51
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Song H, Wang Y, Wang R, Zhang X, Liu Y, Jia G, Chen PR. SFPQ Is an FTO-Binding Protein that Facilitates the Demethylation Substrate Preference. Cell Chem Biol 2020; 27:283-291.e6. [PMID: 31981477 DOI: 10.1016/j.chembiol.2020.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/15/2019] [Accepted: 01/03/2020] [Indexed: 12/25/2022]
Abstract
The fat mass and obesity-associated protein (FTO) is the first identified demethylase of the internal RNA modification N6-methyladenosine (m6A), which also exhibits demethylation activity toward N6,2'-O-dimethyladenosine (m6Am) and N1-methyladenosine (m1A). Demethylation of m6A at specific sites on target transcripts is a key enzymatic function of FTO that modulates diverse physiological and/or pathological processes. However, how FTO selects target RNA and whether additional interaction proteins facilitate this process remain elusive. Herein, via the genetically encoded and site-specific photocrosslinking strategy, we identified the major RNA-binding protein SFPQ as a direct interaction partner of FTO. Our study showed that FTO and SFPQ were located in close proximity throughout the transcriptome and that overexpression of SFPQ led to the demethylation of adjacent m6As, likely through recruiting FTO to these specific RNA sites. These results uncovered a new layer of regulation mechanism that may assist FTO to gain substrate specificity.
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Affiliation(s)
- 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 100871, China
| | - Ye Wang
- 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 100871, China
| | - Ruixiang Wang
- Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Xiao Zhang
- 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 100871, China
| | - Yaping Liu
- 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 100871, China
| | - Guifang Jia
- 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 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, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China.
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52
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Mishra PK, Yoo CM, Hong E, Rhee HW. Photo-crosslinking: An Emerging Chemical Tool for Investigating Molecular Networks in Live Cells. Chembiochem 2020; 21:924-932. [PMID: 31794116 DOI: 10.1002/cbic.201900600] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Studying protein-protein interactions (PPIs) is useful for understanding cellular functions and mechanisms. Evaluating these PPIs under conditions as similar as possible to native conditions can be achieved using photo-crosslinking methods because of their on-demand ability to generate reactive species in situ by irradiation with UV light. Various fusion tag, metabolic incorporation, and amber codon suppression approaches using various crosslinkers containing aryl azide, benzophenone, and diazirines have been applied in live cells. Mass spectrometry and immunological techniques are used to identify crosslinked proteins based on their capture transient and context-dependent interactions. Herein we discuss various incorporation methods and crosslinkers that have been used for interactome mapping in live cells.
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Affiliation(s)
- Pratyush Kumar Mishra
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Chang-Mo Yoo
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 360-4 Dongnae-dong, Dong-gu, Daegu, 41061, Republic of Korea
| | - Hyun Woo Rhee
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
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53
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Dziuba D, Hoffmann J, Hentze MW, Schultz C. A Genetically Encoded Diazirine Analogue for RNA-Protein Photo-crosslinking. Chembiochem 2020; 21:88-93. [PMID: 31658407 PMCID: PMC7003851 DOI: 10.1002/cbic.201900559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Ultraviolent crosslinking is a key experimental step in the numerous protocols that have been developed for capturing and dissecting RNA-protein interactions in living cells. UV crosslinking covalently stalls dynamic interactions between RNAs and the directly contacting RNA-binding proteins and enables stringent denaturing downstream purification conditions needed for the enrichment and biochemical analysis of RNA-protein complexes. Despite its popularity, conventional 254 nm UV crosslinking possesses a set of intrinsic drawbacks, with the low photochemical efficiency being the central caveat. Here we show that genetically encoded photoreactive unnatural amino acids bearing a dialkyl diazirine photoreactive group can address this problem. Using the human iron regulatory protein 1 (IRP1) as a model RNA-binding protein, we show that the photoreactive amino acids can be introduced into the protein without diminishing its RNA-binding properties. A sevenfold increase in the crosslinking efficiency compared to conventional 254 nm UV crosslinking was achieved using the diazirine-based unnatural amino acid DiAzKs. This finding opens an avenue for new applications of the unnatural amino acids in studying RNA-protein interactions.
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Affiliation(s)
- Dmytro Dziuba
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Jan‐Erik Hoffmann
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
| | - Matthias W. Hentze
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
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54
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Yang T, Li X, Li XD. A bifunctional amino acid to study protein–protein interactions. RSC Adv 2020; 10:42076-42083. [PMID: 35516754 PMCID: PMC9057919 DOI: 10.1039/d0ra09110c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
dzANA is a novel bifunctional (photo-reactive and bioorthogonal) amino acid to study protein–protein interactions.
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Affiliation(s)
- Tangpo Yang
- Department of Chemistry
- The University of Hong Kong
- China
| | - Xin Li
- Department of Chemistry
- The University of Hong Kong
- China
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55
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Zheng Q, Zhang L, Zhang Q, Pang Z, Sun Y, Yin Z, Lou Z. Discovery of Interacting Proteins of ABA Receptor PYL5 via Covalent Chemical Capture. ACS Chem Biol 2019; 14:2557-2563. [PMID: 31617999 DOI: 10.1021/acschembio.9b00806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abscisic acid (ABA) is a key phytohormone with diverse functions in plants, and its signal transduction is mainly mediated by ABA receptors termed PYR/PYL/RCARs (hereafter referred to as PYLs) through the PYLs-PP2Cs-SnRK2s regulatory systems. However, the model failed to account for the roles of some important known regulators of ABA physiology. Given the central role of PYLs in ABA signal transduction, we therefore speculated that ABA receptors PYLs might be involved in regulatory pathways other than PP2Cs. Thus, a comprehensive analysis of PYLs-interacting partners could greatly facilitate the identification of unknown regulatory pathways, advancing our knowledge of the ABA signaling mechanism. Herein, we present a strategy involving covalent chemical capture coupled with HPLC-MS/MS analysis, to profile PYL5-interacting partners in plant cell lysates. With this strategy, three new PYL5-interacting partners, ubiquitin receptor RAD23C, COP9 signalosome complex subunit 1 (CSN1), and cyclase-associated protein 1 (CAP1), along with their key binding sites with PYL5 were identified. Among these proteins, CAP1 was verified to interact with PYL5 both in vitro and in vivo. The discovery of a new PYL5 binding partner showed the versatility of covalent chemical cross-linking and laid the foundation for future efforts to further elucidate the ABA signaling mechanism.
