitro. RESULTS EatA and EtpA or their coding sequences were present in 57.0% and 51.5% of the ETEC isolates overall, respectively; and were globally dispersed without significant regional differences in antigen distribution. These antigens also exhibited >93% amino acid sequence identity with even the most divergent proteins retaining the core adhesin and mucinase activity assigned to the prototype molecules. CONCLUSIONS EtpA and EatA are well-conserved molecules in the ETEC pathovar, suggesting that they serve important roles in virulence and that they could be exploited for rational vaccine design.
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Affiliation(s)
- F. Matthew Kuhlmann
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| | - John Martin
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tracy H. Hazen
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Tim J. Vickers
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Madeline Pashos
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Pablo C. Okhuysen
- The Department of Infectious Diseases, Infection Control and Employee Health, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Oscar G. Gómez-Duarte
- Department of Pediatrics, Division of Infectious Diseases, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | | | - Dave Boxrud
- Minnesota Department of Health, St. Paul, Minnesota, United States of America
| | - Felipe del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunonología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Makedonka Mitreva
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David A. Rasko
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James M. Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Medicine Service, Veterans Affairs Medical Center, St. Louis, Missouri, United States of America
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24
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Yang F, Gu Y, Zhou J, Zhang K. Swine waste: A reservoir of high-risk bla NDM and mcr-1. Sci Total Environ 2019; 683:308-316. [PMID: 31132710 DOI: 10.1016/j.scitotenv.2019.05.251] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/05/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Multidrug resistance associated with pigs not only affects pig production but also threatens human health by influencing the farm surrounding and contaminating the food chain. This paper focused on the occurrence and prevalence of high-risk resistance genes (using blaNDM and mcr-1 as marker genes) in two Chinese swine farms, and investigated their fate and seasonal changes in piggery wastewater treatment systems (PWWTSs). Results revealed that blaNDM and mcr-1 were prevalent in both confined swine farms, and even prevailed through various processing stages of PWWTSs. Moreover, the abundance of blaNDM and mcr-1 in winter was higher than that in summer, with 0.01-1.01 logs variation in piggery wastewater. Of concern is that considerable amounts of blaNDM and mcr-1 were present in final effluent that is applied to farmland (up to 102-104copies/mL), raising the risk of propagation to indigenous bacteria. Worse still, those pig-derived isolates harboring the blaNDM/mcr-1 gene were confirmed to spread multidrug resistance to other bacteria, which further increased their dissemination potential in agricultural environment. This study highlights the prevalence of blaNDM and mcr-1 in swine farms, meanwhile, also emphasizes the necessary to mitigate the release and propagation of these high-risk genes from swine farms following land fertilization and wastewater usage.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China
| | - Yanru Gu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150036, China
| | - Jing Zhou
- College of Resources and Environment, Northeast Agricultural University, Harbin 150036, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China.
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25
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Lubeckyj RA, Basharat AR, Shen X, Liu X, Sun L. Large-Scale Qualitative and Quantitative Top-Down Proteomics Using Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry with Nanograms of Proteome Samples. J Am Soc Mass Spectrom 2019; 30:1435-1445. [PMID: 30972727 PMCID: PMC6675661 DOI: 10.1007/s13361-019-02167-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has attracted attention recently for top-down proteomics because it can achieve highly efficient separation and very sensitive detection of proteins. However, separation window and sample loading volume of CZE need to be boosted for a better proteome coverage using CZE-MS/MS. Here, we present an improved CZE-MS/MS system that achieved a 180-min separation window and a 2-μL sample loading volume for top-down characterization of protein mixtures. The system obtained highly efficient separation of proteins with nearly one million theoretical plates for myoglobin and enabled baseline separation of three different proteoforms of myoglobin. The CZE-MS/MS system identified 797 ± 21 proteoforms and 258 ± 7 proteins (n = 2) from an Escherichia coli (E. coli) proteome sample in a single run with only 250 ng of proteins injected. The system still identified 449 ± 40 proteoforms and 173 ± 6 proteins (n = 2) from the E. coli sample when only 25 ng of proteins were injected per run. Single-shot CZE-MS/MS analyses of zebrafish brain cerebellum (Cb) and optic tectum (Teo) regions identified 1730 ± 196 proteoforms (n = 3) and 2024 ± 255 proteoforms (n = 3), respectively, with only 500-ng proteins loaded per run. Label-free quantitative top-down proteomics of zebrafish brain Cb and Teo regions revealed significant differences between Cb and Teo regarding the proteoform abundance. Over 700 proteoforms from 131 proteins had significantly higher abundance in Cb compared to Teo, and these proteins were highly enriched in several biological processes, including muscle contraction, glycolytic process, and mesenchyme migration. Graphical Abstract.
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Affiliation(s)
- Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA.
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26
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Perdigão Neto LV, Corscadden L, Martins RCR, Nagano DS, Cunha MPV, Neves PR, Franco LAM, Moura MLN, Rizek CF, Guimarães T, Boszczowski Í, Rossi F, Levin AS, Stabler RA, Costa SF. Simultaneous colonization by Escherichia coli and Klebsiella pneumoniae harboring mcr-1 in Brazil. Infection 2019; 47:661-664. [PMID: 31025216 DOI: 10.1007/s15010-019-01309-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/17/2019] [Indexed: 10/27/2022]
Abstract
CASE PRESENTATION We present a case report of a woman, concurrently colonized by polymyxin-resistant E. coli and K. pneumoniae. A Brazilian female patient, in her mid-fifties, was hospitalized with schistosomiasis. During hospitalization, polymyxin-resistant E. coli and K. pneumoniae were isolated from surveillance cultures. METHODS Identification, antimicrobial susceptibility testings, PCR for mcr-1, plasmid transfer by conjugation and whole genome sequencing were performed. RESULTS E. coli ST744 and K. pneumoniae ST101 carrying mcr-1 gene were described. Transconjugant E. coli was positive for mcr-1 and IncX4 by PCR. The plasmid is a 33,304-base pair plasmid, and the mcr-1 gene was the only antimicrobial resistance gene present in the plasmid. CONCLUSIONS This study presents a case report of a hospitalized woman, concurrently colonized by mcr-1-harboring E. coli ST744, a different ST from previously described in Brazil, and a K. pneumoniae ST101.
