1
|
The ubiquitination landscape of the influenza A virus polymerase. Nat Commun 2023; 14:787. [PMID: 36774438 PMCID: PMC9922279 DOI: 10.1038/s41467-023-36389-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/30/2023] [Indexed: 02/13/2023] Open
Abstract
During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitination landscape of the IAV polymerase proteins during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG (di-glycyl)-remnant-bearing peptides. We have identified 59 modified lysines across the three subunits, PB2, PB1 and PA of the viral polymerase of which 17 distinctively affect mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, further functional and in silico analysis indicate that ubiquitination at K578 in the PB1 thumb domain is mechanistically linked to dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R differentially affect the generation of recombinant viruses by impeding cRNA and vRNA synthesis, NP binding as well as polymerase dimerization. Collectively, our results demonstrate that the ubiquitin-mediated charge neutralization at PB1-K578 disrupts the interaction to an unstructured loop in the PB2 N-terminus that is required to coordinate polymerase dimerization and facilitate vRNA replication. This provides evidence that IAV exploits the cellular ubiquitin system to modulate the activity of the viral polymerase for viral replication.
Collapse
|
2
|
Lin HJ, James I, Hyer CD, Haderlie CT, Zackrison MJ, Bateman TM, Berg M, Park JS, Daley SA, Zuniga Pina NR, Tseng YJJ, Moody JD, Price JC. Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay. J Proteome Res 2022; 21:2920-2935. [PMID: 36356215 PMCID: PMC9724711 DOI: 10.1021/acs.jproteome.2c00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 11/12/2022]
Abstract
Many of the diseases that plague society today are driven by a loss of protein quality. One method to quantify protein quality is to measure the protein folding stability (PFS). Here, we present a novel mass spectrometry (MS)-based approach for PFS measurement, iodination protein stability assay (IPSA). IPSA quantifies the PFS by tracking the surface-accessibility differences of tyrosine, histidine, methionine, and cysteine under denaturing conditions. Relative to current methods, IPSA increases protein coverage and granularity to track the PFS changes of a protein along its sequence. To our knowledge, this study is the first time the PFS of human serum proteins has been measured in the context of the blood serum (in situ). We show that IPSA can quantify the PFS differences between different transferrin iron-binding states in near in vivo conditions. We also show that the direction of the denaturation curve reflects the in vivo surface accessibility of the amino acid residue and reproducibly reports a residue-specific PFS. Along with IPSA, we introduce an analysis tool Chalf that provides a simple workflow to calculate the residue-specific PFS. The introduction of IPSA increases the potential to use protein structural stability as a structural quality metric in understanding the etiology and progression of human disease. Data is openly available at Chorusproject.org (project ID 1771).
Collapse
Affiliation(s)
- Hsien-Jung
L. Lin
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Isabella James
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Chad D. Hyer
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Connor T. Haderlie
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Michael J. Zackrison
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Tyler M. Bateman
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Monica Berg
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Ji-Sun Park
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - S. Anisha Daley
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Nathan R. Zuniga Pina
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - Yi-Jie J. Tseng
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - James D. Moody
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| | - John C. Price
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah84602, United States
| |
Collapse
|
3
|
Structural mapping techniques distinguish the surfaces of fibrillar 1N3R and 1N4R human tau. J Biol Chem 2021; 297:101252. [PMID: 34592311 PMCID: PMC8551503 DOI: 10.1016/j.jbc.2021.101252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022] Open
Abstract
The rigid core of intracellular tau filaments from Alzheimer's disease (AD), Pick's disease (PiD), and Corticobasal disease (CBD) brains has been shown to differ in their cryo-EM atomic structure. Despite providing critical information on the intimate arrangement of a fraction of htau molecule within the fibrillar scaffold, the cryo-EM studies neither yield a complete picture of tau fibrillar assemblies structure nor contribute insights into the surfaces that define their interactions with numerous cellular components. Here, using proteomic approaches such as proteolysis and molecular covalent painting, we mapped the exposed amino acid stretches at the surface and those constituting the fibrillar core of in vitro-assembled fibrils of human htau containing one N-terminal domain and three (1N3R) or four (1N4R) C-terminal microtubule-binding repeat domains as a result of alternative splicing. Using limited proteolysis, we identified the proteolytic fragments composing the molecular “bar-code” for each type of fibril. Our results are in agreement with structural data reported for filamentous tau from AD, PiD, and CBD cases predigested with the protease pronase. Finally, we report two amino acid stretches, exposed to the solvent in 1N4R not in 1N3R htau, which distinguish the surfaces of these two kinds of fibrils. Our findings open new perspectives for the design of highly specific ligands with diagnostic and therapeutic potential.