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Affiliation(s)
- Qizhen Zheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Liang Zhang
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Qian Zhang
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhengyuan Pang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yang Sun
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zheng Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhiyong Lou
- School of Medicine, Tsinghua University, Beijing 100084, China
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56
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Degp degrades a wide range of substrate proteins in Escherichia coli under stress conditions. Biochem J 2019; 476:3549-3564. [DOI: 10.1042/bcj20190446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022]
Abstract
DegP, a periplasmic dual-functional protease and chaperone in Gram-negative bacteria, is critical for bacterial stress resistance, but the precise underlying mechanisms are not fully understood. Here, we show that the protease function of DegP is critical for Escherichia coli cells to maintain membrane integrity, particularly under heat shock conditions (42°C). Site-directed photo-cross-linking, mass spectrometry and immunoblotting analyses reveal that both periplasmic proteins (e.g. OppA and MalE) and β-barrel outer membrane proteins (OMPs) are DegP-interacting proteins and that OppA is degraded by DegP in vitro and in vivo at 42°C. In addition, OmpA and BamA, chimeric β-barrel OMPs containing a soluble periplasmic domain, are bound to DegP in both unfolded and folded forms, whereas only the unfolded forms are degradable by DegP. The presence of folded OmpA as a substrate of DegP is attributed to its periplasmic domain, which is resistant to DegP degradation and even generally protects pure β-barrel OMPs from degradation in an intra-molecular way. Furthermore, a pair of residues (R262 and V328) in the PDZ domain-1 of DegP play important roles for binding unfolded and folded β-barrel OMPs, with R262 being critical. Our study, together with earlier reports, indicates that DegP plays a critical role in protein quality control in the bacterial periplasm by degrading both periplasmic proteins and β-barrel OMPs under stress conditions and likely also by participating in the folding of chimeric β-barrel OMPs. A working model is proposed to illustrate the finely tuned functions of DegP with respect to different substrate proteins.
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57
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Site-specific acylation of a bacterial virulence regulator attenuates infection. Nat Chem Biol 2019; 16:95-103. [PMID: 31740807 PMCID: PMC8439376 DOI: 10.1038/s41589-019-0392-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/23/2019] [Indexed: 12/27/2022]
Abstract
Microbiota generates millimolar concentrations of short-chain fatty acids (SCFAs) that can modulate host metabolism, immunity and susceptibility to infection. Butyrate in particular can function as a carbon source and anti-inflammatory metabolite, but the mechanism by which it inhibits pathogen virulence has been elusive. Using chemical proteomics, we discovered that several virulence factors encoded by Salmonella pathogenicity island-1 (SPI-1) are acylated by SCFAs. Notably, a transcriptional regulator of SPI-1, HilA, was acylated on several key lysine residues. Subsequent incorporation of stable butyryl-lysine analogs using CRISPR-Cas9 gene editing and unnatural amino acid mutagenesis revealed that site-specific modification of HilA impacts its genomic occupancy, expression of SPI-1 genes and attenuates Salmonella enterica serovar Typhimurium invasion of epithelial cells as well as dissemination in vivo. Moreover, a multiple-site HilA lysine-acylation mutant strain of S. Typhimurium was resistant to butyrate-mediated suppression in vivo. Our results suggest prominent microbiota-derived metabolites may directly acylate virulence factors to inhibit microbial pathogenesis in vivo.
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58
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Hu W, Yuan Y, Wang CH, Tian HT, Guo AD, Nie HJ, Hu H, Tan M, Tang Z, Chen XH. Genetically Encoded Residue-Selective Photo-Crosslinker to Capture Protein-Protein Interactions in Living Cells. Chem 2019. [DOI: 10.1016/j.chempr.2019.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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59
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Won Y, Pagar AD, Patil MD, Dawson PE, Yun H. Recent Advances in Enzyme Engineering through Incorporation of Unnatural Amino Acids. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0163-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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60
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Liu J, Li S, Aslam NA, Zheng F, Yang B, Cheng R, Wang N, Rozovsky S, Wang PG, Wang Q, Wang L. Genetically Encoding Photocaged Quinone Methide to Multitarget Protein Residues Covalently in Vivo. J Am Chem Soc 2019; 141:9458-9462. [PMID: 31184146 DOI: 10.1021/jacs.9b01738] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetically introducing covalent bonds into proteins in vivo with residue specificity is affording innovative ways for protein research and engineering, yet latent bioreactive unnatural amino acids (Uaas) genetically encoded to date react with one to few natural residues only, limiting the variety of proteins and the scope of applications amenable to this technology. Here we report the genetic encoding of (2 R)-2-amino-3-fluoro-3-(4-((2-nitrobenzyl)oxy) phenyl) propanoic acid (FnbY) in Escherichia coli and mammalian cells. Upon photoactivation, FnbY generated a reactive quinone methide (QM), which selectively reacted with nine natural amino acid residues placed in proximity in proteins directly in live cells. In addition to Cys, Lys, His, and Tyr, photoactivated FnbY also reacted with Trp, Met, Arg, Asn, and Gln, which are inaccessible with existing latent bioreactive Uaas. FnbY thus dramatically expanded the number of residues for covalent targeting in vivo. QM has longer half-life than the intermediates of conventional photo-cross-linking Uaas, and FnbY exhibited cross-linking efficiency higher than p-azido-phenylalanine. The photoactivatable and multitargeting reactivity of FnbY with selectivity toward nucleophilic residues will be valuable for addressing diverse proteins and broadening the scope of applications through exploiting covalent bonding in vivo for chemical biology, biotherapeutics, and protein engineering.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Shanshan Li
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States.,Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Nayyar A Aslam
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Bing Yang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Peng G Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
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61
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Fu X, Chang Z. Biogenesis, quality control, and structural dynamics of proteins as explored in living cells via site-directed photocrosslinking. Protein Sci 2019; 28:1194-1209. [PMID: 31002747 DOI: 10.1002/pro.3627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
Protein biogenesis and quality control are essential to maintaining a functional pool of proteins and involve numerous protein factors that dynamically and transiently interact with each other and with the substrate proteins in living cells. Conventional methods are hardly effective for studying dynamic, transient, and weak protein-protein interactions that occur in cells. Herein, we review how the site-directed photocrosslinking approach, which relies on the genetic incorporation of a photoreactive unnatural amino acid into a protein of interest at selected individual amino acid residue positions and the covalent trapping of the interacting proteins upon ultraviolent irradiation, has become a highly efficient way to explore the aspects of protein contacts in living cells. For example, in the past decade, this approach has allowed the profiling of the in vivo substrate proteins of chaperones or proteases under both physiologically optimal and stressful (e.g., acidic) conditions, mapping residues located at protein interfaces, identifying new protein factors involved in the biogenesis of membrane proteins, trapping transiently formed protein complexes, and snapshotting different structural states of a protein. We anticipate that the site-directed photocrosslinking approach will play a fundamental role in dissecting the detailed mechanisms of protein biogenesis, quality control, and dynamics in the future.