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Affiliation(s)
- Lauro Vieira Perdigão Neto
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil.
- , Rua Arruda Alvim, 107, #142, São Paulo, SP, 05410-020, Brazil.
| | - Louise Corscadden
- Department of Infectious and Tropical Diseases, School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Roberta Cristina Ruedas Martins
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Débora Satie Nagano
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Marcos Paulo Vieira Cunha
- School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, 05508-270, Brazil
| | - Patrícia Regina Neves
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Lucas Augusto Moyses Franco
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Maria Luísa Nascimento Moura
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Camila Fonseca Rizek
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Thais Guimarães
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Ícaro Boszczowski
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Flávia Rossi
- Microbiology Laboratory, Hospital das Clínicas, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 155, São Paulo, SP, 05403-000, Brazil
| | - Anna S Levin
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Richard A Stabler
- Department of Infectious and Tropical Diseases, School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Silvia F Costa
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
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27
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Stadler P, Blöschl G, Nemeth L, Oismüller M, Kumpan M, Krampe J, Farnleitner AH, Zessner M. Event-transport of beta-d-glucuronidase in an agricultural headwater stream: Assessment of seasonal patterns by on-line enzymatic activity measurements and environmental isotopes. Sci Total Environ 2019; 662:236-245. [PMID: 30690358 DOI: 10.1016/j.scitotenv.2019.01.143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
Understanding the fate of fecal pollution in the landscape is required for microbial risk analysis. The aim of this study was to assess the patterns and dynamics of beta-d-glucuronidase (GLUC), which has been suggested as a surrogate for fecal pollution monitoring, in a stream draining an agricultural headwater catchment. Automated enzymatic on-site measurements of stream water and sediments were made over two years (2014-2016) to quantify the sources and pathways of GLUC in a stream. The event water fraction of streamflow was estimated by stable isotopes. Samples from field sediments on a hillslope, streambed sediment and stream water were analyzed for GLUC and with a standard E. coli assay. The results showed ten times higher GLUC and E. coli concentrations during the summer than during the winter for all compartments (field and streambed sediments and stream water). The E. coli concentrations in the streambed sediment were approximately 100 times those of the field sediments. Of the total GLUC load in the study period, 39% were transported during hydrological events (increased streamflow due to rainfall or snowmelt); of these, 44% were transported when the stream contained no recent rainwater. The results suggested that a large proportion of the GLUC and E. coli in the stream water stemmed from resuspended streambed sediments. Moreover, the results strongly indicated the existence of remnant populations of GLUC-active organisms in the catchment.
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Affiliation(s)
- Philipp Stadler
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria; Centre for Water Resource Systems, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria.
| | - Günter Blöschl
- Centre for Water Resource Systems, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria; Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria
| | - Lukas Nemeth
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria
| | - Markus Oismüller
- Centre for Water Resource Systems, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria
| | - Monika Kumpan
- Institute for Land & Water Management Research, Federal Agency for Water Management, A-3252 Petzenkirchen, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria
| | - Andreas H Farnleitner
- Centre for Water Resource Systems, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria; Division Water Quality and Health, Karl Landsteiner University of Health Sciences, A-3500 Krems a. d. Donau, Austria; Institute of Chemical and Bioscience Engineering, ICC Water and Health, Research Group 166/5/3TU Wien, Gumpendorferstraße 1a, A-1060 Vienna, Austria
| | - Matthias Zessner
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz 13, A-1040 Vienna, Austria
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28
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Peetz O, Hellwig N, Henrich E, Mezhyrova J, Dötsch V, Bernhard F, Morgner N. LILBID and nESI: Different Native Mass Spectrometry Techniques as Tools in Structural Biology. J Am Soc Mass Spectrom 2019; 30:181-191. [PMID: 30225732 PMCID: PMC6318263 DOI: 10.1007/s13361-018-2061-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Native mass spectrometry is applied for the investigation of proteins and protein complexes worldwide. The challenge in native mass spectrometry is maintaining the features of the proteins of interest, such as oligomeric state, bound ligands, or the conformation of the protein complex, during transfer from solution to gas phase. This is an essential prerequisite to allow conclusions about the solution state protein complex, based on the gas phase measurements. Therefore, soft ionization techniques are required. Widely used for the analysis of protein complexes are nanoelectro spray ionization (nESI) mass spectrometers. A newer ionization method is laser induced liquid bead ion desorption (LILBID), which is based on the release of protein complexes from solution phase via infrared (IR) laser desorption. We use both methods in our lab, depending on the requirements of the biological system we are interested in. Here we benchmark the performance of our LILBID mass spectrometer in comparison to a nESI instrument, regarding sample conditions, buffer and additive tolerances, dissociation mechanism and applicability towards soluble and membrane protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Oliver Peetz
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Nils Hellwig
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J.W. Goethe-University, Frankfurt am Main, Germany.
