101
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Fatty acid synthase cooperates with protrudin to facilitate membrane outgrowth of cellular protrusions. Sci Rep 2017; 7:46569. [PMID: 28429738 PMCID: PMC5399442 DOI: 10.1038/srep46569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Cellular protrusion formation capacity is a key feature of developing neurons and many eukaryotic cells. However, the mechanisms underlying membrane growth in protrusion formation are largely unclear. In this study, photo-reactive unnatural amino acid 3-(3-methyl-3H-diazirin-3-yl)-propamino-carbonyl-Nε-l-lysine was incorporated by a genetic code expansion strategy into protrudin, a protein localized in acidic endosomes and in the endoplasmic reticulum, that induces cellular protrusion and neurite formation. The modified protrudin was used for covalent trapping of protrudin-interacting proteins in living cells. Fatty acid synthase (FASN), which synthesizes free fatty acids, was identified to transiently interact with protrudin. Further characterization revealed a unique cooperation mechanism in which protrudin cooperates with FASN to facilitate cellular protrusion formation. This work reveals a novel mechanism involved in protrusion formation that is dependent on transient interaction between FASN and protrudin, and establishes a creative strategy to investigate transient protein-protein interactions in mammalian cells.
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102
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Lin Z, Xie X, Chen PR. Kicking down the ladder: adding cleavable features to genetically encoded photocrosslinkers. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0452-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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103
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Wang ZA, Zeng Y, Kurra Y, Wang X, Tharp JM, Vatansever EC, Hsu WW, Dai S, Fang X, Liu WR. A Genetically Encoded Allysine for the Synthesis of Proteins with Site-Specific Lysine Dimethylation. Angew Chem Int Ed Engl 2016; 56:212-216. [PMID: 27910233 DOI: 10.1002/anie.201609452] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 01/01/2023]
Abstract
Using the amber suppression approach, Nϵ -(4-azidobenzoxycarbonyl)-δ,ϵ-dehydrolysine, an allysine precursor is genetically encoded in E. coli. Its genetic incorporation followed by two sequential biocompatible reactions allows convenient synthesis of proteins with site-specific lysine dimethylation. Using this approach, dimethyl-histone H3 and p53 proteins have been synthesized and used to probe functions of epigenetic enzymes including histone demethylase LSD1 and histone acetyltransferase Tip60. We confirmed that LSD1 is catalytically active toward H3K4me2 and H3K9me2 but inert toward H3K36me2, and methylation at p53 K372 directly activates Tip60 for its catalyzed acetylation at p53 K120.
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Affiliation(s)
- Zhipeng A Wang
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Xin Wang
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Taxes State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Erol C Vatansever
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Willie W Hsu
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
| | - Susie Dai
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics, Office of the Taxes State Chemist, Department of Veterinary Pathobiology, College Station, TX, 77843, USA
| | - Xinqiang Fang
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou, Fujian, 350002, P.R. China
| | - Wenshe R Liu
- Department of Chemistry, Texas A & M University, Corner of Ross and Spence Streets, College Station, TX 77843, USA
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104
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Wang ZA, Zeng Y, Kurra Y, Wang X, Tharp JM, Vatansever EC, Hsu WW, Dai S, Fang X, Liu WR. A Genetically Encoded Allysine for the Synthesis of Proteins with Site‐Specific Lysine Dimethylation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Zhipeng A. Wang
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Yu Zeng
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Yadagiri Kurra
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Xin Wang
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics Office of the Taxes State Chemist Department of Veterinary Pathobiology College Station TX 77843 USA
| | - Jeffery M. Tharp
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Erol C. Vatansever
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Willie W. Hsu
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
| | - Susie Dai
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics Office of the Taxes State Chemist Department of Veterinary Pathobiology College Station TX 77843 USA
| | - Xinqiang Fang
- Fujian Institute of Research on the Structure of Matter Chinese Academy of Science, Fuzhou Fujian 350002 P.R. China
| | - Wenshe R. Liu
- Department of Chemistry Texas A & M University Corner of Ross and Spence Streets College Station TX 77843 USA
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105
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Ge Y, Fan X, Chen PR. A genetically encoded multifunctional unnatural amino acid for versatile protein manipulations in living cells. Chem Sci 2016; 7:7055-7060. [PMID: 28451140 PMCID: PMC5355830 DOI: 10.1039/c6sc02615j] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/01/2016] [Indexed: 01/20/2023] Open
Abstract
The genetic code expansion strategy allowed incorporation of unnatural amino acids (UAAs) bearing diverse functional groups into proteins, providing a powerful toolkit for protein manipulation in living cells. We report a multifunctional UAA, Nε-p-azidobenzyloxycarbonyl lysine (PABK), that possesses a panel of unique properties capable of fulfilling various protein manipulation purposes. In addition to being used as a bioorthogonal ligation handle, an infrared probe and a photo-affinity reagent, PABK was shown to be chemically decaged by trans-cyclooctenols via a strain-promoted 1,3-dipolar cycloaddition, which provides a new bioorthogonal cleavage strategy for intracellular protein activation. The biocompatibility and efficiency of this method were demonstrated by decaging of a PABK-caged firefly luciferase under living conditions. We further extended this method to chemically rescue a bacterial toxin OspF inside mammalian host cells.
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Affiliation(s)
- Yun Ge
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
| | - Peng R Chen
- Beijing National Laboratory for Molecular Sciences , Synthetic and Functional Biomolecules Center , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
- Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China
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106
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Genetic code expansion for multiprotein complex engineering. Nat Methods 2016; 13:997-1000. [DOI: 10.1038/nmeth.4032] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 09/02/2016] [Indexed: 12/21/2022]
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107
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Mapping of the Communication-Mediating Interface in Nonribosomal Peptide Synthetases Using a Genetically Encoded Photocrosslinker Supports an Upside-Down Helix-Hand Motif. J Mol Biol 2016; 428:4345-4360. [DOI: 10.1016/j.jmb.2016.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/07/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022]
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108
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Yang Y, Song H, Chen PR. Genetically encoded photocrosslinkers for identifying and mapping protein-protein interactions in living cells. IUBMB Life 2016; 68:879-886. [DOI: 10.1002/iub.1560] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/03/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University; Beijing China
- Peking-Tsinghua Center for Life Sciences; Beijing China
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109
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Shang X, Song X, Faller C, Lai R, Li H, Cerny R, Niu W, Guo J. Fluorogenic protein labeling using a genetically encoded unstrained alkene. Chem Sci 2016; 8:1141-1145. [PMID: 28451254 PMCID: PMC5369545 DOI: 10.1039/c6sc03635j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 09/23/2016] [Indexed: 12/26/2022] Open
Abstract
A new fluorogenic bioorthogonal reaction between styrene (an unstrained alkene) and a tetrazine was developed.
We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.
