1
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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2
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Frando A, Grundner C. More than two components: complexities in bacterial phosphosignaling. mSystems 2024; 9:e0028924. [PMID: 38591891 PMCID: PMC11097640 DOI: 10.1128/msystems.00289-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
For over 40 years, the two-component systems (TCSs) have taken front and center in our thinking about the signaling mechanisms by which bacteria sense and respond to their environment. In contrast, phosphorylation on Ser/Thr and Tyr (O-phosphorylation) was long thought to be mostly restricted to eukaryotes and a somewhat accessory signaling mechanism in bacteria. Several recent studies exploring systems aspects of bacterial O-phosphorylation, however, now show that it is in fact pervasive, with some bacterial proteomes as highly phosphorylated as those of eukaryotes. Labile, non-canonical protein phosphorylation sites on Asp, Arg, and His are now also being identified in large numbers in bacteria and first cellular functions are discovered. Other phosphomodifications on Cys, Glu, and Lys remain largely unexplored. The surprising breadth and complexity of bacterial phosphosignaling reveals a vast signaling capacity, the full scope of which we may only now be beginning to understand but whose functions are likely to affect all aspects of bacterial physiology and pathogenesis.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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3
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Zou L, Wang Y, Wang X, Yang X, Zhang Q, Zheng Q. Stable isotope labeling-based two-step derivatization strategy for analysis of Phosphopeptides. J Proteomics 2024; 297:105128. [PMID: 38382841 DOI: 10.1016/j.jprot.2024.105128] [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: 12/10/2023] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
Investigating site-specific protein phosphorylation remains a challenging task. The present study introduces a two-step chemical derivatization method for accurate identification of phosphopeptides. Methylamine neutralizes carboxyl groups, thus reducing the adsorption of non-phosphorylated peptides during enrichment, while dimethylamine offers a cost-effective reagent for stable isotope labeling of phosphorylation sites. The derivatization improves the mass spectra obtained through liquid chromatography-tandem mass spectrometry. The product ions at m/z 58.07 and 64.10 Da, resulting from dimethylamine-d0 and dimethylamine-d6 labeled phosphorylation sites respectively, can serve as report ions. Derivatized phosphopeptides from casein demonstrate enhanced ionization and formation of product ions, yielding a significant increase in the number of identifiable peptides. When using the parallel reaction monitoring technique, it is possible to distinguish isomeric phosphopeptides with the same amino acid sequence but different phosphorylation sites. By employing a proteomic software and screening the report ions, we identified 29 endogenous phosphopeptides in 10 μL of human saliva with high reliability. These findings indicate that the two-step derivatization strategy has great potential in site-specific phosphorylation and large-scale phosphoproteomics research. SIGNIFICANCE: There is a significant need to improve the accuracy of identifying phosphoproteins and phosphopeptides and analyzing them quantitatively. Several chemical derivatization techniques have been developed to label phosphorylation sites, thus enabling the identification and relative quantification of phosphopeptides. Nevertheless, these methods have limitations, such as incomplete conversion or the need for costly isotopic reagents. Building upon previous contributions, our study moves the field forward due to high efficiency in site-specific labeling, cost-effectiveness, improved sensitivity, and comprehensive product ion coverage. Using the two-step derivatization approach, we successfully identified 29 endogenous phosphopeptides in 10 μL of human saliva with high reliability. The outcomes underscore the possibility of the method for site-specific phosphorylation and large-scale phosphoproteomics investigations.
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Affiliation(s)
- Lunfei Zou
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, People's Republic of China
| | - Yao Wang
- Institute of Pathogen and Immunity, Wuhan Centers for Disease Prevention and Control, Wuhan 430024, Hubei, People's Republic of China
| | - Xingdan Wang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, People's Republic of China
| | - Xiaoqiu Yang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, People's Republic of China
| | - Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, People's Republic of China.