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29
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Da Silva WM, Bei J, Amigo N, Valacco MP, Amadio A, Zhang Q, Wu X, Yu T, Larzabal M, Chen Z, Cataldi A. Quantification of enterohemorrhagic Escherichia coli O157:H7 protein abundance by high-throughput proteome. PLoS One 2018; 13:e0208520. [PMID: 30596662 PMCID: PMC6312284 DOI: 10.1371/journal.pone.0208520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/19/2018] [Indexed: 12/22/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a human pathogen responsible for diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS). To promote a comprehensive insight into the molecular basis of EHEC O157:H7 physiology and pathogenesis, the combined proteome of EHEC O157:H7 strains, Clade 8 and Clade 6 isolated from cattle in Argentina, and the standard EDL933 (clade 3) strain has been analyzed. From shotgun proteomic analysis a total of 2,644 non-redundant proteins of EHEC O157:H7 were identified, which correspond approximately 47% of the predicted proteome of this pathogen. Normalized spectrum abundance factor analysis was performed to estimate the protein abundance. According this analysis, 50 proteins were detected as the most abundant of EHEC O157:H7 proteome. COG analysis showed that the majority of the most abundant proteins are associated with translation processes. A KEGG enrichment analysis revealed that Glycolysis / Gluconeogenesis was the most significant pathway. On the other hand, the less abundant detected proteins are those related to DNA processes, cell respiration and prophage. Among the proteins that composed the Type III Secretion System, the most abundant protein was EspA. Altogether, the results show a subset of important proteins that contribute to physiology and pathogenicity of EHEC O157:H7.
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Affiliation(s)
- Wanderson Marques Da Silva
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - Jinlong Bei
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Natalia Amigo
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM (Mass Spectrometry Facility), Faculty of Exact and Natural Sciences, University of Buenos Aires and CONICET (National Research Council), Buenos Aires, Argentina
| | - Ariel Amadio
- Rafaela Experimental Station, National Institute of Agricultural Technology, Rafaela, Santa Fe, Argentina
| | - Qi Zhang
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Xiuju Wu
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Ting Yu
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Mariano Larzabal
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
| | - Zhuang Chen
- AGRO-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Angel Cataldi
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina
- * E-mail:
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30
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Chure G, Lee HJ, Rasmussen A, Phillips R. Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution. J Bacteriol 2018; 200:e00460-18. [PMID: 30201782 PMCID: PMC6222198 DOI: 10.1128/jb.00460-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 12/17/2022] Open
Abstract
Rapid changes in extracellular osmolarity are one of many insults microbial cells face on a daily basis. To protect against such shocks, Escherichia coli and other microbes express several types of transmembrane channels that open and close in response to changes in membrane tension. In E. coli, one of the most abundant channels is the mechanosensitive channel of large conductance (MscL). While this channel has been heavily characterized through structural methods, electrophysiology, and theoretical modeling, our understanding of its physiological role in preventing cell death by alleviating high membrane tension remains tenuous. In this work, we examine the contribution of MscL alone to cell survival after osmotic shock at single-cell resolution using quantitative fluorescence microscopy. We conducted these experiments in an E. coli strain which is lacking all mechanosensitive channel genes save for MscL, whose expression was tuned across 3 orders of magnitude through modifications of the Shine-Dalgarno sequence. While theoretical models suggest that only a few MscL channels would be needed to alleviate even large changes in osmotic pressure, we find that between 500 and 700 channels per cell are needed to convey upwards of 80% survival. This number agrees with the average MscL copy number measured in wild-type E. coli cells through proteomic studies and quantitative Western blotting. Furthermore, we observed zero survival events in cells with fewer than ∼100 channels per cell. This work opens new questions concerning the contribution of other mechanosensitive channels to survival, as well as regulation of their activity.IMPORTANCE Mechanosensitive (MS) channels are transmembrane protein complexes which open and close in response to changes in membrane tension as a result of osmotic shock. Despite extensive biophysical characterization, the contribution of these channels to cell survival remains largely unknown. In this work, we used quantitative video microscopy to measure the abundance of a single species of MS channel in single cells, followed by their survival after a large osmotic shock. We observed total death of the population with fewer than ∼100 channels per cell and determined that approximately 500 to 700 channels were needed for 80% survival. The number of channels we found to confer nearly full survival is consistent with the counts of the numbers of channels in wild-type cells in several earlier studies. These results prompt further studies to dissect the contribution of other channel species to survival.
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Affiliation(s)
- Griffin Chure
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Heun Jin Lee
- Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
| | - Akiko Rasmussen
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Rob Phillips
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Department of Physics, California Institute of Technology, Pasadena, California, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
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31
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Chatterjee B, Thakur SS. Single-Run Mass Spectrometry Analysis Provides Deep Insight into E. coli Proteome. J Am Soc Mass Spectrom 2018; 29:2394-2401. [PMID: 30259409 DOI: 10.1007/s13361-018-2066-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/02/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Single-run mass spectrometry has enabled the detection and quantifications of E. coli proteins. A total of 2068 proteins quantified by intensity-based absolute quantification (iBAQ) Schwanhäusser et al.: (Nature. 473, 337-342, 2011) procedure were obtained with single enzyme-trypsin, without pre-fractionation, by quadruplicate long liquid chromatography runs coupled with high-resolution linear trap quadrupole (LTQ)-Orbitrap Velos mass spectrometry. The single-run of 12 h has ability to cover almost 98% of the quadruplicate LC-MS/MS runs of E. coli proteome and is therefore almost equivalent to quadruplicate LC-MS/MS runs. These quantified proteins are about 52% of the total proteins present in E. coli genome according to Uniprot database. The quantified proteins covered almost all of the proteins in folate biosynthesis. Remarkably greater part of Gene Ontology (GO) Barrell et al.: (Nucleic Acids Res. 37, D396-D403, 2009), Ashburner et al.: (Nat. Genet. 25, 25-29, 2000) annotations, signaling pathways along with protein-protein interactions were covered. Some of the important biological processes-cell cycle, DNA repair, ion transport, ubiquinone biosynthetic process, pseudouridine synthesis, peptidoglycan biosynthetic process, RNA processing, and translation-revealed protein-protein interaction network generated by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) Jensen, et al.:(Nucleic Acids Res 37, D412-D126, 2009) database. Therefore, to achieve the saturation point of detection of maximum number of proteins in single LC-MS/MS run, 12-h liquid chromatography gradient is appropriate. Graphical Abstract ᅟ.