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Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province, 350117, China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Center for Protein Science, Beijing, 100871, China
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62
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Subunit interactions as mediated by “non-interface” residues in living cells for multiple homo-oligomeric proteins. Biochem Biophys Res Commun 2019; 512:100-105. [DOI: 10.1016/j.bbrc.2019.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 03/01/2019] [Indexed: 11/22/2022]
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63
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Miyazaki R, Akiyama Y, Mori H. A photo-cross-linking approach to monitor protein dynamics in living cells. Biochim Biophys Acta Gen Subj 2019; 1864:129317. [PMID: 30851405 DOI: 10.1016/j.bbagen.2019.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Proteins, which comprise one of the major classes of biomolecules that constitute a cell, interact with other cellular factors during both their biogenesis and functional states. Studying not only static but also transient interactions of proteins is important to understand their physiological roles and regulation mechanisms. However, only a limited number of methods are available to analyze the dynamic behaviors of proteins at the molecular level in a living cell. The site-directed in vivo photo-cross-linking approach is an elegant technique to capture protein interactions with high spatial resolution in a living cell. SCOPE OF REVIEW Here, we review the in vivo photo-cross-linking approach including its recent applications and the potential problems to be considered. We also introduce a new in vivo photo-cross-linking-based technique (PiXie) to study protein dynamics with high spatiotemporal resolution. MAJOR CONCLUSIONS In vivo photo-cross-linking enables us to capture weak/transient protein interactions with high spatial resolution, and allows for identification of interacting factors. Moreover, the PiXie approach can be used to monitor rapid folding/assembly processes of proteins in living cells. GENERAL SIGNIFICANCE In vivo photo-cross-linking is a simple method that has been used to analyze the dynamic interactions of many cellular proteins. Originally developed in Escherichia coli, this system has been extended to studies in various organisms, making it a fundamental technique for investigating dynamic protein interactions in many cellular processes. This article is part of a Special issue entitled "Novel major techniques for visualizing 'live' protein molecules" edited by Dr. Daisuke Kohda.
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Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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64
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McKenna R, Lombana TN, Yamada M, Mukhyala K, Veeravalli K. Engineered sigma factors increase full-length antibody expression in Escherichia coli. Metab Eng 2019; 52:315-323. [DOI: 10.1016/j.ymben.2018.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022]
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65
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Liu CJ, Lin CT, Chiang JD, Lin CY, Tay YX, Fan LC, Peng KN, Lin CH, Peng HL. RcsB regulation of the YfdX-mediated acid stress response in Klebsiella pneumoniae CG43S3. PLoS One 2019; 14:e0212909. [PMID: 30818355 PMCID: PMC6394985 DOI: 10.1371/journal.pone.0212909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
In Klebsiella pneumoniae CG43S3, deletion of the response regulator gene rcsB reduced the capsular polysaccharide amount and survival on exposure to acid stress. A comparison of the pH 4.4-induced proteomes between CG43S3 and CG43S3ΔrcsB revealed numerous differentially expressed proteins and one of them, YfdX, which has recently been reported as a periplasmic protein, was absent in CG43S3ΔrcsB. Acid survival analysis was then conducted to determine its role in the acid stress response. Deletion of yfdX increased the sensitivity of K. pneumoniae CG43S3 to a pH of 2.5, and transforming the mutant with a plasmid carrying yfdX restored the acid resistance (AR) levels. In addition, the effect of yfdX deletion was cross-complemented by the expression of the periplasmic chaperone HdeA. Furthermore, the purified recombinant protein YfdX reduced the acid-induced protein aggregation, suggesting that YfdX as well as HdeA functions as a chaperone. The following promoter activity measurement revealed that rcsB deletion reduced the expression of yfdX after the bacteria were subjected to pH 4.4 adaptation. Western blot analysis also revealed that YfdX production was inhibited by rcsB deletion and only the plasmid expressing RcsB or the nonphosphorylated form of RcsB, RcsBD56A, could restore the YfdX production, and the RcsB-mediated complementation was no longer observed when the sensor kinase RcsD gene was deleted. In conclusion, this is the first study demonstrating that YfdX may be involved in the acid stress response as a periplasmic chaperone and that RcsB positively regulates the acid stress response partly through activation of yfdX expression. Moreover, the phosphorylation status of RcsB may affect the YfdX expression under acidic conditions.
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Affiliation(s)
- Chia-Jui Liu
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan, Republic of China
| | - Jo-Di Chiang
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chen-Yi Lin
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Yen-Xi Tay
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Li-Cheng Fan
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Kuan-Nan Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Chih-Huan Lin
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- Institute of Molecular Medicine and Biological Technology, School of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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66
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Regrowth-delay body as a bacterial subcellular structure marking multidrug-tolerant persisters. Cell Discov 2019; 5:8. [PMID: 30675381 PMCID: PMC6341109 DOI: 10.1038/s41421-019-0080-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 02/08/2023] Open
Abstract
Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. This structure, that dissolves when the cell resumes growth, is able to be viewed as a marker of persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.
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67
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Protease-Mediated Protein Quality Control for Bacterial Acid Resistance. Cell Chem Biol 2019; 26:144-150.e3. [DOI: 10.1016/j.chembiol.2018.10.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/10/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022]
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68
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Zheng Q, Pang Z, Liu J, Zhou Y, Sun Y, Yin Z, Lou Z. Photoaffinity palladium reagents for capture of protein–protein interactions. Org Biomol Chem 2019; 17:6369-6373. [DOI: 10.1039/c9ob01048c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A straightforward strategy using palladium-mediated reagents to reliably incorporate different photoaffinity groups into peptides/proteins for crosslinking of interacting partners is described.