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Optoelectronic Materials & Technology, Jianghan University, Wuhan 430056, Hubei, People's Republic of China
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4
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Daly L, Byrne DP, Perkins S, Brownridge PJ, McDonnell E, Jones AR, Eyers PA, Eyers CE. Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. J Proteome Res 2023; 22:3754-3772. [PMID: 37939282 PMCID: PMC10696596 DOI: 10.1021/acs.jproteome.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Protein tyrosine sulfation (sY) is a post-translational modification (PTM) catalyzed by Golgi-resident tyrosyl protein sulfo transferases (TPSTs). Information on sY in humans is currently limited to ∼50 proteins, with only a handful having verified sites of sulfation. As such, the contribution of sulfation to the regulation of biological processes remains poorly defined. Mass spectrometry (MS)-based proteomics is the method of choice for PTM analysis but has yet to be applied for systematic investigation of the "sulfome", primarily due to issues associated with discrimination of sY-containing from phosphotyrosine (pY)-containing peptides. In this study, we developed an MS-based workflow for sY-peptide characterization, incorporating optimized Zr4+ immobilized metal-ion affinity chromatography (IMAC) and TiO2 enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of fragmentation regimes (CID, HCD, EThcD, ETciD, UVPD) highlighted differences in the generation of site-determining product ions and allowed us to develop a strategy for differentiating sulfated peptides from nominally isobaric phosphopeptides based on low collision energy-induced neutral loss. Application of our "sulfomics" workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically, and reveals new interplay between enzymes relevant to both protein and glycan sulfation.
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Affiliation(s)
- Leonard
A. Daly
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Simon Perkins
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Euan McDonnell
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Andrew R. Jones
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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5
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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6
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Wang Y, Pan Y, Yan Z, Zhong Z, Zhang L, Zhang W. Magnetic resin composites for the enrichment of proteins, peptides and phosphopeptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3984-3990. [PMID: 37534964 DOI: 10.1039/d3ay01068f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
There is growing interest in the development of materials for enriching proteins and phosphoproteins from complex sample matrices for mass spectrometric analysis. Herein, we designed and synthesized two types of magnetic resin composites, i.e., MTS9200@Fe3O4 and FPA90CL@Fe3O4, and assessed their applications as adsorbents for enriching proteins, peptides and phosphopeptides. With the combination of Fe3+-IMAC interaction (MTS9200) or electrostatic attraction (FPA90CL) of resins and the adsorption of Fe3O4, the prepared composites exhibited higher capacities for adsorbing a protein (bovine serum albumin, at 195.71 and 135.03 mg g-1 for MTS9200@Fe3O4 and FPA90CL@Fe3O4, respectively) than MTS9200, FPA90CL and Fe3O4. In addition, due to the contributions of the hydrophobic skeleton of resins and Fe3O4, the magnetic resin composites allowed for efficient enrichment of peptides. Moreover, through Fe3+-IMAC interaction or electrostatic attraction of resins and Fe-O MOAC interaction of Fe3O4 with phosphate groups, phosphopeptides could also be captured. Furthermore, we employed the prepared composites for enriching proteins and phosphopeptides from human serum, where 466 and 506 proteins, and 434 and 356 phosphorylation sites, were detected from human serum after being processed with FPA90CL@Fe3O4 and MTS9200@Fe3O4, respectively. Together, our work revealed the great potential of magnetic resin composites as enrichment materials for proteomics and phosphoproteomics analysis.
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Affiliation(s)
- Yu Wang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yini Pan
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhichao Yan
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhihua Zhong
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, Department of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
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7
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Makwana MV, Dos Santos Souza C, Pickup BT, Thompson MJ, Lomada SK, Feng Y, Wieland T, Jackson RFW, Muimo R. Chemical Tools for Studying Phosphohistidine: Generation of Selective τ-Phosphohistidine and π-Phosphohistidine Antibodies. Chembiochem 2023; 24:e202300182. [PMID: 37183567 DOI: 10.1002/cbic.202300182] [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: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Nonhydrolysable stable analogues of τ-phosphohistidine (τ-pHis) and π-pHis have been designed, aided by electrostatic surface potential calculations, and subsequently synthesized. The τ-pHis and π-pHis analogues (phosphopyrazole 8 and pyridyl amino amide 13, respectively) were used as haptens to generate pHis polyclonal antibodies. Both τ-pHis and π-pHis conjugates in the form of BSA-glutaraldehyde-τ-pHis and BSA-glutaraldehyde-π-pHis were synthesized and characterized by 31 P NMR spectroscopy. Commercially available τ-pHis (SC56-2) and π-pHis (SC1-1; SC50-3) monoclonal antibodies were used to show that the BSA-G-τ-pHis and BSA-G-π-pHis conjugates could be used to assess the selectivity of pHis antibodies in a competitive ELISA. Subsequently, the selectivity of the pHis antibodies generated by using phosphopyrazole 8 and pyridyl amino amide 13 as haptens was assessed by competitive ELISA against His, pSer, pThr, pTyr, τ-pHis and π-pHis. Antibodies generated by using phosphopyrazole 8 as a hapten were found to be selective for τ-pHis, and antibodies generated by using pyridyl amino amide 13 were found to be selective for π-pHis. Both τ- and π-pHis antibodies were shown to be effective in immunological experiments, including ELISA, western blot, and immunofluorescence. The τ-pHis antibody was also shown to be useful in the immunoprecipitation of proteins containing pHis.