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Affiliation(s)
- X Shang
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - X Song
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - C Faller
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - R Lai
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - H Li
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - R Cerny
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - W Niu
- Department of Chemical & Biomolecular Engineering , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
| | - J Guo
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA .
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110
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Chang Z. The function of the DegP (HtrA) protein: Protease versus chaperone. IUBMB Life 2016; 68:904-907. [PMID: 27670951 DOI: 10.1002/iub.1561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/06/2016] [Indexed: 11/06/2022]
Abstract
The DegP (or HtrA) is a highly conserved family of proteins functioning in all living organisms. It was initially identified as a protease functioning in the periplasmic space of the Gram-negative bacterial cells. It was later reported to also exhibit chaperone activity and thus has been designated as a bifunctional protein. However, recent studies demonstrated that in living cells it more likely functions only as a protease with hardly detectable chaperone activities. In this review, I will summarize the evidences clarifying that DegP more likely only functions as a protease rather than as a chaperone in cells. © 2016 IUBMB Life, 68(11):904-907, 2016.
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Affiliation(s)
- Zengyi Chang
- Center for Protein Science, State Key Laboratory of Protein and Plant Gene Studies, School of Life Sciences, Center for History and Philosophy of Science, Peking University, Beijing, China.
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111
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Lee Y, Jeong J, Lee G, Moon JH, Lee MK. Covalent and Oriented Surface Immobilization of Antibody Using Photoactivatable Antibody Fc-Binding Protein Expressed in Escherichia coli. Anal Chem 2016; 88:9503-9509. [DOI: 10.1021/acs.analchem.6b02071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yeolin Lee
- Hazards Monitoring Bionano Research
Center, ‡Disease Target Structure Research
Center, Korea Research Institute of Bioscience and Biotechnology, and §Department of
Nanobiotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jiyun Jeong
- Hazards Monitoring Bionano Research
Center, ‡Disease Target Structure Research
Center, Korea Research Institute of Bioscience and Biotechnology, and §Department of
Nanobiotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Gabi Lee
- Hazards Monitoring Bionano Research
Center, ‡Disease Target Structure Research
Center, Korea Research Institute of Bioscience and Biotechnology, and §Department of
Nanobiotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jeong Hee Moon
- Hazards Monitoring Bionano Research
Center, ‡Disease Target Structure Research
Center, Korea Research Institute of Bioscience and Biotechnology, and §Department of
Nanobiotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Myung Kyu Lee
- Hazards Monitoring Bionano Research
Center, ‡Disease Target Structure Research
Center, Korea Research Institute of Bioscience and Biotechnology, and §Department of
Nanobiotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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112
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Comparative proteomics reveal distinct chaperone-client interactions in supporting bacterial acid resistance. Proc Natl Acad Sci U S A 2016; 113:10872-7. [PMID: 27621474 DOI: 10.1073/pnas.1606360113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
HdeA and HdeB constitute the essential chaperone system that functions in the unique periplasmic space of Gram-negative enteric bacteria to confer acid resistance. How this two-chaperone machinery cooperates to protect a broad range of client proteins from acid denaturation while avoiding nonspecific binding during bacterial passage through the highly acidic human stomach remains unclear. We have developed a comparative proteomic strategy that combines the genetically encoded releasable protein photocross-linker with 2D difference gel electrophoresis, which allows an unbiased side-by-side comparison of the entire client pools from these two acid-activated chaperones in Escherichia coli Our results reveal distinct client specificities between HdeA and HdeB in vivo that are determined mainly by their different responses to pH stimulus. The intracellular acidity serves as an environmental cue to determine the folding status of both chaperones and their clients, enabling specific chaperone-client binding and release under defined pH conditions. This cooperative and synergistic mode of action provides an efficient, economical, flexible, and finely tuned protein quality control strategy for coping with acid stress.
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113
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Yang Y, Song H, He D, Zhang S, Dai S, Lin S, Meng R, Wang C, Chen PR. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label. Nat Commun 2016; 7:12299. [PMID: 27460181 PMCID: PMC4974458 DOI: 10.1038/ncomms12299] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Coupling photocrosslinking reagents with mass spectrometry has become a powerful tool for studying protein–protein interactions in living systems, but it still suffers from high rates of false-positive identifications as well as the lack of information on interaction interface due to the challenges in deciphering crosslinking peptides. Here we develop a genetically encoded photo-affinity unnatural amino acid that introduces a mass spectrometry-identifiable label (MS-label) to the captured prey proteins after photocrosslinking and prey–bait separation. This strategy, termed IMAPP (In-situ cleavage and MS-label transfer After Protein Photocrosslinking), enables direct identification of photo-captured substrate peptides that are difficult to uncover by conventional genetically encoded photocrosslinkers. Taking advantage of the MS-label, the IMAPP strategy significantly enhances the confidence for identifying protein–protein interactions and enables simultaneous mapping of the binding interface under living conditions. Mapping protein-protein interaction using crosslinking and mass spectroscopy strategies is hampered by a high rate of false-positive results. Here, the authors develop a genetically encoded photo-affinity probe for accurate identification of protein interaction partners and crosslinking sites.
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Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuai Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shizhong Dai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shixian Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Rong Meng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
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114
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De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
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Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
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115
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Wang Y, Wang R, Jin F, Liu Y, Yu J, Fu X, Chang Z. A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria. J Biol Chem 2016; 291:16720-9. [PMID: 27298319 DOI: 10.1074/jbc.m115.710715] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 11/06/2022] Open
Abstract
β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis.
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Affiliation(s)
- Yan Wang
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences
| | - Rui Wang
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences
| | - Feng Jin
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yang Liu
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences
| | - Jiayu Yu
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences
| | - Xinmiao Fu
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, and
| | - Zengyi Chang
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, and
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116
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Crnković A, Suzuki T, Söll D, Reynolds NM. Pyrrolysyl-tRNA synthetase, an aminoacyl-tRNA synthetase for genetic code expansion. CROAT CHEM ACTA 2016; 89:163-174. [PMID: 28239189 PMCID: PMC5321558 DOI: 10.5562/cca2825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetic code expansion (GCE) has become a central topic of synthetic biology. GCE relies on engineered aminoacyl-tRNA synthetases (aaRSs) and a cognate tRNA species to allow codon reassignment by co-translational insertion of non-canonical amino acids (ncAAs) into proteins. Introduction of such amino acids increases the chemical diversity of recombinant proteins endowing them with novel properties. Such proteins serve in sophisticated biochemical and biophysical studies both in vitro and in vivo, they may become unique biomaterials or therapeutic agents, and they afford metabolic dependence of genetically modified organisms for biocontainment purposes. In the Methanosarcinaceae the incorporation of the 22nd genetically encoded amino acid, pyrrolysine (Pyl), is facilitated by pyrrolysyl-tRNA synthetase (PylRS) and the cognate UAG-recognizing tRNAPyl. This unique aaRS•tRNA pair functions as an orthogonal translation system (OTS) in most model organisms. The facile directed evolution of the large PylRS active site to accommodate many ncAAs, and the enzyme's anticodon-blind specific recognition of the cognate tRNAPyl make this system highly amenable for GCE purposes. The remarkable polyspecificity of PylRS has been exploited to incorporate >100 different ncAAs into proteins. Here we review the Pyl-OT system and selected GCE applications to examine the properties of an effective OTS.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Noah M. Reynolds
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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117
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Xu H, Wang Y, Lu J, Zhang B, Zhang Z, Si L, Wu L, Yao T, Zhang C, Xiao S, Zhang L, Xia Q, Zhou D. Re-exploration of the Codon Context Effect on Amber Codon-Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue-White Screening Assay. Chembiochem 2016; 17:1250-6. [PMID: 27028123 DOI: 10.1002/cbic.201600117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022]
Abstract
The effect of codon context on amber codon-guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re-explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ-α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X-gal. Large-scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual-luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria.