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Affiliation(s)
- Bhaswati Chatterjee
- National Institute of Pharmaceutical Education and Research (NIPER), NIPER-Hyderabad, (Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India), Balanagar, Hyderabad, Telangana, 500 037, India.
| | - Suman S Thakur
- Centre for Cellular and Molecular Biology, Proteomics and Cell Signaling, Lab E409, Uppal Road, Hyderabad, 500007, India.
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Meier F, Brunner AD, Koch S, Koch H, Lubeck M, Krause M, Goedecke N, Decker J, Kosinski T, Park MA, Bache N, Hoerning O, Cox J, Räther O, Mann M. Online Parallel Accumulation-Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer. Mol Cell Proteomics 2018; 17:2534-2545. [PMID: 30385480 PMCID: PMC6283298 DOI: 10.1074/mcp.tir118.000900] [Citation(s) in RCA: 467] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Indexed: 11/06/2022] Open
Abstract
In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.
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Affiliation(s)
- Florian Meier
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Scarlet Koch
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Heiner Koch
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Markus Lubeck
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Michael Krause
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Niels Goedecke
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Jens Decker
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Thomas Kosinski
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., Manning Road, Billerica, Massachusetts 01821
| | - Nicolai Bache
- Evosep Biosystems, Thriges Pl. 6, 5000 Odense, Denmark
| | - Ole Hoerning
- Evosep Biosystems, Thriges Pl. 6, 5000 Odense, Denmark
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Oliver Räther
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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Drali R, Berrazeg M, Zidouni LL, Hamitouche F, Abbas AA, Deriet A, Mouffok F. Emergence of mcr-1 plasmid-mediated colistin-resistant Escherichia coli isolates from seawater. Sci Total Environ 2018; 642:90-94. [PMID: 29894885 DOI: 10.1016/j.scitotenv.2018.05.387] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Colistin is currently regarded as one of the 'last-resort' antibiotics used for the treatment of critical infections caused by multidrug-resistant Gram-negative pathogens. Recently, there have been numerous reports of the emergence of a transferable plasmid-mediated colistin resistance gene, mcr-1 in patients, animals, food, and environment. Here, we characterize the support of colistin resistance among environmental isolates collected from seawater of Algiers coast. Our study was carried out on 246 isolates resistant to colistin (MIC > 2 μg/L). The mcr-1 gene was identified in only two isolates; M49 and M78. The two strains were identified as Escherichia coli and were non-susceptible to amoxicillin, ticarcillin, piperacillin, gentamicin, nalidixic acid, tigecycline, tetracycline, trimethoprim-sulfamethoxazole and colistin. For the latter, isolates M49 and M78 showed MIC values of 4 μg/mL and 8 μg/mL, respectively. Only the strain M78 was intermediary resistant to tobramycin. The two E. coli strains belonged to two different sequence types (STs): ST23 for M49 and ST115 for M78. The mcr-1 gene was present on a non-conjugative plasmid in the two strains.
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Affiliation(s)
- Rezak Drali
- Unité Environnement, Institut Pasteur d'Algérie, Alger 16000, Algeria.
| | - Meryem Berrazeg
- Unité de Microbiologie, Institut Pasteur d'Algérie, Antenne d'Oran 31000, Algeria; Département de Biologie, Faculté des Sciences de la Nature et de la vie, Université Oran1, 31000, Algeria
| | | | - Fella Hamitouche
- Unité Environnement, Institut Pasteur d'Algérie, Alger 16000, Algeria
| | - Amina Aicha Abbas
- Dépar tement de Biologie, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger 16000, Algeria
| | - Abdelhamid Deriet
- Unité Environnement, Institut Pasteur d'Algérie, Alger 16000, Algeria
| | - Fawzia Mouffok
- Unité Environnement, Institut Pasteur d'Algérie, Alger 16000, Algeria
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34
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Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI. ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinformatics 2018; 34:3557-3565. [PMID: 29741573 PMCID: PMC6184454 DOI: 10.1093/bioinformatics/bty370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Accepted: 05/03/2018] [Indexed: 01/27/2023] Open
Abstract
Motivation Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the Saccharomyces cerevisiae and Escherichia coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. Results We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S.cerevisiae and E.coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution. Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (P-value < 10-10) and -0.46 (P-value < 10-10) for S.cerevisiae and E.coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant. Availability and implementation ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rostam M Razban
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Amy I Gilson
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Niamh Durfee
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hendrik Strobelt
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Kasper Dinkla
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Jeong-Mo Choi
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hanspeter Pfister
- School of Engineering & Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Eugene I Shakhnovich
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
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35
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Abstract
Single-molecule digital enzyme assay using micron-sized droplet array is a promising analysis method to quantify biomolecules at extremely low concentrations. However, multiplex digital enzyme assays are still difficult to access because the best buffer conditions can vary largely among enzymes. In addition, the best conditions for flurogenic compounds to retain high quantum efficiency and to avoid leakage into the oil phase can be also very different. In this study, digital enzyme assay was performed using an array of nanometer-sized droplets of 200 aL volume, termed 'nanocell'. Due to the small reaction volume, nanocell enhanced the accumulation rate of fluorescent products by a factor of 100 when compared with micron-sized reactors. Nanocell also enabled oil-free sealing of reactors: when flushed with an air flow, nanocell displayed water droplets under air, allowing enzymes to catalyze the reaction at the same rate as in oil-sealed reactors. Dual digital enzyme assay was also demonstrated using β-galactosidase and alkaline phosphatase (ALP) at pH 7.4, which is far from the optimum condition for ALP. Even under such a non-optimum condition, ALP molecules were successfully detected. Nanocell could largely expand the applicability of digital bioassay for enzymes under non-optimum conditions or enzymes of low turnover rate. The sealing of the reactor with air would also expand the applicability, allowing the use of fluorescent dyes that leak into oil.