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Affiliation(s)
- Mehul V Makwana
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
- Department of Infection Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Cleide Dos Santos Souza
- Sheffield Instituate of Translational Neuroscience, The University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK
| | - Barry T Pickup
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
| | - Mark J Thompson
- Department of Oncology and Metabolism, Medical School, The University Of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Santosh K Lomada
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Yuxi Feng
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Thomas Wieland
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Richard F W Jackson
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
| | - Richmond Muimo
- Department of Infection Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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8
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Singh S, Tian W, Severance ZC, Chaudhary SK, Anokhina V, Mondal B, Pergu R, Singh P, Dhawa U, Singha S, Choudhary A. Proximity-inducing modalities: the past, present, and future. Chem Soc Rev 2023; 52:5485-5515. [PMID: 37477631 DOI: 10.1039/d2cs00943a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Living systems use proximity to regulate biochemical processes. Inspired by this phenomenon, bifunctional modalities that induce proximity have been developed to redirect cellular processes. An emerging example of this class is molecules that induce ubiquitin-dependent proteasomal degradation of a protein of interest, and their initial development sparked a flurry of discovery for other bifunctional modalities. Recent advances in this area include modalities that can change protein phosphorylation, glycosylation, and acetylation states, modulate gene expression, and recruit components of the immune system. In this review, we highlight bifunctional modalities that perform functions other than degradation and have great potential to revolutionize disease treatment, while also serving as important tools in basic research to explore new aspects of biology.
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Affiliation(s)
- Sameek Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Wenzhi Tian
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Zachary C Severance
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Viktoriya Anokhina
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Basudeb Mondal
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Prashant Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Uttam Dhawa
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santanu Singha
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
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9
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Cao Y, Liu XT, Mao PZ, Chen ZL, Tarn C, Dong MQ. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers. J Proteome Res 2023; 22:2593-2607. [PMID: 37494005 DOI: 10.1021/acs.jproteome.3c00037] [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] [Indexed: 07/27/2023]
Abstract
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting of cross-linkable sites. Some restrict NHS ester cross-linkable sites to lysine (K) and protein N-terminus, referred to as K only for short, whereas others additionally include serine (S), threonine (T), and tyrosine (Y) by default. Here, by setting amino acids with chemically inert side chains such as glycine (G), valine (V), and leucine (L) as cross-linkable sites, which serves as a negative control, we show that software-identified STY-cross-links are only as reliable as GVL-cross-links. This is true across different NHS ester cross-linkers including DSS, DSSO, and DSBU, and across different search engines including MeroX, xiSearch, and pLink. Using a published data set originated from synthetic peptides, we demonstrate that STY-cross-links indeed have a high false discovery rate. Further analysis revealed that depending on the data and the search engine used to analyze the data, up to 65% of the STY-cross-links identified are actually K-K cross-links of the same peptide pairs, up to 61% are actually K-mono-links, and the rest tend to contain short peptides at high risk of false identification.
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Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Xin-Tong Liu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Peng-Zhi Mao
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ching Tarn
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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10
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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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11
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Heininen J, Erbacher C, Kotiaho T, Kostiainen R, Teppo J. Enzymatic Phosphorylation of Oxidized Tyrosine Residues. J Proteome Res 2023. [PMID: 37146082 DOI: 10.1021/acs.jproteome.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Post-translational modifications (PTMs) alter the function and fate of proteins and cells in almost every conceivable way. Protein modifications can occur as a result of specific regulating actions of enzymes, such as tyrosine kinases phosphorylating tyrosine residues or by nonenzymatic reactions, such as oxidation related to oxidative stress and diseases. While many studies have addressed the multisite, dynamic, and network-like properties of PTMs, only little is known of the interplay of the same site modifications. In this work, we studied the enzymatic phosphorylation of oxidized tyrosine (l-DOPA) residues using synthetic insulin receptor peptides, in which tyrosine residues were replaced with l-DOPA. The phosphorylated peptides were identified by liquid chromatography-high-resolution mass spectrometry and the site of phosphorylation by tandem mass spectrometry. The results clearly show that the oxidized tyrosine residues are phosphorylated, displaying a specific immonium ion peak in the MS2 spectra. Furthermore, we detected this modification in our reanalysis (MassIVE ID: MSV000090106) of published bottom-up phosphoproteomics data. The modification, where both oxidation and phosphorylation take place at the same amino acid, has not yet been published in PTM databases. Our data indicate that there can be multiple PTMs that do not exclude each other at the same modification site.