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Affiliation(s)
- Qizhen Zheng
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Zhengyuan Pang
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Jingwei Liu
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yi Zhou
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yang Sun
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Zheng Yin
- Center of Basic Molecular Science
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Zhiyong Lou
- Collaborative Innovation Center of Biotherapy and MOE Key Laboratory of Protein Science
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
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69
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Cheng L, Kang X, Wang D, Gao Y, Yi L, Xi Z. The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation. Org Biomol Chem 2019; 17:5675-5679. [DOI: 10.1039/c9ob00528e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation were used for producing a FRET-based dyad in living cells as a proof-of-concept study.
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Affiliation(s)
- Longhuai Cheng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xueying Kang
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Dan Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Yasi Gao
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Long Yi
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
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70
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Yu XC, Hu Y, Ding J, Li H, Jin C. Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone. J Biol Chem 2018; 294:3192-3206. [PMID: 30573682 DOI: 10.1074/jbc.ra118.006398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
The role of protein structural disorder in biological functions has gained increasing attention in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of "conditionally disordered" proteins, because it is inactive in its well-structured state and becomes activated via an order-to-disorder transition under acid stress. However, the mechanism for unfolding-induced activation remains unclear because of a lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Herein, we used advanced solution NMR methods to characterize the activated-state conformation of HdeA under acidic conditions and identify its client-binding sites. We observed that the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions. Furthermore, using the pH-dependent chemical exchange saturation transfer (CEST) NMR method, we identified three acid-sensitive regions that act as structural locks in regulating the exposure of the two client-binding sites during the activation process, revealing a multistep activation mechanism of HdeA's chaperone function at the atomic level. Our results highlight the role of intrinsic protein disorder in chaperone function and the self-inhibitory role of ordered structures under nonstress conditions, offering new insights for improving our understanding of protein structure-function paradigms.
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Affiliation(s)
- Xing-Chi Yu
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences
| | - Hongwei Li
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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71
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Horne JE, Walko M, Calabrese AN, Levenstein MA, Brockwell DJ, Kapur N, Wilson AJ, Radford SE. Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers. Angew Chem Int Ed Engl 2018; 57:16688-16692. [PMID: 30393918 PMCID: PMC6348423 DOI: 10.1002/anie.201809149] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/30/2018] [Indexed: 12/31/2022]
Abstract
Analysing protein complexes by chemical crosslinking-mass spectrometry (XL-MS) is limited by the side-chain reactivities and sizes of available crosslinkers, their slow reaction rates, and difficulties in crosslink enrichment, especially for rare, transient or dynamic complexes. Here we describe two new XL reagents that incorporate a methanethiosulfonate (MTS) group to label a reactive cysteine introduced into the bait protein, and a residue-unbiased diazirine-based photoactivatable XL group to trap its interacting partner(s). Reductive removal of the bait transfers a thiol-containing fragment of the crosslinking reagent onto the target that can be alkylated and located by MS sequencing and exploited for enrichment, enabling the detection of low abundance crosslinks. Using these reagents and a bespoke UV LED irradiation platform, we show that maximum crosslinking yield is achieved within 10 seconds. The utility of this "tag and transfer" approach is demonstrated using a well-defined peptide/protein regulatory interaction (BID80-102 /MCL-1), and the dynamic interaction interface of a chaperone/substrate complex (Skp/OmpA).
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Affiliation(s)
- Jim E. Horne
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Martin Walko
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Mark A. Levenstein
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- School of Mechanical EngineeringUniversity of LeedsLeedsLS2 9JTUK
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Nikil Kapur
- School of Mechanical EngineeringUniversity of LeedsLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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72
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Horne JE, Walko M, Calabrese AN, Levenstein MA, Brockwell DJ, Kapur N, Wilson AJ, Radford SE. Rapid Mapping of Protein Interactions Using Tag‐Transfer Photocrosslinkers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jim E. Horne
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Martin Walko
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Mark A. Levenstein
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- School of Mechanical EngineeringUniversity of Leeds Leeds LS2 9JT UK
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Nikil Kapur
- School of Mechanical EngineeringUniversity of Leeds Leeds LS2 9JT UK
| | - Andrew J. Wilson
- School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular BiologyUniversity of Leeds Leeds LS2 9JT UK
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73
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Stull F, Hipp H, Stockbridge RB, Bardwell JCA. In vivo chloride concentrations surge to proteotoxic levels during acid stress. Nat Chem Biol 2018; 14:1051-1058. [PMID: 30323217 PMCID: PMC6193267 DOI: 10.1038/s41589-018-0143-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/29/2018] [Indexed: 11/23/2022]
Abstract
To successfully colonize the intestine, bacteria must survive passage through the stomach. The permeability of the outer membrane renders the periplasm of Gram-negative bacteria vulnerable to stomach acid, which inactivates proteins. Here we report that the semipermeable nature of the outer membrane allows the development of a strong Donnan equilibrium across this barrier at low pH. As a result, when bacteria are exposed to conditions that mimic gastric juice, periplasmic chloride concentrations rise to levels that exceed 0.6 M. At these chloride concentrations, proteins readily aggregate in vitro. The acid sensitivity of strains lacking acid-protective chaperones is enhanced by chloride, suggesting that these chaperones protect periplasmic proteins both from acidification and from the accompanying accumulation of chloride. These results illustrate how organisms have evolved chaperones to respond to the substantial chemical threat imposed by otherwise innocuous chloride concentrations that are amplified to proteotoxic levels by low-pH-induced Donnan equilibrium effects.
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Affiliation(s)
- Frederick Stull
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Hannah Hipp
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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74
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018; 57:14350-14361. [PMID: 30144241 DOI: 10.1002/anie.201805869] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Protein-protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site-specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein-protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site-specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity-dependent manner, thereby chemically stabilizing low-affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine-tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein-protein interactions in living systems.