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Affiliation(s)
- Huan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Yan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Jiaqi Lu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ziwei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Longlong Si
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ling Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Tianzhuo Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Chuanling Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
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118
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The Activity of Escherichia coli Chaperone SurA Is Regulated by Conformational Changes Involving a Parvulin Domain. J Bacteriol 2016; 198:921-9. [PMID: 26728192 DOI: 10.1128/jb.00889-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/29/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The periplasmic chaperone SurA is critical for the biogenesis of outer membrane proteins (OMPs) and, thus, the maintenance of membrane integrity in Escherichia coli. The activity of this modular chaperone has been attributed to a core chaperone module, with only minor importance assigned to the two SurA peptidyl-prolyl isomerase (PPIase) domains. In this work, we used synthetic phenotypes and covalent tethering to demonstrate that the activity of SurA is regulated by its PPIase domains and, furthermore, that its activity is correlated with the conformational state of the chaperone. When combined with mutations in the β-barrel assembly machine (BAM), SurA mutations resulting in deletion of the second parvulin domain (P2) inhibit OMP assembly, suggesting that P2 is involved in the regulation of SurA. The first parvulin domain (P1) potentiates this autoinhibition, as mutations that covalently tether the P1 domain to the core chaperone module severely impair OMP assembly. Furthermore, these inhibitory mutations negate the suppression of and biochemically stabilize the protein specified by a well-characterized gain-of-function mutation in P1, demonstrating that SurA cycles between distinct conformational and functional states during the OMP assembly process. IMPORTANCE This work reveals the reversible autoinhibition of the SurA chaperone imposed by a heretofore underappreciated parvulin domain. Many β-barrel-associated outer membrane (OM) virulence factors, including the P-pilus and type I fimbriae, rely on SurA for proper assembly; thus, a mechanistic understanding of SurA function and inhibition may facilitate antibiotic intervention against Gram-negative pathogens, such as uropathogenic Escherichia coli, E. coli O157:H7, Shigella, and Salmonella. In addition, SurA is important for the assembly of critical OM biogenesis factors, such as the lipopolysaccharide (LPS) transport machine, suggesting that specific targeting of SurA may provide a useful means to subvert the OM barrier.
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119
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Song X, Shang X, Ju T, Cerny R, Niu W, Guo J. A photoactivatable Src homology 2 (SH2) domain. RSC Adv 2016. [DOI: 10.1039/c6ra06211c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A photoactivatable SH2 domain that can be potentially applied as an optogenetic tool to the photocontrol of phosphotyrosine-associated biological processes.
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Affiliation(s)
- X. Song
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - X. Shang
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - T. Ju
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - R. Cerny
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - W. Niu
- Department of Chemical & Biomolecular Engineering
- University of Nebraska-Lincoln
- Lincoln
- USA
| | - J. Guo
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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120
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Yang T, Li XM, Bao X, Fung YME, Li XD. Photo-lysine captures proteins that bind lysine post-translational modifications. Nat Chem Biol 2015; 12:70-2. [PMID: 26689789 DOI: 10.1038/nchembio.1990] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022]
Abstract
Post-translational modifications (PTMs) have key roles in regulating protein-protein interactions in living cells. However, it remains a challenge to identify these PTM-mediated interactions. Here we develop a new lysine-based photo-reactive amino acid, termed photo-lysine. We demonstrate that photo-lysine, which is readily incorporated into proteins by native mammalian translation machinery, can be used to capture and identify proteins that recognize lysine PTMs, including 'readers' and 'erasers' of histone modifications.
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Affiliation(s)
- Tangpo Yang
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiucong Bao
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yi Man Eva Fung
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
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121
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Zhai Z, Wu Q, Zheng W, Liu M, Pielak GJ, Li C. Roles of structural plasticity in chaperone HdeA activity are revealed by 19F NMR. Chem Sci 2015; 7:2222-2228. [PMID: 29910910 PMCID: PMC5975942 DOI: 10.1039/c5sc04297f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 11/21/2022] Open
Abstract
Multiple conformations of acid chaperone HdeA and their roles in activity.
HdeA, a minimal ATP-independent acid chaperone, is crucial for the survival of enteric pathogens as they transit the acidic (pH 1–3) environment of the stomach. Although protein disorder (unfolding) and structural plasticity have been elegantly linked to HdeA function, the details of the linkage are lacking. Here, we apply 19F NMR to reveal the structural transition associated with activation. We find that unfolding is necessary but not sufficient for activation. Multiple conformations are present in the functional state at low pH, but the partially folded conformation is essential for HdeA chaperone activity, and HdeA's intrinsic disulfide bond is required to maintain the partially folded conformation. The results show that both disorder and order are key to function. The ability of 19F NMR to reveal and quantify multiple conformational states makes it a powerful tool for studying other chaperones.
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Affiliation(s)
- Zining Zhai
- Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , National Center for Magnetic Resonance in Wuhan , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , P. R. China . .,University of Chinese Academy of Sciences , Beijing , P. R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , National Center for Magnetic Resonance in Wuhan , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , P. R. China .
| | - Wenwen Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , National Center for Magnetic Resonance in Wuhan , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , P. R. China . .,University of Chinese Academy of Sciences , Beijing , P. R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , National Center for Magnetic Resonance in Wuhan , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , P. R. China .
| | - Gary J Pielak
- Department of Chemistry and Department of Biochemistry and Biophysics , University of North Carolina , Chapel Hill , NC , USA.,Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , National Center for Magnetic Resonance in Wuhan , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , P. R. China .
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122
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Ding J, Yang C, Niu X, Hu Y, Jin C. HdeB chaperone activity is coupled to its intrinsic dynamic properties. Sci Rep 2015; 5:16856. [PMID: 26593705 PMCID: PMC4655364 DOI: 10.1038/srep16856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/21/2015] [Indexed: 11/09/2022] Open
Abstract
Enteric bacteria encounter extreme acidity when passing through hosts' stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2-3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4-5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes, and therefore its functional mechanism is apparently different from HdeA.