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Affiliation(s)
- Juho Heininen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Catharina Erbacher
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Tapio Kotiaho
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Risto Kostiainen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Jaakko Teppo
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
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12
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Zhang S, Li JY, Gao W, Qiao JQ, Lian HZ. Magnetic Ti 3C 2 MXene Nanosheets Prepared for Enrichment of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2023; 15:16505-16514. [PMID: 36947132 DOI: 10.1021/acsami.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
MXenes have received lots of attention since discovered and have been applied in various fields. In this work, Ti3C2-Fe3O4 composites with exposed non-modified Ti3C2 MXene nanosheets were designed and prepared by an in situ growth strategy and then applied in the enrichment of phosphopeptides. The two-dimensional composites could interact with the phosphopeptides through a metal oxide affinity chromatography mechanism provided by Ti-O and Fe-O bonds and a hydrophilic interaction chromatography mechanism by surface hydroxyl groups. This magnetic nanomaterial with a specific surface area of 66.1 m2·g-1 had high sensitivity to phosphopeptides (0.5 nmol·L-1) and high selectivity (1:1000 of the molar ratio of β-casein to bovine serum albumin). Non-fat milk was adopted as a real sample to preliminarily examine the applicability of the Ti3C2-Fe3O4-based protocol. Subsequently, Qingkailing injection, a kind of traditional Chinese medicine injection, was introduced to further explore the suitability of the nanocomposites for phosphopeptide enrichment from more complex matrices and satisfactory results were obtained.
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Affiliation(s)
- Sen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Jia-Yuan Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Wei Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Jun-Qin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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13
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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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14
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Widespread protein N-phosphorylation in organism revealed by SiO2@DpaZn beads based mild-acidic enrichment method. Talanta 2023; 251:123740. [DOI: 10.1016/j.talanta.2022.123740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022]
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15
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Wang S, Chen YZ, Fu S, Zhao Y. In silico approaches uncovering the systematic function of N-phosphorylated proteins in human cells. Comput Biol Med 2022; 151:106280. [PMID: 36375414 DOI: 10.1016/j.compbiomed.2022.106280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/12/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Phosphorylation plays a key role in the regulation of protein function. In addition to the extensively studied O-phosphorylation of serine, threonine, and tyrosine, emerging evidence suggests that the non-canonical phosphorylation of histidine, lysine, and arginine termed N-phosphorylation, exists widely in eukaryotes. At present, the study of N-phosphorylation is still in its infancy, and its regulatory role and specific biological functions in mammalian cells are still unknown. Here, we report the in silico analysis of the systematic biological significance of N-phosphorylated proteins in human cells. The protein structural and functional domain enrichment analysis revealed that N-phosphorylated proteins are rich in RNA recognition motif, nucleotide-binding and alpha-beta plait domains. The most commonly enriched biological pathway is the metabolism of RNA. Besides, arginine phosphorylated (pArg) proteins are highly related to DNA repair, while histidine phosphorylated (pHis) proteins may play a role in the regulation of the cell cycle, and lysine phosphorylated (pLys) proteins are linked to cellular stress response, intracellular signal transduction, and intracellular transport, which are of great significance for maintaining cell homeostasis. Protein-protein interaction (PPI) network analysis revealed important hub proteins (i.e., SRSF1, HNRNPA1, HNRNPC, SRSF7, HNRNPH1, SRSF2, SRSF11, HNRNPD, SRRM2 and YBX1) which are closely related to neoplasms, nervous system diseases, and virus infection and have potential as therapeutic targets. Those proteins with clinical significance are worthy of attention, and the rational considerations of N-phosphorylation in occurrence and progression of diseases might be beneficial for further translational applications.