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Affiliation(s)
- Takao Ono
- Department of Applied Chemistry
, Graduate School of Engineering
, The University of Tokyo
,
Japan
.
| | - Takanori Ichiki
- Department of Materials Engineering
, Graduate School of Engineering
, The University of Tokyo
,
Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry
, Graduate School of Engineering
, The University of Tokyo
,
Japan
.
- ImPACT Program
, Japan Science and Technology Agency
,
Saitama 332-0012
, Japan
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36
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Wu Y, Chen J, Liu Z, Wang F. Identification of pyridoxal phosphate-modified proteins using mass spectrometry. Rapid Commun Mass Spectrom 2018; 32:195-200. [PMID: 29164709 DOI: 10.1002/rcm.8030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Pyridoxal 5'-phosphate (PLP) cooperates with a variety of enzymes in all organisms for many important biological processes. The development of mass spectrometry-based methodology for high-throughput modification analyses could provide an alternative way for PLP identification. The present study aims to identify PLP modification. METHODS More PLP site-determining information was obtained by introducing multistage activation (MSA)-assisted collision-induced dissociation (CID). We then utilized immobilized metal ion affinity chromatography (IMAC) with Ti4+ to enrich the PLP peptides. In addition, alkaline phosphatase (ALP) was used to remove the phosphoryl group and further confirm the PLP modification site. RESULTS MSA was able to greatly enhance the identification and localization of PLP modification. We applied this strategy to analyze PLP-modified proteins in Escherichia coli samples and accurately determine PLP site K270 in tryptophanase. CONCLUSIONS MSA-assisted CID was used to provide better identification of PLP-modified peptides. Furthermore, tryptophanase with PLP modification at K270 in E. coli was identified with Ti4+ -IMAC enrichment followed by ALP treatment. This method provides a promising alternative for investigating biological functions of PLP-modified proteins.
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Affiliation(s)
- Yue Wu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
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37
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Robson SA, Takeuchi K, Boeszoermenyi A, Coote PW, Dubey A, Hyberts S, Wagner G, Arthanari H. Mixed pyruvate labeling enables backbone resonance assignment of large proteins using a single experiment. Nat Commun 2018; 9:356. [PMID: 29367739 PMCID: PMC5783931 DOI: 10.1038/s41467-017-02767-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022] Open
Abstract
Backbone resonance assignment is a critical first step in the investigation of proteins by NMR. This is traditionally achieved with a standard set of experiments, most of which are not optimal for large proteins. Of these, HNCA is the most sensitive experiment that provides sequential correlations. However, this experiment suffers from chemical shift degeneracy problems during the assignment procedure. We present a strategy that increases the effective resolution of HNCA and enables near-complete resonance assignment using this single HNCA experiment. We utilize a combination of 2-13C and 3-13C pyruvate as the carbon source for isotope labeling, which suppresses the one bond (1Jαβ) coupling providing enhanced resolution for the Cα resonance and amino acid-specific peak shapes that arise from the residual coupling. Using this approach, we can obtain near-complete (>85%) backbone resonance assignment of a 42 kDa protein using a single HNCA experiment.
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Affiliation(s)
- Scott A Robson
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Andras Boeszoermenyi
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Paul W Coote
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Abhinav Dubey
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Sven Hyberts
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
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38
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Abstract
Bacterial Hsp90 is an ATP-dependent molecular chaperone involved in protein remodeling and activation. The E. coli Hsp90, Hsp90Ec, collaborates in protein remodeling with another ATP-dependent chaperone, DnaK, the E. coli Hsp70. Both Hsp90Ec and DnaK hydrolyze ATP and client (substrate) proteins stimulate the hydrolysis. Additionally, ATP hydrolysis by the combination of Hsp90Ec and DnaK is synergistically stimulated in the presence of client (substrate). Here, we describe two steady-state ATPase assays used to monitor ATP hydrolysis by Hsp90Ec and DnaK as well as the synergistic stimulation of ATP hydrolysis by the combination of Hsp90Ec and DnaK in the presence of a client (substrate). The first assay is a spectrophotometric assay based on enzyme-coupled reactions that utilize the ADP formed during ATP hydrolysis to oxidize NADH. The second assay is a more sensitive method that directly quantifies the radioactive inorganic phosphate released following the hydrolysis of [γ-33P] ATP or [γ-32P] ATP.