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Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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75
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
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76
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Fu X, Wang Y, Shao H, Ma J, Song X, Zhang M, Chang Z. DegP functions as a critical protease for bacterial acid resistance. FEBS J 2018; 285:3525-3538. [DOI: 10.1111/febs.14627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 06/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Heqi Shao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Jing Ma
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Xinwen Song
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Meng Zhang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
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77
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Coin I. Application of non-canonical crosslinking amino acids to study protein-protein interactions in live cells. Curr Opin Chem Biol 2018; 46:156-163. [PMID: 30077876 DOI: 10.1016/j.cbpa.2018.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
The genetic incorporation of non-canonical amino acids (ncAAs) equipped with photo-crosslinking and chemical crosslinking moieties has found broad application in the study of protein-protein interactions from a unique perspective in live cells. We highlight here applications of photo-activatable ncAAs to map protein interaction surfaces and to capture protein-protein interactions, and we describe recent efforts to efficiently couple photo-crosslinking with mass spectrometric analysis. In addition, we describe recent advances in the development and application of ncAAs for chemical crosslinking, including protein stapling, photo-control of protein conformation, two-dimensional crosslinking, and stabilization of transient and low-affinity protein-protein interactions. We expect that the field will keep growing in the near future and enable the tackling of ambitious biological questions.
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Affiliation(s)
- Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04301 Leipzig, Germany.
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78
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Hoffmann JE, Dziuba D, Stein F, Schultz C. A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation. Biochemistry 2018; 57:4747-4752. [PMID: 29932646 DOI: 10.1021/acs.biochem.8b00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mapping of weak and hence transient interactions between low-abundance interacting molecules is still a major challenge in systems biology and protein biochemistry. Therefore, additional system-wide acting tools are needed to determine protein interactomics. Most important are reagents that can be applied at any kind of protein interface and the possibility to enrich cross-linked fragments with high efficiency. In this study, we report the synthesis of a novel noncanonical amino acid that features a diazirine group for ultraviolet cross-linking as well as an alkyne group for labeling by click chemistry. This bifunctional amino acid, called PrDiAzK, may be inserted into almost any protein interface with minimal structural perturbation using genetic code expansion. We demonstrate that PrDiAzK can be site-selectively incorporated into proteins in both bacterial and mammalian cell cultures, and we show that PrDiAzK allows protein labeling as well as cross-linking. In addition, we tested PrDiAzK for proteome-wide incorporation via stochastic orthogonal recoding of translation, implying potential applications in system-wide mapping of protein-protein interactions in the future.
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Affiliation(s)
- Jan-Erik Hoffmann
- Department of Physiology & Pharmacology , Oregon Health & Science University , L334, 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239-3098 , United States
| | - Dmytro Dziuba
- European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Frank Stein
- European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Carsten Schultz
- Department of Physiology & Pharmacology , Oregon Health & Science University , L334, 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239-3098 , United States.,European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
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79
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Guan F, Yu J, Yu J, Liu Y, Li Y, Feng XH, Huang KC, Chang Z, Ye S. Lateral interactions between protofilaments of the bacterial tubulin homolog FtsZ are essential for cell division. eLife 2018; 7:35578. [PMID: 29889022 PMCID: PMC6050046 DOI: 10.7554/elife.35578] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023] Open
Abstract
The prokaryotic tubulin homolog FtsZ polymerizes into protofilaments, which further assemble into higher-order structures at future division sites to form the Z-ring, a dynamic structure essential for bacterial cell division. The precise nature of interactions between FtsZ protofilaments that organize the Z-ring and their physiological significance remain enigmatic. In this study, we solved two crystallographic structures of a pair of FtsZ protofilaments, and demonstrated that they assemble in an antiparallel manner through the formation of two different inter-protofilament lateral interfaces. Our in vivo photocrosslinking studies confirmed that such lateral interactions occur in living cells, and disruption of the lateral interactions rendered cells unable to divide. The inherently weak lateral interactions enable FtsZ protofilaments to self-organize into a dynamic Z-ring. These results have fundamental implications for our understanding of bacterial cell division and for developing antibiotics that target this key process.
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Affiliation(s)
- Fenghui Guan
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Jiayu Yu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jie Yu
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Yang Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ying Li
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Xin-Hua Feng
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Zengyi Chang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Ye
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
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80
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Tian Y, Lin Q. Genetic encoding of 2-aryl-5-carboxytetrazole-based protein photo-cross-linkers. Chem Commun (Camb) 2018; 54:4449-4452. [PMID: 29652063 DOI: 10.1039/c8cc02431f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Three γ-heteroatom-substituted N-methylpyrroletetrazole-lysines (mPyTXKs) were synthesized and subsequently incorporated into proteins site-specifically via genetic code expansion. The γ-seleno-substituted derivative, mPyTSeK, showed excellent incorporation efficiency in Escherichia coli and allowed site-selective photo-cross-linking of the GST dimer. Furthermore, the mPyTSeK-cross-linked GST dimer can be cleaved under mild oxidative conditions. The incorporation of mPyTXKs into proteins in mammalian cells was also demonstrated. Lastly, the recombinantly expressed mPyTSeK-encoded Grb2 was shown to covalently capture its interaction partner, EGFR, in mammalian cell lysate, which was subsequently released after treatment with H2O2.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.
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81
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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82
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Shang X, Chen Y, Wang N, Niu W, Guo J. Oxidation-induced generation of a mild electrophile for proximity-enhanced protein-protein crosslinking. Chem Commun (Camb) 2018; 54:4172-4175. [PMID: 29629441 PMCID: PMC5908726 DOI: 10.1039/c8cc01639a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy to introduce a reactive electrophile into proteins through the conversion of a chemically inert group into a bioreactive group in response to an inducer molecule. This strategy was demonstrated by oxidation-induced and proximity-enhanced protein-protein crosslinking in the presence of a large excess of free nucleophile.