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Affiliation(s)
- Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Yu Zong Chen
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Songsen Fu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
| | - Yufen Zhao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China; Key Lab of Bioorganic Phosphorus Chemistry&Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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16
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Xie Z, Feng Q, Zhang S, Yan Y, Deng C, Ding CF. Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis. Proteomics 2022; 22:e2200070. [PMID: 36100958 DOI: 10.1002/pmic.202200070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 11/08/2022]
Abstract
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
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Affiliation(s)
- Zehu Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shun Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Chunhui Deng
- Department of Chemistry, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
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17
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How phosphorylation impacts intrinsically disordered proteins and their function. Essays Biochem 2022; 66:901-913. [PMID: 36350035 PMCID: PMC9760426 DOI: 10.1042/ebc20220060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
Phosphorylation is the most common post-translational modification (PTM) in eukaryotes, occurring particularly frequently in intrinsically disordered proteins (IDPs). These proteins are highly flexible and dynamic by nature. Thus, it is intriguing that the addition of a single phosphoryl group to a disordered chain can impact its function so dramatically. Furthermore, as many IDPs carry multiple phosphorylation sites, the number of possible states increases, enabling larger complexities and novel mechanisms. Although a chemically simple and well-understood process, the impact of phosphorylation on the conformational ensemble and molecular function of IDPs, not to mention biological output, is highly complex and diverse. Since the discovery of the first phosphorylation site in proteins 75 years ago, we have come to a much better understanding of how this PTM works, but with the diversity of IDPs and their capacity for carrying multiple phosphoryl groups, the complexity grows. In this Essay, we highlight some of the basic effects of IDP phosphorylation, allowing it to serve as starting point when embarking on studies into this topic. We further describe how recent complex cases of multisite phosphorylation of IDPs have been instrumental in widening our view on the effect of protein phosphorylation. Finally, we put forward perspectives on the phosphorylation of IDPs, both in relation to disease and in context of other PTMs; areas where deep insight remains to be uncovered.
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18
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Kim HJ, Jung H, Kim S, Seo JK, Kee JM. Identification of a Target Site for Covalent Inhibition of Protein Phosphohistidine Phosphatase 1. ACS Med Chem Lett 2022; 13:1911-1915. [DOI: 10.1021/acsmedchemlett.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Hyeong Jun Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hoyoung Jung
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Soyeon Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Graduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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19
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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21
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Sakai Y, Hanafusa H, Hisamoto N, Matsumoto K. Histidine dephosphorylation of the Gβ protein GPB-1 promotes axon regeneration in C. elegans. EMBO Rep 2022; 23:e55076. [PMID: 36278516 PMCID: PMC9724660 DOI: 10.15252/embr.202255076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 12/12/2022] Open
Abstract
Histidine phosphorylation is an emerging noncanonical protein phosphorylation in animals, yet its physiological role remains largely unexplored. The protein histidine phosphatase (PHPT1) was recently identified for the first time in mammals. Here, we report that PHIP-1, an ortholog of PHPT1 in Caenorhabditis elegans, promotes axon regeneration by dephosphorylating GPB-1 Gβ at His-266 and inactivating GOA-1 Goα signaling, a negative regulator of axon regeneration. Overexpression of the histidine kinase NDK-1 also inhibits axon regeneration via GPB-1 His-266 phosphorylation. Thus, His-phosphorylation plays an antiregenerative role in C. elegans. Furthermore, we identify a conserved UNC-51/ULK kinase that functions in autophagy as a PHIP-1-binding protein. We demonstrate that UNC-51 phosphorylates PHIP-1 at Ser-112 and activates its catalytic activity and that this phosphorylation is required for PHIP-1-mediated axon regeneration. This study reveals a molecular link from ULK to protein histidine phosphatase, which facilitates axon regeneration by inhibiting trimeric G protein signaling.
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Affiliation(s)
- Yoshiki Sakai
- Division of Biological Science, Graduate School of ScienceNagoya UniversityNagoyaJapan
| | - Hiroshi Hanafusa
- Division of Biological Science, Graduate School of ScienceNagoya UniversityNagoyaJapan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of ScienceNagoya UniversityNagoyaJapan
| | - Kunihiro Matsumoto
- Division of Biological Science, Graduate School of ScienceNagoya UniversityNagoyaJapan
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22
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Complex Relationships between HIV-1 Integrase and Its Cellular Partners. Int J Mol Sci 2022; 23:ijms232012341. [PMID: 36293197 PMCID: PMC9603942 DOI: 10.3390/ijms232012341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
RNA viruses, in pursuit of genome miniaturization, tend to employ cellular proteins to facilitate their replication. HIV-1, one of the most well-studied retroviruses, is not an exception. There is numerous evidence that the exploitation of cellular machinery relies on nucleic acid-protein and protein-protein interactions. Apart from Vpr, Vif, and Nef proteins that are known to regulate cellular functioning via interaction with cell components, another viral protein, integrase, appears to be crucial for proper virus-cell dialog at different stages of the viral life cycle. The goal of this review is to summarize and systematize existing data on known cellular partners of HIV-1 integrase and their role in the HIV-1 life cycle.