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Affiliation(s)
- Joel R Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5144, NIH, Bethesda, MD, 20892, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5144, NIH, Bethesda, MD, 20892, USA.
| | - Shannon M Doyle
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5144, NIH, Bethesda, MD, 20892, USA.
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39
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Peschke M, Le Goff M, Koningstein GM, Karyolaimos A, de Gier JW, van Ulsen P, Luirink J. SRP, FtsY, DnaK and YidC Are Required for the Biogenesis of the E. coli Tail-Anchored Membrane Proteins DjlC and Flk. J Mol Biol 2017; 430:389-403. [PMID: 29246766 DOI: 10.1016/j.jmb.2017.12.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 11/19/2022]
Abstract
Tail-anchored membrane proteins (TAMPs) are relatively simple membrane proteins characterized by a single transmembrane domain (TMD) at their C-terminus. Consequently, the hydrophobic TMD, which acts as a subcellular targeting signal, emerges from the ribosome only after termination of translation precluding canonical co-translational targeting and membrane insertion. In contrast to the well-studied eukaryotic TAMPs, surprisingly little is known about the cellular components that facilitate the biogenesis of bacterial TAMPs. In this study, we identify DjlC and Flk as bona fide Escherichia coli TAMPs and show that their TMDs are necessary and sufficient for authentic membrane targeting of the fluorescent reporter mNeonGreen. Using strains conditional for the expression of known E. coli membrane targeting and insertion factors, we demonstrate that the signal recognition particle (SRP), its receptor FtsY, the chaperone DnaK and insertase YidC are each required for efficient membrane localization of both TAMPs. A close association between the TMD of DjlC and Flk with both the Ffh subunit of SRP and YidC was confirmed by site-directed in vivo photo-crosslinking. In addition, our data suggest that the hydrophobicity of the TMD correlates with the dependency on SRP for efficient targeting.
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Affiliation(s)
- Markus Peschke
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands
| | - Mélanie Le Goff
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands
| | - Gregory M Koningstein
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands
| | - Alexandros Karyolaimos
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden
| | - Peter van Ulsen
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands
| | - Joen Luirink
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands.
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40
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Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:2614-2634. [PMID: 28875426 PMCID: PMC5709234 DOI: 10.1007/s13361-017-1781-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). Graphical Abstract ᅟ.
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Affiliation(s)
- Arseniy M Belov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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41
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Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:2614-2634. [PMID: 28875426 DOI: 10.1007/s13361-13017-11781-13361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/25/2023]
Abstract
Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). Graphical Abstract ᅟ.
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Affiliation(s)
- Arseniy M Belov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - David M Horn
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | | | - Barry L Karger
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
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42
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White JA, Haghighi C, Brunner J, Estrada M, Lal M, Chen D. Preformulation studies with the Escherichia coli double mutant heat-labile toxin adjuvant for use in an oral vaccine. J Immunol Methods 2017; 451:83-89. [PMID: 28939395 PMCID: PMC5703769 DOI: 10.1016/j.jim.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 11/25/2022]
Abstract
Double mutant heat-labile toxin (dmLT) is a promising adjuvant for oral vaccine administration. The aims of our study were to develop sensitive methods to detect low concentrations of dmLT and to use the assays in preformulation studies to determine whether dmLT remains stable under conditions encountered by an oral vaccine. We developed a sandwich ELISA specific for intact dmLT and a sensitive SDS-PAGE densitometry method, and tested stability of dmLT in glass and plastic containers, in saliva, at the pH of stomach fluid, and in high-osmolarity buffers. The developed ELISA has a quantification range of 62.5 to 0.9 ng/mL and lower limit of detection of 0.3 ng/mL; the limit of quantification of the SDS-PAGE is 10 μg/mL. This work demonstrates the application of dmLT assays in preformulation studies to development of an oral vaccine containing dmLT. Assays reported here will facilitate the understanding and use of dmLT as an adjuvant.
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Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, Martin V, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. Genome Med 2017; 9:70. [PMID: 28738847 PMCID: PMC5525225 DOI: 10.1186/s13073-017-0457-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare-associated infections. Here, we describe the value derived from a longitudinal epidemiological and genomic surveillance study of drug-resistant Escherichia coli in a LTCF in the United Kingdom (UK). METHODS Forty-five of 90 (50%) residents were recruited and followed for six months in 2014. Participants were screened weekly for carriage of extended-spectrum beta-lactamase (ESBL) producing E. coli. Participants positive for ESBL E. coli were also screened for ESBL-negative E. coli. Phenotypic antibiotic susceptibility of E. coli was determined using the Vitek2 instrument and isolates were sequenced on an Illumina HiSeq2000 instrument. Information was collected on episodes of clinical infection and antibiotic consumption. RESULTS Seventeen of 45 participants (38%) carried ESBL E. coli. Twenty-three of the 45 participants (51%) had 63 documented episodes of clinical infection treated with antibiotics. Treatment with antibiotics was associated with higher risk of carrying ESBL E. coli. ESBL E. coli was mainly sequence type (ST)131 (16/17, 94%). Non-ESBL E. coli from these 17 cases was more genetically diverse, but ST131 was found in eight (47%) cases. Whole-genome analysis of 297 ST131 E. coli from the 17 cases demonstrated highly related strains from six participants, indicating acquisition from a common source or person-to-person transmission. Five participants carried highly related strains of both ESBL-positive and ESBL-negative ST131. Genome-based comparison of ST131 isolates from the LTCF study participants with ST131 associated with bloodstream infection at a nearby acute hospital and in hospitals across England revealed sharing of highly related lineages between the LTCF and a local hospital. CONCLUSIONS This study demonstrates the power of genomic surveillance to detect multidrug-resistant pathogens and confirm their connectivity within a healthcare network.