Collapse
|
4
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
5
|
Lee SY, Lee S, Park SB, Kim KY, Hong J, Kang D. Development of a parallel microbore hollow fiber enzyme reactor platform for online 18O-labeling: Application to lectin-specific lung cancer N-glycoproteome. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1100-1101:58-64. [PMID: 30292950 DOI: 10.1016/j.jchromb.2018.09.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/29/2018] [Accepted: 09/28/2018] [Indexed: 11/19/2022]
Abstract
We introduce a simple online 18O-labeling protocol for protein samples that uses a parallelizing microbore hollow fiber enzyme reactor (mHFER) as an alternative tool for online proteolytic digestion. Online 18O-labeling is performed by separately attaching two mHFERs in parallel to a 10-port switching valve with a high-pressure syringe pump and two syringes containing 16O- or 18O-water. 16O-/18O-labeled peptides are formed in this manner and simultaneously analyzed online using nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) without any residual trypsin activity. The usefulness of a parallel mHFER platform (P-mHFER) in 18O-labeling was tested using both cytochrome C and alpha-1-acid-glycoprotein to verify the incorporation level of two 18O atoms into tryptic peptides and to provide a quantitative assessment with varied mixing ratios. Additionally, our 18O-labeling approach was used to study the serum N-glycoproteome from lung cancer patients and controls to evaluate the applicability of lectin-based quantitative N-glycoproteomics. We successfully quantified 76 peptides (from 62 N-glycoproteins). Nineteen of these peptides from lung cancer serum were up-/down-regulated at least 2.5-fold compared to controls. As a result, the P-mHFER-based online 18O-labeling platform presented here can be a simple and reproducible way to allow quantitative proteomic analysis of diverse proteome samples.
Collapse
Affiliation(s)
- Sun Young Lee
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Seonjeong Lee
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Bum Park
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, P.O. Box 107, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Ki Young Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, P.O. Box 107, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jongki Hong
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea.
| | - Dukjin Kang
- Center for Bioanalysis, Division of Chemical and Medical Metrology, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
6
|
Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing. BMC Genomics 2015; 16:79. [PMID: 25758772 PMCID: PMC4342091 DOI: 10.1186/s12864-015-1284-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique. RESULTS We first compared the accuracy and sensitivity of both sequencers using plasmid DNA and different ratios of wild type and mutant plasmid. Illumina MiSeq sequencing reads were one and a half times more accurate than those of the Ion Torrent PGM. The majority of sequencing errors were substitutions on the Illumina MiSeq and insertions and deletions, mostly in homopolymer regions, on the Ion Torrent PGM. To evaluate the suitability of the two techniques for determining the genome diversity of influenza A virus, we generated plasmid-derived PR8 virus and grew this virus in vitro. We also optimized an RT-PCR protocol to obtain uniform coverage of all eight genomic RNA segments. The sequencing reads obtained with both sequencers could successfully be assembled de novo into the segmented influenza virus genome. After mapping of the reads to the reference genome, we found that the detection limit for reliable recognition of variants in the viral genome required a frequency of 0.5% or higher. This threshold exceeds the background error rate resulting from the RT-PCR reaction and the sequencing method. Most of the variants in the PR8 virus genome were present in hemagglutinin, and these mutations were detected by both sequencers. CONCLUSIONS Our approach underlines the power and limitations of two commonly used next-generation sequencers for the analysis of influenza virus gene diversity. We conclude that the Illumina MiSeq platform is better suited for detecting variant sequences whereas the Ion Torrent PGM platform has a shorter turnaround time. The data analysis pipeline that we propose here will also help to standardize variant calling in small RNA genomes based on next-generation sequencing data.