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Affiliation(s)
- Jienv Ding
- College of Life Sciences, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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123
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Ren W, Truong TM, Ai HW. Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases. Sci Rep 2015; 5:12632. [PMID: 26220470 PMCID: PMC4518261 DOI: 10.1038/srep12632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/03/2015] [Indexed: 11/08/2022] Open
Abstract
We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.
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Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Tan M. Truong
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, California 92521, United States
- Cell, Molecular, and Developmental Biology Graduate Program, University of California-Riverside, Riverside, California 92521, United States
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124
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Suss O, Reichmann D. Protein plasticity underlines activation and function of ATP-independent chaperones. Front Mol Biosci 2015; 2:43. [PMID: 26284255 PMCID: PMC4516975 DOI: 10.3389/fmolb.2015.00043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/13/2015] [Indexed: 12/31/2022] Open
Abstract
One of the key issues in biology is to understand how cells cope with protein unfolding caused by changes in their environment. Self-protection is the natural immediate response to any sudden threat and for cells the critical issue is to prevent aggregation of existing proteins. Cellular response to stress is therefore indistinguishably linked to molecular chaperones, which are the first line of defense and function to efficiently recognize misfolded proteins and prevent their aggregation. One of the major protein families that act as cellular guards includes a group of ATP-independent chaperones, which facilitate protein folding without the consumption of ATP. This review will present fascinating insights into the diversity of ATP-independent chaperones, and the variety of mechanisms by which structural plasticity is utilized in the fine-tuning of chaperone activity, as well as in crosstalk within the proteostasis network. Research into this intriguing class of chaperones has introduced new concepts of stress response to a changing cellular environment, and paved the way to uncover how this environment affects protein folding.
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Affiliation(s)
- Ohad Suss
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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125
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Song Z, Takaoka Y, Kioi Y, Komatsu K, Tamura T, Miki T, Hamachi I. Extended Affinity-guided DMAP Chemistry with a Finely Tuned Acyl Donor for Intracellular FKBP12 Labeling. CHEM LETT 2015. [DOI: 10.1246/cl.141065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhining Song
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yoshiyuki Kioi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Kazuhiro Komatsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Takayuki Miki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Japan Science and Technology Agency (JST), CREST
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126
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Cho SH, Szewczyk J, Pesavento C, Zietek M, Banzhaf M, Roszczenko P, Asmar A, Laloux G, Hov AK, Leverrier P, Van der Henst C, Vertommen D, Typas A, Collet JF. Detecting envelope stress by monitoring β-barrel assembly. Cell 2015; 159:1652-64. [PMID: 25525882 DOI: 10.1016/j.cell.2014.11.045] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/06/2014] [Accepted: 11/24/2014] [Indexed: 01/29/2023]
Abstract
The cell envelope protects bacteria from their surroundings. Defects in its integrity or assembly are sensed by signal transduction systems, allowing cells to rapidly adjust. The Rcs phosphorelay responds to outer membrane (OM)- and peptidoglycan-related stress in enterobacteria. We elucidated how the OM lipoprotein RcsF, the upstream Rcs component, senses envelope stress and activates the signaling cascade. RcsF interacts with BamA, the major component of the β-barrel assembly machinery. In growing cells, BamA continuously funnels RcsF through the β-barrel OmpA, displaying RcsF on the cell surface. This process spatially separates RcsF from the downstream Rcs component, which we show is the inner membrane protein IgaA. The Rcs system is activated when BamA fails to bind RcsF and funnel it to OmpA. Newly synthesized RcsF then remains periplasmic, interacting with IgaA to activate the cascade. Thus RcsF senses envelope damage by monitoring the activity of the Bam machinery.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Joanna Szewczyk
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Christina Pesavento
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matylda Zietek
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paula Roszczenko
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Abir Asmar
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Géraldine Laloux
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Ann-Kristin Hov
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Pauline Leverrier
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Charles Van der Henst
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jean-François Collet
- WELBIO, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium.
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127
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Joerger RD, Choi S. Contribution of the hdeB-like gene (SEN1493) to survival of Salmonella enterica enteritidis Nal(R) at pH 2. Foodborne Pathog Dis 2015; 12:353-9. [PMID: 25659065 DOI: 10.1089/fpd.2014.1878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Periplasmic proteins are particularly vulnerable to denaturation upon entry into a highly acid environment. In Escherichia coli, a level of protection of these proteins is afforded by acid-inducible chaperonins encoded by hdeAB. In contrast, Salmonella enterica only harbors an hdeB-like gene and it is currently not known what function it plays in this genus. In the present study, the hdeB-like gene was deleted in Salmonella enterica Enteritidis Nal(R) and Salmonella enterica Kentucky 3795. When grown overnight in tryptic soy broth (TSB) medium buffered at pH 5.5 and then exposed to TSB pH 2 for 20 min, Enteritidis wild-type strain experienced a 0.5-log10 reduction in colony-forming units, whereas the deletion strain's surviving cells were reduced by 1.6 log10. No difference in survival was observed in the corresponding Salmonella enterica Kentucky 3795 strains treated the same way. Exposure of the strains to pH 2.5 or 3 resulted in the same log reduction regardless of the presence of the hdeB-like gene. When wild-type and deletion strains of both serovars were grown in medium buffered at pH 7 prior to exposure to the acidic pHs, no difference in survival with respect to serovar or presence/absence of the hdeB-like gene was found. Salmonella enterica Enteritidis Nal(R) carrying its own or the intragenic region upstream of the hdeB-like from Salmonella enterica Kentucky 3795 cloned in front of the gfp gene from pFPV25 showed maximum fluorescence when grown at pH 5.5, whereas the corresponding plasmid-carrying Salmonella enterica Kentucky strains did not exhibit fluorescence regardless of the pH of the growth medium. Therefore, the hdeB-like gene in Salmonella enterica Enteritidis, but not in Salmonella enterica Kentucky 3795, contributed to survival at pH 2 and its expression is responsive to the pH of the medium.