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Affiliation(s)
- Hayley J. Brodrick
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Kathy E. Raven
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Nicholas M. Brown
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Veronique Martin
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Department of Medical Microbiology, Pathology Sciences Building 1, Southmead Hospital, Bristol, BS10 5NB UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
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Dohmen W, Schmitt H, Bonten M, Heederik D. Air exposure as a possible route for ESBL in pig farmers. Environ Res 2017; 155:359-364. [PMID: 28273621 DOI: 10.1016/j.envres.2017.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Livestock can carry extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, with blaCTX-M-1 being most prevalent. ESBL carriage in farmers is associated with ESBL carriage in animals, with direct animal-human contact considered as the dominant route of transmission. However, inhalation of stable air might represent another route of transmission. We, therefore, quantified presence of blaCTX-M group 1 genes (CTX-M-gr1) in dust and the association with CTX-M-gr1 carriage in pig farmers, family members and employees. We included 131 people living and/or working on 32 conventional Dutch pig production farms (farmers, family members and employees) during two sampling moments over a 12-month interval. Human stool samples, rectal swabs from 60 pigs per farm, and 2-5 dust samples collected using an electrostatic dust collector (EDC) (as a proxy for presence of viable CTX-M-gr1 carrying bacteria in air) were obtained per farm. Presence of ESBL-producing Escherichia Coli (E. coli) in stool samples and rectal swabs was determined by selective plating and CTX-M-gr1 was identified by PCR. Dust samples were analyzed directly by PCR for presence of CTX-M-gr1. Questionnaires were used to collect information on nature, intensity and duration of animal contact. Overall human prevalence of CTX-M-gr1 carriage was 3.6%. CTX-M-gr1 was detected in dust on 26% of the farms and in pigs on 35% of the farms, on at least one sampling moment. Human CTX-M-gr1 carriage and presence of CTX-M-gr1 in dust were associated univariately (OR=12.4, 95% CI=2.7-57.1). In multivariate analysis human CTX-M-gr1 carriage was associated with the number of working hours per week (OR=1.03, 95% CI=1.00-1.06), presence of CTX-M-gr1 carrying pigs on the farm (OR=7.4, 95% CI=1.1-49.7) and presence of CTX-M-gr1 in dust (OR=3.5, 95% CI=0.6-20.9). These results leave open the possibility of airborne CTX-M-gr1 transmission from animals to humans next to direct contact.
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Affiliation(s)
- Wietske Dohmen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marc Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
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45
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Mediavilla-Gradolph C, Sáinz-Rodriguez R, Valverde-Troya M, de Toro-Peinado I, Bermudez-Ruíz MP, Palop-Borrás B. [Evaluation of an immunochromatographic test for the detection of OXA-48 carbapenemase]. Rev Esp Quimioter 2017; 30:45-49. [PMID: 27897435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE Detection and differentiation of various types of carbapenemases is crucial to their control and dissemination. OXA-48 is the most common carbapenemase in Spain and in our environment. The aim of this study is the evaluation of a new immunochromatographic test OXA-48 Card letitest (Coris, BioConcept Belgium) to detect this carbapenemase from solid media. METHODS During the last year 151 strains of carbapenemase producing bacteria have been isolated, of which 136 were OXA-48 (126 Klebsiella pneumoniae, 1 Klebsiella oxytoca, 5 Escherichia coli, 4 Enterobacter cloacae), and 15 producing other carbapenemases . These 15 strains with other 73 carrying other resistance mechanisms (54 extended-spectrum β-lactamases producers and 19 with other mechanisms) were used as negative controls. RESULTS One hundred and thirty six strains carrying OXA-48 were positive with the test OXA-48 Card letitest and the 88 species used as controls were negative, resulting in a sensitivity and specificity of 100%. CONCLUSIONS The OXA-48 Card letitest is simple, quick, safe and cheap (approx. 6€/test) and can be used in microbiology laboratories to confirm the production of OXA-48 carbapenemase in clinical isolates.
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Affiliation(s)
| | | | | | | | | | - B Palop-Borrás
- Begoña Palop-Borrás, Laboratorio de Microbiología, Hospital Regional Universitario de Málaga, Avda. Carlos Haya, s/n 29010 Málaga, Spain.
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Amigo N, Zhang Q, Amadio A, Zhang Q, Silva WM, Cui B, Chen Z, Larzabal M, Bei J, Cataldi A. Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain. PLoS One 2016; 11:e0166883. [PMID: 27880834 PMCID: PMC5120812 DOI: 10.1371/journal.pone.0166883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 11/04/2016] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS), and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS) through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6), obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3). Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE), phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.
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Affiliation(s)
- Natalia Amigo
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Qi Zhang
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Ariel Amadio
- Rafaela Experimental Station, National Institute of Agricultural Technology. Rafaela, Santa Fe, Argentina
| | - Qunjie Zhang
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Wanderson M. Silva
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Baiyuan Cui
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Zhongjian Chen
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Mariano Larzabal
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Jinlong Bei
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
- * E-mail:
| | - Angel Cataldi
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
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Dufour YS, Gillet S, Frankel NW, Weibel DB, Emonet T. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells. PLoS Comput Biol 2016; 12:e1005041. [PMID: 27599206 PMCID: PMC5012591 DOI: 10.1371/journal.pcbi.1005041] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/29/2016] [Indexed: 01/26/2023] Open
Abstract
Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. Cell-to-cell variations in protein numbers due to random fluctuations at the molecular level lead to cell-to-cell variations in behavior. To maintain predictable responses, signaling networks have evolved robustness against noise, but in some situations phenotypic diversity in a clonal population can be beneficial as a bet hedging or division of labor strategy. Investigating of how random molecular fluctuations affect cell behavior requires to measure biological parameters at different scales. Here, we report a new experiment that allows the measure of both protein numbers and behavior in cells that are free to move in their environment. Using Escherichia coli, a model system for the study of cellular behavior, we investigated the effects variations in the numbers of the chemo-receptor modification enzymes on single-cell swimming behavior. We found that the mean and variance of the behavior can be adjusted independently in the population by adjusting protein expression. This mechanism allows for the genetic selection of phenotypic diversity without disrupting correlations in protein expression that are important for the overall robustness of the chemotaxis system.