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23
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O’Shaughnessy WJ, Dewangan PS, Paiz EA, Reese ML. Not your Mother's MAPKs: Apicomplexan MAPK function in daughter cell budding. PLoS Pathog 2022; 18:e1010849. [PMID: 36227859 PMCID: PMC9560070 DOI: 10.1371/journal.ppat.1010849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Reversible phosphorylation by protein kinases is one of the core mechanisms by which biological signals are propagated and processed. Mitogen-activated protein kinases, or MAPKs, are conserved throughout eukaryotes where they regulate cell cycle, development, and stress response. Here, we review advances in our understanding of the function and biochemistry of MAPK signaling in apicomplexan parasites. As expected for well-conserved signaling modules, MAPKs have been found to have multiple essential roles regulating both Toxoplasma tachyzoite replication and sexual differentiation in Plasmodium. However, apicomplexan MAPK signaling is notable for the lack of the canonical kinase cascade that normally regulates the networks, and therefore must be regulated by a distinct mechanism. We highlight what few regulatory relationships have been established to date, and discuss the challenges to the field in elucidating the complete MAPK signaling networks in these parasites.
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Affiliation(s)
- William J. O’Shaughnessy
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - Pravin S. Dewangan
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - E. Ariana Paiz
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael L. Reese
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biochemistry, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America,* E-mail:
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24
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Zhao J, Zhuang M, Liu J, Zhang M, Zeng C, Jiang B, Wu J, Song X. pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties. BMC Bioinformatics 2022; 23:399. [PMID: 36171552 PMCID: PMC9520798 DOI: 10.1186/s12859-022-04938-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome, however only hundreds of pHis sites have been discovered to date. Due to the inherent disadvantages of experimental methods, it is an urgent task for developing efficient computational approaches to identify pHis sites. Results Here, we present a novel tool, pHisPred, for accurately identifying pHis sites from protein sequences. We manually collected the largest number of experimental validated pHis sites to build benchmark datasets. Using randomized tenfold CV, the weighted SVM-RBF model shows the best performance than other four commonly used classification models (LR, KNN, RF, and MLP). From ten thousands of features, 140 and 150 most informative features were individually selected out for eukaryotic and prokaryotic models. The average AUC and F1-score values of pHisPred were (0.81, 0.40) and (0.78, 0.46) for tenfold CV on the eukaryotic and prokaryotic training datasets, respectively. In addition, pHisPred significantly outperforms other tools on testing datasets, in particular on the eukaryotic one. Conclusion We implemented a python program of pHisPred, which is freely available for non-commercial use at https://github.com/xiaofengsong/pHisPred. Moreover, users can use it to train new models with their own data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04938-x.
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Affiliation(s)
- Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Minhui Zhuang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Cong Zeng
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
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25
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Hu Y, Jiang B. Selective enrichment tandem β-elimination assisted strategy for N-phosphorylation analysis. Talanta 2022; 247:123580. [DOI: 10.1016/j.talanta.2022.123580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/27/2022]
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26
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Kim S, Backe SJ, Wengert LA, Johnson AE, Isakov RV, Bratslavsky MS, Woodford MR. O-GlcNAcylation suppresses TRAP1 activity and promotes mitochondrial respiration. Cell Stress Chaperones 2022; 27:573-585. [PMID: 35976490 PMCID: PMC9485411 DOI: 10.1007/s12192-022-01293-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/03/2022] Open
Abstract
The molecular chaperone TNF-receptor-associated protein-1 (TRAP1) controls mitochondrial respiration through regulation of Krebs cycle and electron transport chain activity. Post-translational modification (PTM) of TRAP1 regulates its activity, thereby controlling global metabolic flux. O-GlcNAcylation is one PTM that is known to impact mitochondrial metabolism, however the major effectors of this regulatory PTM remain inadequately resolved. Here we demonstrate that TRAP1-O-GlcNAcylation decreases TRAP1 ATPase activity, leading to increased mitochondrial metabolism. O-GlcNAcylation of TRAP1 occurs following mitochondrial import and provides critical regulatory feedback, as the impact of O-GlcNAcylation on mitochondrial metabolism shows TRAP1-dependence. Mechanistically, loss of TRAP1-O-GlcNAcylation decreased TRAP1 binding to ATP, and interaction with its client protein succinate dehydrogenase (SDHB). Taken together, TRAP1-O-GlcNAcylation serves to regulate mitochondrial metabolism by the reversible attenuation of TRAP1 chaperone activity.