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Affiliation(s)
- X Shang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
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83
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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84
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Serfling R, Seidel L, Böttke T, Coin I. Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells. J Vis Exp 2018. [PMID: 29683449 DOI: 10.3791/57069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA. However, directed evolution of tRNA or AARS using large libraries and dead/alive selection methods are not feasible in mammalian cells. Here, a facile and robust fluorescence-based assay to evaluate the efficiency of orthogonal pairs in mammalian cells is presented. The assay allows screening tens to hundreds of AARS/tRNA variants with a moderate effort and within a reasonable time. Use of this assay to generate new tRNAs that significantly improve the efficiency of the pyrrolysine orthogonal system is described, along with the application of ncAAs to the study of G-protein coupled receptors (GPCRs), which are challenging objects for ncAA mutagenesis. First, by systematically incorporating a photo-crosslinking ncAA throughout the extracellular surface of a receptor, binding sites of different ligands on the intact receptor are mapped directly in the live cell. Second, by incorporating last-generation ncAAs into a GPCR, ultrafast catalyst-free receptor labeling with a fluorescent dye is demonstrated, which exploits bioorthogonal strain-promoted inverse Diels Alder cycloaddition (SPIEDAC) on the live cell. As ncAAs can be generally applied to any protein independently on its size, the method is of general interest for a number of applications. In addition, ncAA incorporation does not require any special equipment and is easily performed in standard biochemistry labs.
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Affiliation(s)
- Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Lisa Seidel
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig;
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85
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Kleiner RE, Hang LE, Molloy KR, Chait BT, Kapoor TM. A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells. Cell Chem Biol 2018; 25:110-120.e3. [PMID: 29104064 PMCID: PMC5775914 DOI: 10.1016/j.chembiol.2017.10.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/03/2017] [Accepted: 09/28/2017] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions mediate essential cellular processes, however the detection of native interactions is challenging since they are often low affinity and context dependent. Here, we develop a chemical proteomics approach in vivo CLASPI [iCLASPI] (in vivo crosslinking-assisted and stable isotope labeling by amino acids in cell culture [SILAC]-based protein identification) relying upon photo-crosslinking, amber suppression, and SILAC-based quantitative proteomics to profile context-dependent protein-protein interactions in living cells. First, we use iCLASPI to profile in vivo binding partners of the N-terminal tails of soluble histone H3 or H4. We identify known histone chaperones and modifying proteins, thereby validating our approach, and find an interaction between soluble histone H3 and UBR7, an E3 ubiquitin ligase, mediated by UBR7's PHD domain. Furthermore, we apply iCLASPI to profile the context-dependent protein-protein interactions of chromatin-associated histone H3 at different cell-cycle stages, and identify ANP32A as a mitosis-specific interactor. Our results demonstrate that the iCLASPI approach can provide a general strategy for identifying native, context-dependent direct protein-protein interactions using photo-crosslinking and quantitative proteomics.
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Affiliation(s)
- Ralph E Kleiner
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Lisa E Hang
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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86
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Seidel L, Coin I. Mapping of Protein Interfaces in Live Cells Using Genetically Encoded Crosslinkers. Methods Mol Biol 2018; 1728:221-235. [PMID: 29405001 DOI: 10.1007/978-1-4939-7574-7_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the topology of protein-protein interactions is a matter of fundamental importance in the biomedical field. Biophysical approaches such as X-ray crystallography and nuclear magnetic resonance can investigate in detail only isolated protein complexes that are reconstituted in an artificial environment. Alternative methods are needed to investigate protein interactions in a physiological context, as well as to characterize protein complexes that elude the direct structural characterization. We describe here a general strategy to investigate protein interactions at the molecular level directly in the live mammalian cell, which is based on the genetic incorporation of photo- and chemical crosslinking noncanonical amino acids. First a photo-crosslinking amino acid is used to map putative interaction surfaces and determine which positions of a protein come into proximity of an associated partner. In a second step, the subset of residues that belong to the binding interface are substituted with a chemical crosslinker that reacts selectively with proximal cysteines strategically placed in the interaction partner. This allows determining inter-molecular spatial constraints that provide the basis for building accurate molecular models. In this chapter, we illustrate the detailed application of this experimental strategy to unravel the binding modus of the 40-mer neuropeptide hormone Urocortin1 to its class B G-protein coupled receptor, the corticotropin releasing factor receptor type 1. The approach is in principle applicable to any protein complex independent of protein type and size, employs established techniques of noncanonical amino acid mutagenesis, and is feasible in any molecular biology laboratory.
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Affiliation(s)
- Lisa Seidel
- Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Irene Coin
- Institute of Biochemistry, University of Leipzig, Leipzig, Germany.
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87
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Hoffmann C, Neumann H, Neumann-Staubitz P. Trapping Chromatin Interacting Proteins with Genetically Encoded, UV-Activatable Crosslinkers In Vivo. Methods Mol Biol 2018; 1728:247-262. [PMID: 29405003 DOI: 10.1007/978-1-4939-7574-7_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The installation of unnatural amino acids into proteins of living cells is an enabling technology that facilitates an enormous number of applications. UV-activatable crosslinker amino acids allow the formation of a covalent bond between interaction partners in living cells with nearly perfect spatial and temporal control. Here, we describe how this method can be employed to map chromatin interactions and to follow these interactions across the cell cycle in synchronized yeast populations. This method thereby provides unprecedented insights into the molecular events controlling chromatin reorganization in mitosis. As similar tools are available for other organisms, it should be possible to derive similar strategies for these and for other synchronizable processes.
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Affiliation(s)
- Christian Hoffmann
- Georg August University Göttingen, Göttingen, Germany
- Accurion GmbH, Stresemannstr. 30, 37079, Göttingen, Germany
| | - Heinz Neumann
- Georg August University Göttingen, Göttingen, Germany.
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.
| | - Petra Neumann-Staubitz
- Georg August University Göttingen, Göttingen, Germany.
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.
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88
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Miyazaki R, Myougo N, Mori H, Akiyama Y. A photo-cross-linking approach to monitor folding and assembly of newly synthesized proteins in a living cell. J Biol Chem 2017; 293:677-686. [PMID: 29158258 DOI: 10.1074/jbc.m117.817270] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/03/2017] [Indexed: 11/06/2022] Open
Abstract
Many proteins form multimeric complexes that play crucial roles in various cellular processes. Studying how proteins are correctly folded and assembled into such complexes in a living cell is important for understanding the physiological roles and the qualitative and quantitative regulation of the complex. However, few methods are suitable for analyzing these rapidly occurring processes. Site-directed in vivo photo-cross-linking is an elegant technique that enables analysis of protein-protein interactions in living cells with high spatial resolution. However, the conventional site-directed in vivo photo-cross-linking method is unsuitable for analyzing dynamic processes. Here, by combining an improved site-directed in vivo photo-cross-linking technique with a pulse-chase approach, we developed a new method that can analyze the folding and assembly of a newly synthesized protein with high spatiotemporal resolution. We demonstrate that this method, named the pulse-chase and in vivo photo-cross-linking experiment (PiXie), enables the kinetic analysis of the formation of an Escherichia coli periplasmic (soluble) protein complex (PhoA). We also used our new technique to investigate assembly/folding processes of two membrane complexes (SecD-SecF in the inner membrane and LptD-LptE in the outer membrane), which provided new insights into the biogenesis of these complexes. Our PiXie method permits analysis of the dynamic behavior of various proteins and enables examination of protein-protein interactions at the level of individual amino acid residues. We anticipate that our new technique will have valuable utility for studies of protein dynamics in many organisms.