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Affiliation(s)
- Rolf D Joerger
- Department of Animal and Food Sciences, University of Delaware , Newark, Delaware
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128
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Lin A, Merkley ED, Clowers BH, Hutchison JR, Kreuzer HW. Effects of bacterial inactivation methods on downstream proteomic analysis. J Microbiol Methods 2015; 112:3-10. [PMID: 25620019 DOI: 10.1016/j.mimet.2015.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/18/2022]
Abstract
Inactivation of pathogenic microbial samples is often necessary for the protection of researchers and to comply with local and federal regulations. By its nature, biological inactivation causes changes to microbial samples, potentially affecting observed experimental results. While inactivation-induced damage to materials such as DNA has been evaluated, the effect of various inactivation strategies on proteomic data, to our knowledge, has not been discussed. To this end, we inactivated samples of Yersinia pestis and Escherichia coli by autoclave, ethanol, or irradiation treatment to determine how inactivation changes liquid chromatography-tandem mass spectrometry data quality as well as apparent protein content of cells. Proteomic datasets obtained from aliquots of samples inactivated by different methods were highly similar, with Pearson correlation coefficients ranging from 0.822 to 0.985 and 0.816 to 0.985 for E. coli and Y. pestis, respectively, suggesting that inactivation had only slight impacts on the set of proteins identified. In addition, spectral quality metrics such as distributions of various database search algorithm scores remained constant across inactivation methods, indicating that inactivation does not appreciably degrade spectral quality. Though overall changes resulting from inactivation were small, there were detectable trends. For example, one-sided Fischer exact tests determined that periplasmic proteins decrease in observed abundance after sample inactivation by autoclaving (α=1.71×10(-2) for E. coli, α=4.97×10(-4) for Y. pestis) and irradiation (α=9.43×10(-7) for E. coli, α=1.21×10(-5) for Y. pestis) when compared to controls that were not inactivated. Based on our data, if sample inactivation is necessary, we recommend inactivation with ethanol treatment with secondary preference given to irradiation.
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Affiliation(s)
- Andy Lin
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Eric D Merkley
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Brian H Clowers
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry, Washington State University, Pullman, WA 99164, United States
| | - Janine R Hutchison
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Helen W Kreuzer
- Signatures Sciences & Technology Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
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129
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Siegrist MS, Swarts BM, Fox DM, Lim SA, Bertozzi CR. Illumination of growth, division and secretion by metabolic labeling of the bacterial cell surface. FEMS Microbiol Rev 2015; 39:184-202. [PMID: 25725012 DOI: 10.1093/femsre/fuu012] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cell surface is the essential interface between a bacterium and its surroundings. Composed primarily of molecules that are not directly genetically encoded, this highly dynamic structure accommodates the basic cellular processes of growth and division as well as the transport of molecules between the cytoplasm and the extracellular milieu. In this review, we describe aspects of bacterial growth, division and secretion that have recently been uncovered by metabolic labeling of the cell envelope. Metabolite derivatives can be used to label a variety of macromolecules, from proteins to non-genetically-encoded glycans and lipids. The embedded metabolite enables precise tracking in time and space, and the versatility of newer chemoselective detection methods offers the ability to execute multiple experiments concurrently. In addition to reviewing the discoveries enabled by metabolic labeling of the bacterial cell envelope, we also discuss the potential of these techniques for translational applications. Finally, we offer some guidelines for implementing this emerging technology.
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Affiliation(s)
- M Sloan Siegrist
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Benjamin M Swarts
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Douglas M Fox
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Shion An Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, CA 94720, USA Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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130
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Ahlstrom LS, Law SM, Dickson A, Brooks CL. Multiscale modeling of a conditionally disordered pH-sensing chaperone. J Mol Biol 2015; 427:1670-80. [PMID: 25584862 DOI: 10.1016/j.jmb.2015.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/09/2014] [Accepted: 01/06/2015] [Indexed: 11/26/2022]
Abstract
The pH-sensing chaperone HdeA promotes the survival of enteropathogenic bacteria during transit through the harshly acidic environment of the mammalian stomach. At low pH, HdeA transitions from an inactive, folded, dimer to chaperone-active, disordered, monomers to protect against the acid-induced aggregation of periplasmic proteins. Toward achieving a detailed mechanistic understanding of the pH response of HdeA, we develop a multiscale modeling approach to capture its pH-dependent thermodynamics. Our approach combines pK(a) (logarithmic acid dissociation constant) calculations from all-atom constant pH molecular dynamics simulations with coarse-grained modeling and yields new, atomic-level, insights into HdeA chaperone function that can be directly tested by experiment. "pH triggers" that significantly destabilize the dimer are each located near the N-terminus of a helix, suggesting that their neutralization at low pH destabilizes the helix macrodipole as a mechanism of monomer disordering. Moreover, we observe a non-monotonic change in the pH-dependent stability of HdeA, with maximal stability of the dimer near pH5. This affect is attributed to the protonation Glu37, which exhibits an anomalously high pK(a) value and is located within the hydrophobic dimer interface. Finally, the pH-dependent binding pathway of HdeA comprises a partially unfolded, dimeric intermediate that becomes increasingly stable relative to the native dimer at lower pH values and displays key structural features for chaperone-substrate interaction. We anticipate that the insights from our model will help inform ongoing NMR and biochemical investigations.
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Affiliation(s)
- Logan S Ahlstrom
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sean M Law
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Alex Dickson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA.
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131
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De Biase D, Lund PA. The Escherichia coli Acid Stress Response and Its Significance for Pathogenesis. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:49-88. [PMID: 26003933 DOI: 10.1016/bs.aambs.2015.03.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Escherichia coli has a remarkable ability to survive low pH and possesses a number of different genetic systems that enable it to do this. These may be expressed constitutively, typically in stationary phase, or induced by growth under a variety of conditions. The activities of these systems have been implicated in the ability of E. coli to pass the acidic barrier of the stomach and to become established in the gastrointestinal tract, something causing serious infections. However, much of the work characterizing these systems has been done on standard laboratory strains of E. coli and under conditions which do not closely resemble those found in the human gut. Here we review what is known about acid resistance in E. coli as a model laboratory organism and in the context of its lifestyle as an inhabitant-sometimes an unwelcome one-of the human gut.
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132
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Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment - Expanding the chemistry in biology. Chem Sci 2015; 6:50-69. [PMID: 28553457 PMCID: PMC5424465 DOI: 10.1039/c4sc01534g] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022] Open
Abstract
Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of 'non-sense' codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.