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Affiliation(s)
- Seungchan Kim
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Laura A Wengert
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Anna E Johnson
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Roman V Isakov
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Michael S Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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27
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Makwana MV, Williamson MP, Jackson RFW, Muimo R. Quantitation of phosphohistidine in proteins in a mammalian cell line by 31P NMR. PLoS One 2022; 17:e0273797. [PMID: 36048825 PMCID: PMC9436146 DOI: 10.1371/journal.pone.0273797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
There is growing evidence to suggest that phosphohistidines are present at significant levels in mammalian cells and play a part in regulating cellular activity, in particular signaling pathways related to cancer. Because of the chemical instability of phosphohistidine at neutral or acid pH, it remains unclear how much phosphohistidine is present in cells. Here we describe a protocol for extracting proteins from mammalian cells in a way that avoids loss of covalent phosphates from proteins, and use it to measure phosphohistidine concentrations in human bronchial epithelial cell (16HBE14o-) lysate using 31P NMR spectroscopic analysis. Phosphohistidine is determined on average to be approximately one third as abundant as phosphoserine and phosphothreonine combined (and thus roughly 15 times more abundant than phosphotyrosine). The amount of phosphohistidine, and phosphoserine/phosphothreonine per gram of protein from a cell lysate was determined to be 23 μmol/g and 68 μmol/g respectively. The amount of phosphohistidine, and phosphoserine/phosphothreonine per cell was determined to be 1.8 fmol/cell, and 5.8 fmol/cell respectively. Phosphorylation is largely at the N3 (tele) position. Typical tryptic digest conditions result in loss of most of the phosphohistidine present, which may explain why the amounts reported here are greater than is generally seen using mass spectroscopy assays. The results further strengthen the case for a functional role of phosphohistidine in eukaryotic cells.
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Affiliation(s)
- Mehul V. Makwana
- Department of Chemistry, The University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
| | - Mike P. Williamson
- School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | | | - Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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28
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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29
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Lima MA, Rudd TR, Fernig DG, Yates EA. Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220391. [PMID: 35919982 PMCID: PMC9346353 DOI: 10.1098/rsif.2022.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.
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Affiliation(s)
- M A Lima
- Centre for Glycosciences, Keele University, Keele ST5 5BG, UK.,School of Life Sciences, Keele University, Keele ST5 5BG, UK
| | - T R Rudd
- Analytical and Biological Science Department, National Institute of Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - D G Fernig
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - E A Yates
- School of Life Sciences, Keele University, Keele ST5 5BG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
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30
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Srinivasan A, Sing JC, Gingras AC, Röst HL. Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry. J Proteome Res 2022; 21:1789-1799. [PMID: 35877786 DOI: 10.1021/acs.jproteome.2c00172] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based profiling of the phosphoproteome is a powerful method of identifying phosphorylation events at a systems level. Most phosphoproteomics studies have used data-dependent acquisition (DDA) mass spectrometry as their method of choice. In this Perspective, we review some recent studies benchmarking DDA and DIA methods for phosphoproteomics and discuss data analysis options for DIA phosphoproteomics. In order to evaluate the impact of data-dependent and data-independent acquisition (DIA) on identification and quantification, we analyze a previously published phosphopeptide-enriched data set consisting of 10 replicates acquired by DDA and DIA each. We find that though more unique identifications are made in DDA data, phosphopeptides are identified more consistently across replicates in DIA. We further discuss the challenges of identifying chromatographically coeluting phosphopeptide isomers and investigate the impact on reproducibility of identifying high-confidence site-localized phosphopeptides in replicates.