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Affiliation(s)
- Ryoji Miyazaki
- From the Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naomi Myougo
- From the Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Mori
- From the Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- From the Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
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89
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Sharma V, Zeng Y, Wang WW, Qiao Y, Kurra Y, Liu WR. Evolving the N-Terminal Domain of Pyrrolysyl-tRNA Synthetase for Improved Incorporation of Noncanonical Amino Acids. Chembiochem 2017; 19:26-30. [PMID: 29096043 DOI: 10.1002/cbic.201700268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/10/2022]
Abstract
By evolving the N-terminal domain of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) that directly interacts with tRNAPyl , a mutant clone displaying improved amber-suppression efficiency for the genetic incorporation of Nϵ -(tert-butoxycarbonyl)-l-lysine threefold more than the wild type was identified. The identified mutations were R19H/H29R/T122S. Direct transfer of these mutations to two other PylRS mutants that were previously evolved for the genetic incorporation of Nϵ -acetyl-l-lysine and Nϵ -(4-azidobenzoxycarbonyl)-l-δ,ϵ-dehydrolysine also improved the incorporation efficiency of these two noncanonical amino acids. As the three identified mutations were found in the N-terminal domain of PylRS that was separated from its catalytic domain for charging tRNAPyl with a noncanonical amino acid, they could potentially be introduced to all other PylRS mutants to improve the incorporation efficiency of their corresponding noncanonical amino acids. Therefore, it represents a general strategy to optimize the pyrrolysine incorporation system-based noncanonical amino-acid mutagenesis.
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Affiliation(s)
- Vangmayee Sharma
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - W Wesley Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yuchen Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagiri Kurra
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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90
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Ye J, Liu J, Li C, Zhou P, Wu S, Ou H. Heterogeneous photocatalysis of tris(2-chloroethyl) phosphate by UV/TiO 2: Degradation products and impacts on bacterial proteome. WATER RESEARCH 2017; 124:29-38. [PMID: 28738271 DOI: 10.1016/j.watres.2017.07.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/27/2017] [Accepted: 07/15/2017] [Indexed: 05/22/2023]
Abstract
The widespread, persistent and toxic organophosphorus esters (OPEs) have become one category of emerging environmental contaminants. Thus, it is in urgent need to develop a cost-effective and safe treatment technology for OPEs control. The current study is a comprehensive attempt to use UV/TiO2 heterogeneous photocatalysis for the degradation of a water dissolved OPEs, tris(2-chloroethyl) phosphate (TCEP). A pseudo-first order degradation reaction with a kobs of 0.3167 min-1 was observed, while hydroxyl radical may be the dominating reactive oxidative species. As the reaction proceeded, TCEP was transformed to a series of hydroxylated and dechlorinated products. The degradation efficiency was significantly affected by pH value, natural organic matters and anions, implying that the complete mineralization of TCEP would be difficult to achieve in actual water treatment process. Based on the proteomics analysis regarding the metabolism reactions, pathways and networks, the significant activation of transmembrane transport and energy generation in Escherichia coli exposed to preliminary degrading products suggested that they can be transported and utilized through cellular metabolism. Furthermore, the descending trend of stress resistance exhibited that the toxicity of products was obviously weakened as the treatment proceeded. In conclusion, hydroxylation and dechlorination of TCEP with incomplete mineralization were likewise effective for its detoxification, indicating that UV/TiO2 will be an alternative treatment method for OPEs control.
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Affiliation(s)
- Jinshao Ye
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China; Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA
| | - Juan Liu
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Chongshu Li
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Pulin Zhou
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Shuang Wu
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Huase Ou
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China.
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91
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Yu XC, Yang C, Ding J, Niu X, Hu Y, Jin C. Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress. Biochemistry 2017; 56:5748-5757. [PMID: 29016106 DOI: 10.1021/acs.biochem.7b00724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial acid-resistant chaperone HdeA is a "conditionally disordered" protein that functions at low pH when it undergoes a transition from a well-folded dimer to an unfolded monomer. The dimer dissociation and unfolding processes result in exposure of hydrophobic surfaces that allows binding to a broad range of client proteins. To fully elucidate the chaperone mechanism of HdeA, it is crucial to understand how the activated HdeA interacts with its native substrates during acid stress. Herein, we present a nuclear magnetic resonance study of the pH-dependent HdeA-substrate interactions. Our results show that the activation of HdeA is not only induced by acidification but also regulated by the presence of unfolded substrates. The variable extent of unfolding of substrates differentially regulates the HdeA-substrate interaction, and the binding further affects the HdeA conformation. Finally, we show that HdeA binds its substrates heterogeneously, and the "amphiphilic" model for HdeA-substrate interaction is discussed.
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Affiliation(s)
- Xing-Chi Yu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Jienv Ding
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Changwen Jin
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
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92
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; 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; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; 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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93
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He D, Xie X, Yang F, Zhang H, Su H, Ge Y, Song H, Chen PR. Quantitative and Comparative Profiling of Protease Substrates through a Genetically Encoded Multifunctional Photocrosslinker. Angew Chem Int Ed Engl 2017; 56:14521-14525. [DOI: 10.1002/anie.201708151] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dan He
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xiao Xie
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences; Wuhan University; Wuhan 430072 China
| | - Yun Ge
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; 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; Department of Chemical Biology; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; 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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94
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Yang Y, Song H, He D, Zhang S, Dai S, Xie X, Lin S, Hao Z, Zheng H, Chen PR. Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells. Nat Protoc 2017; 12:2147-2168. [DOI: 10.1038/nprot.2017.090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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95
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Abstract
As an important epigenetic mark, lysine methylations play critical roles in the regulation of both chromatin and non-chromatin proteins. There are three levels of lysine methylation, mono-, di-, and trimethylation. Each one has turned out to be biologically distinctive. For the biochemical characterization of proteins with lysine methylation, multiple chemical biology methods have been developed. This concept article will highlight these developments and their applications in epigenetic investigation of protein functions.