Collapse
|
7
|
Zheng J, Tan BH, Sugrue R, Tang K. Current approaches on viral infection: proteomics and functional validations. Front Microbiol 2012; 3:393. [PMID: 23162545 PMCID: PMC3499792 DOI: 10.3389/fmicb.2012.00393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022] Open
Abstract
Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way.
Collapse
Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University Singapore
| | | | | | | |
Collapse
|
8
|
Targeting of the influenza A virus polymerase PB1-PB2 interface indicates strain-specific assembly differences. J Virol 2011; 85:13298-309. [PMID: 21957294 DOI: 10.1128/jvi.00868-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Assembly of the heterotrimeric influenza virus polymerase complex from the individual subunits PB1, PA, and PB2 is a prerequisite for viral replication. The conserved protein-protein interaction sites have been suggested as potential drug targets. To characterize the PB1-PB2 interface, we fused the PB1-binding domain of PB2 to green fluorescent protein (PB2(1-37)-GFP) and determined its competitive inhibitory effect on the polymerase activity of influenza A virus strains. Coexpression of PB2(1-37)-GFP in a polymerase reconstitution system led to substantial inhibition of the polymerase of A/WSN/33 (H1N1). Surprisingly, polymerases of other strains, including A/SC35M (H7N7), A/Puerto Rico/8/34 (H1N1), A/Hamburg/4/2009 (H1N1), and A/Thailand/1(KAN-1)/2004 (H5N1), showed various degrees of resistance. Individual exchange of polymerase subunits and the nucleoprotein between the sensitive WSN polymerase and the insensitive SC35M polymerase mapped the resistance to both PB1 and PA of SC35M polymerase. While PB2(1-37)-GFP bound equally well to the PB1 subunits of both virus strains, PB1-PA dimers of SC35M polymerase showed impaired binding compared to PB1-PA dimers of WSN polymerase. The use of PA(SC35M/WSN) chimeras revealed that the reduced affinity of the SC35M PB1-PA dimer was mediated by the N-terminal 277 amino acids of PA. Based on these observations, we speculate that the PB1-PA dimer formation of resistant polymerases shields the PB2(1-37) binding site, whereas sensitive polymerases allow this interaction, suggesting different assembly strategies of the trimeric polymerase complex between different influenza A virus strains.
Collapse
|
9
|
Liu N, Wu H, Liu H, Chen G, Cai Z. Microwave-Assisted 18O-Labeling of Proteins Catalyzed by Formic Acid. Anal Chem 2010; 82:9122-6. [PMID: 20939519 DOI: 10.1021/ac101888f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ning Liu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Hanzhi Wu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Hongxia Liu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Guonan Chen
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Zongwei Cai
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| |
Collapse
|
10
|
Leung BW, Chen H, Brownlee GG. Correlation between polymerase activity and pathogenicity in two duck H5N1 influenza viruses suggests that the polymerase contributes to pathogenicity. Virology 2010; 401:96-106. [PMID: 20211480 DOI: 10.1016/j.virol.2010.01.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 01/29/2010] [Indexed: 10/19/2022]
Abstract
The influenza RNA polymerase is known to be important in pathogenicity and adaptation of avian influenza viruses to mammalian hosts. However, the molecular mechanisms responsible are only partly understood. Here we investigated the role of the polymerase in two different, closely related, H5N1 influenza viruses - a high pathogenic, A/duck/Fujian/01/2002 (FJ) strain and a low pathogenic, A/duck/Guangxi/53/2002 (GX) strain. The polymerase activity of the FJ strain was significantly greater than the GX strain. Experiments with hybrid polymerase constructs - both in vitro and in ribonucleoprotein cell-based assays, suggested that the PA and to a lesser extent the PB2 subunits of the polymerase, were responsible for increased polymerase activity of the high pathogenic strain. However, promoter binding was inversely correlated with polymerase activity implying that excessive promoter binding inhibited polymerase activity by preventing promoter clearance. Overall, we suggest that the influenza polymerase is one of the determinants of pathogenicity of duck H5N1 viruses.
Collapse
Affiliation(s)
- Bo Wah Leung
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | |
Collapse
|