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Affiliation(s)
- Anaëlle Dumas
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Lukas Lercher
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher D Spicer
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Benjamin G Davis
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
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133
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Zhang J, Men Y, Lv S, Yi L, Chen JF. Protein tetrazinylation via diazonium coupling for covalent and catalyst-free bioconjugation. Org Biomol Chem 2015; 13:11422-5. [DOI: 10.1039/c5ob02053k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports an efficient reagent 1 for direct and covalent introduction of tetrazines onto the surface of proteins and viruses under mild conditions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yuwen Men
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shanshan Lv
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Jian-Feng Chen
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
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134
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Götzke H, Muheim C, Altelaar AFM, Heck AJR, Maddalo G, Daley DO. Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics. Mol Cell Proteomics 2014; 14:216-26. [PMID: 25403562 DOI: 10.1074/mcp.m114.043216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How proteins are trafficked, folded, and assembled into functional units in the cell envelope of Gram-negative bacteria is of significant interest. A number of chaperones have been identified, however, the molecular roles of these chaperones are often enigmatic because it has been challenging to assign substrates. Recently we discovered a novel periplasmic chaperone, called YfgM, which associates with PpiD and the SecYEG translocon and operates in a network that contains Skp and SurA. The aim of the study presented here was to identify putative substrates of YfgM. We reasoned that substrates would be incorrectly folded or trafficked when YfgM was absent from the cell, and thus more prone to proteolysis (the loss-of-function rationale). We therefore used a comparative proteomic approach to identify cell envelope proteins that were lower in abundance in a strain lacking yfgM, and strains lacking yfgM together with either skp or surA. Sixteen putative substrates were identified. The list contained nine inner membrane proteins (CusS, EvgS, MalF, OsmC, TdcB, TdcC, WrbA, YfhB, and YtfH) and seven periplasmic proteins (HdeA, HdeB, AnsB, Ggt, MalE, YcgK, and YnjE), but it did not include any lipoproteins or outer membrane proteins. Significantly, AnsB (an asparaginase) and HdeB (a protein involved in the acid stress response), were lower in abundance in all three strains lacking yfgM. For both genes, we ruled out the possibility that they were transcriptionally down-regulated, so it is highly likely that the corresponding proteins are misfolded/mistargeted and turned-over in the absence of YfgM. For HdeB we validated this conclusion in a pulse-chase experiment. The identification of HdeB and other cell envelope proteins as potential substrates will be a valuable resource for follow-up experiments that aim to delineate molecular the function of YfgM.
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Affiliation(s)
- Hansjörg Götzke
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Claudio Muheim
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - A F Maarten Altelaar
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gianluca Maddalo
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Daniel O Daley
- From the ‡Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden;
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135
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Yang T, Liu Z, Li XD. Developing diazirine-based chemical probes to identify histone modification 'readers' and 'erasers'. Chem Sci 2014; 6:1011-1017. [PMID: 29560188 PMCID: PMC5811097 DOI: 10.1039/c4sc02328e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 10/24/2014] [Indexed: 01/06/2023] Open
Abstract
New chemical tools to ‘trap’ post translational modification (PTM)-mediated protein–protein interactions.
Post translational modifications (PTMs, e.g., phosphorylation, acetylation and methylation) of histone play important roles in regulating many fundamental cellular processes such as gene transcription, DNA replication and damage repair. While ‘writer’ and ‘eraser’ enzymes modify histones by catalyzing the addition and removal of histone PTMs, ‘reader’ proteins recognize these modified histones and ‘translate’ the PTMs by executing distinct cellular programs. Therefore, identification of the regulating enzymes and binding partners of histone PTMs is essential for understanding their regulatory mechanisms and cellular functions. Here we report the development of diazirine-based photoaffinity probes for identification of ‘readers’ and ‘erasers’ of histone PTMs. When compared with previously described benzophenone-based photoaffinity probes, the present probes demonstrate significantly improved photo-cross-linking rates, yields and specificities for capturing proteins that recognize a trimethylation mark on histone H3 lysine 4 (H3K4Me3). Furthermore, we show that the diazirine-based probes can also be used to identify enzymes that catalyse the removal of histone lysine acetylation and malonylation. This study provides new chemical tools for examining PTM-mediated protein–protein interactions and broadens the scope of our photo-cross-linking strategy from finding histone PTM ‘readers’ to identifying dynamic and transient interactions between PTMs and their ‘erasers’.
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Affiliation(s)
- Tangpo Yang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Zheng Liu
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
| | - Xiang David Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , China .
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136
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Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JCA, Jakob U. HdeB functions as an acid-protective chaperone in bacteria. J Biol Chem 2014; 290:65-75. [PMID: 25391835 DOI: 10.1074/jbc.m114.612986] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Enteric bacteria such as Escherichia coli utilize various acid response systems to counteract the acidic environment of the mammalian stomach. To protect their periplasmic proteome against rapid acid-mediated damage, bacteria contain the acid-activated periplasmic chaperones HdeA and HdeB. Activation of HdeA at pH 2 was shown to correlate with its acid-induced dissociation into partially unfolded monomers. In contrast, HdeB, which has high structural similarities to HdeA, shows negligible chaperone activity at pH 2 and only modest chaperone activity at pH 3. These results raised intriguing questions concerning the physiological role of HdeB in bacteria, its activation mechanism, and the structural requirements for its function as a molecular chaperone. In this study, we conducted structural and biochemical studies that revealed that HdeB indeed works as an effective molecular chaperone. However, in contrast to HdeA, whose chaperone function is optimal at pH 2, the chaperone function of HdeB is optimal at pH 4, at which HdeB is still fully dimeric and largely folded. NMR, analytical ultracentrifugation, and fluorescence studies suggest that the highly dynamic nature of HdeB at pH 4 alleviates the need for monomerization and partial unfolding. Once activated, HdeB binds various unfolding client proteins, prevents their aggregation, and supports their refolding upon subsequent neutralization. Overexpression of HdeA promotes bacterial survival at pH 2 and 3, whereas overexpression of HdeB positively affects bacterial growth at pH 4. These studies demonstrate how two structurally homologous proteins with seemingly identical in vivo functions have evolved to provide bacteria with the means for surviving a range of acidic protein-unfolding conditions.
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Affiliation(s)
- Jan-Ulrik Dahl
- From the Department of Molecular, Cellular, and Developmental Biology and
| | - Philipp Koldewey
- From the Department of Molecular, Cellular, and Developmental Biology and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Loïc Salmon
- From the Department of Molecular, Cellular, and Developmental Biology and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Scott Horowitz
- From the Department of Molecular, Cellular, and Developmental Biology and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - James C A Bardwell
- From the Department of Molecular, Cellular, and Developmental Biology and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1048
| | - Ursula Jakob
- From the Department of Molecular, Cellular, and Developmental Biology and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109-1048
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137
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Tuley A, Wang YS, Fang X, Kurra Y, Rezenom YH, Liu WR. The genetic incorporation of thirteen novel non-canonical amino acids. Chem Commun (Camb) 2014; 50:2673-5. [PMID: 24473369 DOI: 10.1039/c3cc49068h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Thirteen novel non-canonical amino acids were synthesized and tested for suppression of an amber codon using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair. Suppression was observed with varied efficiencies. One non-canonical amino acid in particular contains an azide that can be applied for site-selective protein labeling.
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Affiliation(s)
- Alfred Tuley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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138
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Zhang J, Ma D, Du D, Xi Z, Yi L. An efficient reagent for covalent introduction of alkynes into proteins. Org Biomol Chem 2014; 12:9528-31. [DOI: 10.1039/c4ob01873g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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139
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Chen XH, Xiang Z, Hu YS, Lacey VK, Cang H, Wang L. Genetically encoding an electrophilic amino acid for protein stapling and covalent binding to native receptors. ACS Chem Biol 2014; 9:1956-61. [PMID: 25010185 PMCID: PMC4168779 DOI: 10.1021/cb500453a] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Covalent bonds can be generated within
and between proteins by
an unnatural amino acid (Uaa) reacting with a natural residue through
proximity-enabled bioreactivity. Until now, Uaas have been developed
to react mainly with cysteine in proteins. Here we genetically encoded
an electrophilic Uaa capable of reacting with histidine and lysine,
thereby expanding the diversity of target proteins and the scope of
the proximity-enabled protein cross-linking technology. In addition
to efficient cross-linking of proteins inter- and intramolecularly,
this Uaa permits direct stapling of a protein α-helix in a recombinant
manner and covalent binding of native membrane receptors in live cells.