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Affiliation(s)
- Zhipeng A. Wang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R. Liu
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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96
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Zhang Z, Xu H, Si L, Chen Y, Zhang B, Wang Y, Wu Y, Zhou X, Zhang L, Zhou D. Construction of an inducible stable cell line for efficient incorporation of unnatural amino acids in mammalian cells. Biochem Biophys Res Commun 2017; 489:490-496. [DOI: 10.1016/j.bbrc.2017.05.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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97
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Kang K, Park J, Kim E. Tetrazine ligation for chemical proteomics. Proteome Sci 2017; 15:15. [PMID: 28674480 PMCID: PMC5485739 DOI: 10.1186/s12953-017-0121-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/15/2017] [Indexed: 12/12/2022] Open
Abstract
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical proteomics.
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Affiliation(s)
- Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104 Republic of Korea
| | - Jongmin Park
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St, CPZN 5206, Boston, Massachusetts 02114 USA
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499 Republic of Korea
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98
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Gilbert C, Howarth M, Harwood CR, Ellis T. Extracellular Self-Assembly of Functional and Tunable Protein Conjugates from Bacillus subtilis. ACS Synth Biol 2017; 6:957-967. [PMID: 28230977 DOI: 10.1021/acssynbio.6b00292] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics, and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis. Using this approach, we demonstrate how self-conjugation of a secreted industrial enzyme, XynA, dramatically increases its resilience to boiling, and we show that cellular consortia can be engineered to self-assemble functional protein-protein conjugates with tunable composition. This novel genetically encoded modular system provides a flexible strategy for protein conjugation harnessing the substantial advantages of extracellular self-assembly.
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Affiliation(s)
- Charlie Gilbert
- Centre
for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, U.K
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Colin R. Harwood
- Centre
for Bacterial Cell Biology, Baddiley-Clark Building, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K
| | - Tom Ellis
- Centre
for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, U.K
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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99
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The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic. NPJ Microgravity 2017. [PMID: 28649637 PMCID: PMC5460176 DOI: 10.1038/s41526-017-0020-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microorganisms impact spaceflight in a variety of ways. They play a positive role in biological systems, such as waste water treatment but can be problematic through buildups of biofilms that can affect advanced life support. Of special concern is the possibility that during extended missions, the microgravity environment will provide positive selection for undesirable genomic changes. Such changes could affect microbial antibiotic sensitivity and possibly pathogenicity. To evaluate this possibility, Escherichia coli (lac plus) cells were grown for over 1000 generations on Luria Broth medium under low-shear modeled microgravity conditions in a high aspect rotating vessel. This is the first study of its kind to grow bacteria for multiple generations over an extended period under low-shear modeled microgravity. Comparisons were made to a non-adaptive control strain using growth competitions. After 1000 generations, the final low-shear modeled microgravity-adapted strain readily outcompeted the unadapted lac minus strain. A portion of this advantage was maintained when the low-shear modeled microgravity strain was first grown in a shake flask environment for 10, 20, or 30 generations of growth. Genomic sequencing of the 1000 generation strain revealed 16 mutations. Of the five changes affecting codons, none were neutral. It is not clear how significant these mutations are as individual changes or as a group. It is concluded that part of the long-term adaptation to low-shear modeled microgravity is likely genomic. The strain was monitored for acquisition of antibiotic resistance by VITEK analysis throughout the adaptation period. Despite the evidence of genomic adaptation, resistance to a variety of antibiotics was never observed.
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Zhang S, He D, Lin Z, Yang Y, Song H, Chen PR. Conditional Chaperone-Client Interactions Revealed by Genetically Encoded Photo-cross-linkers. Acc Chem Res 2017; 50:1184-1192. [PMID: 28467057 DOI: 10.1021/acs.accounts.6b00647] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The cell envelope is an integral and essential component of Gram-negative bacteria. As the front line during host-pathogen interactions, it is directly challenged by host immune responses as well as other harsh extracellular stimuli. The high permeability of the outer-membrane and the lack of ATP energy system render it difficult to maintain important biological activities within the periplasmic space under stress conditions. The HdeA/B chaperone machinery is the only known acid resistant system found in bacterial periplasm, enabling enteric pathogens to survive through the highly acidic human stomach and establish infections in the intestine. These two homologous chaperones belong to a fast growing family of conditionally disordered chaperones that conditionally lose their well-defined three-dimensional structures to exert biological activities. Upon losing ordered structures, these proteins commit promiscuous binding of diverse clients in response to environmental stimulation. For example, HdeA and HdeB are well-folded inactive dimers at neutral pH but become partially unfolded to protect a wide array of acid-denatured proteins upon acid stress. Whether these conditionally disordered chaperones possess client specificities remains unclear. This is in part due to the lack of efficient tools to investigate such versatile and heterogeneous protein-protein interactions under living conditions. Genetically encoded protein photo-cross-linkers have offered a powerful strategy to capture protein-protein interactions, showing great potential in profiling protein interaction networks, mapping binding interfaces, and probing dynamic changes in both physiological and pathological settings. Despite great success, photo-cross-linkers that can simultaneously capture the promiscuous binding partners and directly identify the interaction interfaces remain technically challenging. Furthermore, methods for side-by-side profiling and comparing the condition-dependent client pools from two homologous chaperones are lacking. Herein, we introduce our recent efforts in developing a panel of versatile genetically encoded photo-cross-linkers to study the disorder-mediated chaperone-client interactions in living cells. In particular, we have developed a series of proteomic-based strategies relying on these new photo-cross-linkers to systematically compare the client profiles of HdeA and HdeB, as well as to map their interaction interfaces. These studies revealed the mode-of-action, particularly the client specificity, of these two conditionally disordered chaperones. In the end, some recent elegant work from other groups that applied the genetically encoded photo-cross-linking strategy to illuminate important protein-protein interactions within bacterial cell envelope is also discussed.
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Affiliation(s)
- Shuai Zhang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dan He
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhi Lin
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Yang
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haiping Song
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R. Chen
- Beijing National
Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules
Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
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