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Affiliation(s)
- Yann S Dufour
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Sébastien Gillet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas W Frankel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
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48
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Abstract
We present a method suitable for quantitative analysis of intracellular proteins, metabolites and secondary messengers of single bacterial cells. The method integrates the concept of immunoassays on a microfluidic device that facilitates single cell trapping and isolating in a small volume of a few tens of picoliters. Combination of the benefits of microfluidic systems for single cell analysis with the high analytical selectivity and sensitivity of immunoassays enables the detection of even low abundant intracellular analytes which occur only at a few hundred copies per bacterium.
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Affiliation(s)
- Simone Stratz
- Department of Biosystems Science and Engineering, ETH Zurich, Vladimir-Prelog-Weg 3, Zurich, 8091, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Vladimir-Prelog-Weg 3, Zurich, 8091, Switzerland.
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49
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O’Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLoS Comput Biol 2016; 12:e1004998. [PMID: 27351952 PMCID: PMC4924638 DOI: 10.1371/journal.pcbi.1004998] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
The costs and benefits of protein expression are balanced through evolution. Expression of un-utilized protein (that have no benefits in the current environment) incurs a quantifiable fitness costs on cellular growth rates; however, the magnitude and variability of un-utilized protein expression in natural settings is unknown, largely due to the challenge in determining environment-specific proteome utilization. We address this challenge using absolute and global proteomics data combined with a recently developed genome-scale model of Escherichia coli that computes the environment-specific cost and utility of the proteome on a per gene basis. We show that nearly half of the proteome mass is unused in certain environments and accounting for the cost of this unused protein expression explains >95% of the variance in growth rates of Escherichia coli across 16 distinct environments. Furthermore, reduction in unused protein expression is shown to be a common mechanism to increase cellular growth rates in adaptive evolution experiments. Classification of the unused protein reveals that the unused protein encodes several nutrient- and stress- preparedness functions, which may convey fitness benefits in varying environments. Thus, unused protein expression is the source of large and pervasive fitness costs that may provide the benefit of hedging against environmental change. An overarching endeavor in systems biology is to characterize and understand the allocation of an organism’s proteome. Common approaches to characterize proteome allocation are based on annotations of protein functions or transcriptional regulatory targets. Here, we develop a novel approach based on model-predicted proteome utilization. This approach reveals that in many environments, a large fraction of the proteome is unused. Unused protein expression is known to incur costs on organismal fitness. We show that changes in the allocation of the proteome to used versus unused fractions can account for the variability in growth rates observed across environments and is a common mechanism to increase growth rates in laboratory evolution experiments. We compare our approach to classify the proteome based on model-predicted utilization to more traditional approaches to reveal biological functions and transcriptional regulators underlying the expression of unused protein. Expression of these functions may reflect ecological trade-offs between growth, nutrient-readiness, and stress resistance.
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Affiliation(s)
- Edward J. O’Brien
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology program, University of California, San Diego, La Jolla, California, United States of America
| | - Jose Utrilla
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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Abstract
In vivo isotopic labeling coupled with high-resolution proteomics is used to investigate primary metabolism in techniques such as stable isotope probing (protein-SIP) and peptide-based metabolic flux analysis (PMFA). Isotopic enrichment of carbon substrates and intracellular metabolism determine the distribution of isotopes within amino acids. The resulting amino acid mass distributions (AMDs) are convoluted into peptide mass distributions (PMDs) during protein synthesis. With no a priori knowledge on metabolic fluxes, the PMDs are therefore unknown. This complicates labeled peptide identification because prior knowledge on PMDs is used in all available peptide identification software. An automated framework for the identification and quantification of PMDs for nonuniformly labeled samples is therefore lacking. To unlock the potential of peptide labeling experiments for high-throughput flux analysis and other complex labeling experiments, an unsupervised peptide identification and quantification method was developed that uses discrete deconvolution of mass distributions of identified peptides to inform on the mass distributions of otherwise unidentifiable peptides. Uniformly (13)C-labeled Escherichia coli protein was used to test the developed feature reconstruction and deconvolution algorithms. The peptide identification was validated by comparing MS(2)-identified peptides to peptides identified from PMDs using unlabeled E. coli protein. Nonuniformly labeled Glycine max protein was used to demonstrate the technology on a representative sample suitable for flux analysis. Overall, automatic peptide identification and quantification were comparable or superior to manual extraction, enabling proteomics-based technology for high-throughput flux analysis studies.
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Affiliation(s)
- Joshua E Goldford
- Biotechnology Institute, University of Minnesota , Saint Paul, Minnesota 55108, United States
| | - Igor G L Libourel
- Biotechnology Institute, University of Minnesota , Saint Paul, Minnesota 55108, United States
- Department of Plant Biology, 1500 Gortner Avenue, University of Minnesota , Saint Paul, Minnesota 55108, United States
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