The target diversity, recombinant stapling, and covalent targeting
of endogenous proteins enabled by this versatile Uaa should prove
valuable in developing novel research tools, biological diagnostics,
and therapeutics by exploiting covalent protein linkages for specificity,
irreversibility, and stability.
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Affiliation(s)
- Xiao-Hua Chen
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Zheng Xiang
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying S. Hu
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Vanessa K. Lacey
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Hu Cang
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Lei Wang
- The Jack
H. Skirball Center for Chemical Biology and Proteomics and ‡Waitt Advanced
Biophotonics Center, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, United States
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140
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Abstract
Substantial efforts in the past decade have resulted in the systematic expansion of genetic codes, allowing for the direct ribosomal incorporation of ∼100 unnatural amino acids into bacteria, yeast, mammalian cells, and animals. Here, we illustrate the versatility of expanded genetic codes in biology and bioengineering, focusing on the application of expanded genetic codes to problems in protein, cell, synthetic, and experimental evolutionary biology. As the expanded genetic code field continues to develop, its place as a foundational technology in the whole of biological sciences will solidify.
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Affiliation(s)
- Xiang Li
- Department of Biomedical Engineering, University of California at Irvine, 3120 Natural Sciences II, Irvine, CA 92697 (USA)
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141
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Lin S, He D, Long T, Zhang S, Meng R, Chen PR. Genetically encoded cleavable protein photo-cross-linker. J Am Chem Soc 2014; 136:11860-3. [PMID: 25084056 DOI: 10.1021/ja504371w] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have developed a genetically encoded, selenium-based cleavable photo-cross-linker that allows for the separation of bait and prey proteins after protein photo-cross-linking. We have further demonstrated the efficient capture of the in situ generated selenenic acid on the cleaved prey proteins. Our strategy involves tagging the selenenic acid with an alkyne-containing dimethoxyaniline molecule and subsequently labeling with an azide-bearing fluorophore or biotin probe. This cleavage-and-capture after protein photo-cross-linking strategy allows for the efficient capture of prey proteins that are readily accessible by two-dimensional gel-based proteomics and mass spectrometry analysis.
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Affiliation(s)
- Shixian Lin
- Beijing National Laboratory for Molecular Sciences, Synthetic and functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, and Molecular Engineering, Peking University , Beijing 100871, China
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142
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Genetic code expansion and bioorthogonal labelling enables cell specific proteomics in an animal. Curr Opin Chem Biol 2014; 21:154-60. [DOI: 10.1016/j.cbpa.2014.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 11/20/2022]
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143
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Pavic K, Rios P, Dzeyk K, Koehler C, Lemke EA, Köhn M. Unnatural amino acid mutagenesis reveals dimerization as a negative regulatory mechanism of VHR's phosphatase activity. ACS Chem Biol 2014; 9:1451-9. [PMID: 24798147 DOI: 10.1021/cb500240n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vaccinia H1-related (VHR) phosphatase is a dual specificity phosphatase that is required for cell-cycle progression and plays a role in cell growth of certain cancers. Therefore, it represents a potential drug target. VHR is structurally and biochemically well characterized, yet its regulatory principles are still poorly understood. Understanding its regulation is important, not only to comprehend VHR's biological mechanisms and roles but also to determine its potential and druggability as a target in cancer. Here, we investigated the functional role of the unique "variable insert" region in VHR by selectively introducing the photo-cross-linkable amino acid para-benzoylphenylalanine (pBPA) using the amber suppression method. This approach led to the discovery of VHR dimerization, which was further confirmed using traditional chemical cross-linkers. Phe68 in VHR was discovered as a residue involved in the dimerization. We demonstrate that VHR can dimerize inside cells, and that VHR catalytic activity is reduced upon dimerization. Our results suggest that dimerization could occlude the active site of VHR, thereby blocking its accessibility to substrates. These findings indicate that the previously unknown transient self-association of VHR acts as a means for the negative regulation of its catalytic activity.
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Affiliation(s)
- Karolina Pavic
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Pablo Rios
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kristina Dzeyk
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christine Koehler
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A. Lemke
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Maja Köhn
- Genome Biology Unit, ‡Proteomics Core Facility and §Structural and Computational Biology
Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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144
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Lund P, Tramonti A, De Biase D. Coping with low pH: molecular strategies in neutralophilic bacteria. FEMS Microbiol Rev 2014; 38:1091-125. [PMID: 24898062 DOI: 10.1111/1574-6976.12076] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 02/26/2014] [Accepted: 03/14/2014] [Indexed: 12/31/2022] Open
Abstract
As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.
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Affiliation(s)
- Peter Lund
- School of Biosciences, University of Birmingham, Birmingham, UK
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145
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Götzke H, Palombo I, Muheim C, Perrody E, Genevaux P, Kudva R, Müller M, Daley DO. YfgM is an ancillary subunit of the SecYEG translocon in Escherichia coli. J Biol Chem 2014; 289:19089-97. [PMID: 24855643 DOI: 10.1074/jbc.m113.541672] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein secretion in Gram-negative bacteria is essential for both cell viability and pathogenesis. The vast majority of secreted proteins exit the cytoplasm through a transmembrane conduit called the Sec translocon in a process that is facilitated by ancillary modules, such as SecA, SecDF-YajC, YidC, and PpiD. In this study we have characterized YfgM, a protein with no annotated function. We found it to be a novel ancillary subunit of the Sec translocon as it co-purifies with both PpiD and the SecYEG translocon after immunoprecipitation and blue native/SDS-PAGE. Phenotypic analyses of strains lacking yfgM suggest that its physiological role in the cell overlaps with the periplasmic chaperones SurA and Skp. We, therefore, propose a role for YfgM in mediating the trafficking of proteins from the Sec translocon to the periplasmic chaperone network that contains SurA, Skp, DegP, PpiD, and FkpA.
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Affiliation(s)
- Hansjörg Götzke
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Isolde Palombo
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Claudio Muheim
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Elsa Perrody
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, and Université Paul Sabatier, 31062 Toulouse, France, and
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, and Université Paul Sabatier, 31062 Toulouse, France, and
| | - Renuka Kudva
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare, Spemann Graduate School of Biology and Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Matthias Müller
- Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare, Spemann Graduate School of Biology and Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Daniel O Daley
- From the Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden,
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146
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Trentini DB, Fuhrmann J, Mechtler K, Clausen T. Chasing Phosphoarginine Proteins: Development of a Selective Enrichment Method Using a Phosphatase Trap. Mol Cell Proteomics 2014; 13:1953-64. [PMID: 24825175 DOI: 10.1074/mcp.o113.035790] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Indexed: 01/30/2023] Open
Abstract
Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was never studied using modern mass spectrometry methods, owing to technical difficulties arising from the acid lability of phosphoarginine. As shown recently, the McsB and YwlE proteins from Bacillus subtilis function as a highly specific protein arginine kinase and phosphatase couple, shaping the phosphoarginine proteome. Using a B. subtilis ΔywlE strain as a source for arginine-phosphorylated proteins, we were able to adapt mass spectrometry (MS) protocols to the special chemical properties of the arginine modification. Despite this progress, the analysis of protein arginine phosphorylation in eukaryotes is still challenging, given the great abundance of serine/threonine phosphorylations that would compete with phosphoarginine during the phosphopeptide enrichment procedure, as well as during data-dependent MS acquisition. We thus set out to establish a method for the selective enrichment of arginine-phosphorylated proteins as an initial step in the phosphoproteomic analysis. For this purpose, we developed a substrate-trapping mutant of the YwlE phosphatase that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. By testing a number of active site substitutions, we identified a YwlE mutant (C9A) that stably binds to arginine-phosphorylated proteins. We further improved the substrate-trapping efficiency by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captured arginine-phosphorylated proteins from complex B. subtilis ΔywlE cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications. In conclusion, we present a novel tool for the selective enrichment and subsequent MS analysis of arginine phosphorylation, which is a largely overlooked protein modification that might be important for eukaryotic cell signaling.
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Affiliation(s)
- Débora Broch Trentini
- From the ‡Research Institute of Molecular Pathology - IMP, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
| | - Jakob Fuhrmann
- From the ‡Research Institute of Molecular Pathology - IMP, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
| | - Karl Mechtler
- From the ‡Research Institute of Molecular Pathology - IMP, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria; §Institute of Molecular Biotechnology of the Austrian Academy of Sciences - IMBA, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Tim Clausen
- From the ‡Research Institute of Molecular Pathology - IMP, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria;
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147
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Tharp JM, Wang YS, Lee YJ, Yang Y, Liu WR. Genetic incorporation of seven ortho-substituted phenylalanine derivatives. ACS Chem Biol 2014; 9:884-90. [PMID: 24451054 PMCID: PMC3997995 DOI: 10.1021/cb400917a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Seven
phenylalanine derivatives with small ortho substitutions
were genetically encoded in Escherichia coli and
mammalian cells at an amber codon using a previously reported,
rationally designed pyrrolysyl-tRNA synthetase mutant (PylRS(N346A/C348A))
coupled with tRNACUAPyl. Ortho substitutions of the phenylalanine
derivatives reported herein include three halides, methyl, methoxy,
nitro, and nitrile. These compounds have the potential for use in
multiple biochemical and biophysical applications. Specifically, we
demonstrated that o-cyano-phenylalanine could be
used as a selective sensor to probe the local environment of proteins
and applied this to study protein folding/unfolding. For six of these
compounds this constitutes the first report of their genetic incorporation
in living cells. With these compounds the total number of substrates
available for PylRS(N346A/C348A) is increased to nearly 40, which
demonstrates that PylRS(N346A/C348A) is able to recognize phenylalanine
with a substitution at any side-chain aromatic position as a substrate.
To our knowledge, PylRS(N346A/C348A) is the only aminoacyl-tRNA synthetase
with such a high substrate promiscuity.
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Affiliation(s)
- Jeffery M. Tharp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yanyan Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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148
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Schmidt MJ, Weber A, Pott M, Welte W, Summerer D. Structural basis of furan-amino acid recognition by a polyspecific aminoacyl-tRNA-synthetase and its genetic encoding in human cells. Chembiochem 2014; 15:1755-60. [PMID: 24737732 DOI: 10.1002/cbic.201402006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 11/05/2022]
Abstract
The site-selective introduction of photo-crosslinking groups into proteins enables the discovery and mapping of weak and/or transient protein interactions with high spatiotemporal resolution, both in vitro and in vivo. We report the genetic encoding of a furan-based, photo-crosslinking amino acid in human cells; it can be activated with red light, thus offering high penetration depths in biological samples. This is achieved by activation of the amino acid and charging to its cognate tRNA by a pyrrolysyl-tRNA-synthetase (PylRS) mutant with broad polyspecificity. To gain insights into the recognition of this amino acid and to provide a rationale for its polyspecificity, we solved three crystal structures of the PylRS mutant: in its apo-form, in complex with adenosine 5'-(β,γ-imido)triphosphate (AMP-PNP) and in complex with the AMP ester of the furan amino acid. These structures provide clues for the observed polyspecificity and represent a promising starting point for the engineering of PylRS mutants with further increased substrate scope.
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Affiliation(s)
- Moritz J Schmidt
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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149
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Preston GW, Radford SE, Ashcroft AE, Wilson AJ. Analysis of amyloid nanostructures using photo-cross-linking: in situ comparison of three widely used photo-cross-linkers. ACS Chem Biol 2014; 9:761-8. [PMID: 24372480 PMCID: PMC3964826 DOI: 10.1021/cb400731s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Photoinduced cross-linking (PIC) has become a powerful tool in chemical biology for the identification and mapping of stable or transient interactions between biomacromolecules and their (unknown) ligands. However, the value of PIC for in vitro and in vivo structural proteomics can be realized only if cross-linking reports accurately on biomacromolecule secondary, tertiary, and quaternary structures with residue-specific resolution. Progress in this area requires rigorous and comparative studies of PIC reagents, but despite widespread use of PIC, these have rarely been performed. The use of PIC to report reliably on noncovalent structure is therefore limited, and its potentials have yet to be fully realized. In the present study, we compared the abilities of three probes, phenyl trifluoromethyldiazirine (TFMD), benzophenone (BP), and phenylazide (PA), to record structural information within a biomolecular complex. For this purpose, we employed a self-assembled amyloid-like peptide nanostructure as a tightly and specifically packed model environment in which to photolyze the reagents. Information about PIC products was gathered using mass spectrometry and ion mobility spectrometry, and the data were interpreted using a mechanism-oriented approach. While all three PIC groups appeared to generate information within the packed peptide environment, the data highlight technical limitations of BP and PA. On the other hand, TFMD displayed accuracy and generated straightforward results. Thus TFMD, with its robust and rapid photochemistry, was shown to be an ideal probe for cross-linking of peptide nanostructures. The implications of our findings for detailed analyses of complex systems, including those that are transiently populated, are discussed.
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Affiliation(s)
- George W. Preston
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sheena E. Radford
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Alison. E. Ashcroft
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Andrew J. Wilson
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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150
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 787] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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