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Affiliation(s)
- Aparna Srinivasan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Justin C Sing
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Hannes L Röst
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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31
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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32
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Brandi J, Noberini R, Bonaldi T, Cecconi D. Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications. J Chromatogr A 2022; 1678:463352. [PMID: 35896048 DOI: 10.1016/j.chroma.2022.463352] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Post-translational modifications (PTMs) occur during or after protein biosynthesis and increase the functional diversity of proteome. They comprise phosphorylation, acetylation, methylation, glycosylation, ubiquitination, sumoylation (among many other modifications), and influence all aspects of cell biology. Mass-spectrometry (MS)-based proteomics is the most powerful approach for PTM analysis. Despite this, it is challenging due to low abundance and labile nature of many PTMs. Hence, enrichment of modified peptides is required for MS analysis. This review provides an overview of most common PTMs and a discussion of current enrichment methods for MS-based proteomics analysis. The traditional affinity strategies, including immunoenrichment, chromatography and protein pull-down, are outlined together with their strengths and shortcomings. Moreover, a special attention is paid to chemical enrichment strategies, such as capture by chemoselective probes, metabolic and chemoenzymatic labelling, which are discussed with an emphasis on their recent progress. Finally, the challenges and future trends in the field are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy.
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy.
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
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33
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Paris J, Theisen A, Marzullo BP, Haris A, Morgan TE, Barrow MP, O’Hara J, O’Connor PB. Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1126-1133. [PMID: 35604791 PMCID: PMC9264387 DOI: 10.1021/jasms.1c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.
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Affiliation(s)
- Johanna Paris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bryan P. Marzullo
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E. Morgan
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John O’Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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34
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Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
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Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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35
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Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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36
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Lei Q, Murshed A, Ogbuehi AC, Peng Q, Zhang Y, Sun F, Zhong Q, Jin L, Wang H. Highly selective titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles for the enrichment of intact phosphoproteins. J Sep Sci 2022; 45:3054-3062. [PMID: 35754361 DOI: 10.1002/jssc.202200351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/11/2022]
Abstract
Phosphorylation is one of the most important protein post-translational modifications, which possesses dramatic regulatory effects on the function of proteins. In consideration of the low abundance and low stoichiometry of phosphorylation and non-specific signal suppression, efficient capture of the phosphoproteins from complex biological samples is critical to meet the need of protein profiling. In this work, a facile preparation of titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles were developed for the enrichment of intact phosphoproteins. The prepared magnetic nanoparticles were characterized by various instruments and had a spherical shape with an average diameter of 300 nm. The adsorption isotherms were investigated and the maximum capacity for β-casein was calculated to be 961.5 mg/g. Standard protein mixtures and biological samples (non-fat milk and human serum) were selected to test the enrichment performance. Sodium dodecyl sulfate-poly acrylamide gel electrophoresis analysis demonstrated the excellent enrichment performance with high selectivity. With the superparamagnetic property, titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles were convenient for the practical application and clinical promotion, thus having a promising prospect in the field of phosphoprotein research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qin Lei
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai, 200072, China
| | - Abduh Murshed
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai, 200072, China
| | - Anthony Chukwunonso Ogbuehi
- Faculty of Physics, University of Münster, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Str. 9, Münster, 48149, Germany
| | - Qian Peng
- Faculty of Medical Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yiqing Zhang
- Faculty of Medical Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai, 200072, China
| | - Qi Zhong
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai, 200072, China
| | - Lei Jin
- Faculty of Medical Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Hao Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai, 200072, China
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37
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Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
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Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
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38
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Histidine phosphorylation in human cells; a needle or phantom in the haystack? Nat Methods 2022; 19:827-828. [PMID: 35726056 DOI: 10.1038/s41592-022-01524-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 12/29/2022]
Abstract
It has been suggested that in mammalian cells histidine residues in proteins may become as frequently phosphorylated as serine, threonine and tyrosine, and may play a key role in mammalian signaling. Here we applied a robust workflow that earlier allowed us to detect histidine phosphorylation in bacteria unambiguously, to probe for histidine phosphorylation in four human cell lines. Initially, seemingly hundreds of protein histidine phosphorylations were picked up in all studied human cell lines. However, careful examination of the data, and several control experiments, led us to the conclusion that >99% of these initially assigned pHis sites were not genuine, and should be site localized to neighboring Ser/Thr residues. Nevertheless, our methods are selective enough to detect just a handful of genuine pHis sites in mammalian cells, representing well-known enzymatic intermediates. Consequently, we do not find any evidence in our data supporting that protein histidine phosphorylation plays a role in mammalian signaling.
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39
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Liu L, Weiß A, Saul VV, Schermuly RT, Pleschka S, Schmitz ML. Comparative kinase activity profiling of pathogenic influenza A viruses reveals new anti- and pro-viral protein kinases. J Gen Virol 2022; 103. [PMID: 35771598 DOI: 10.1099/jgv.0.001762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Constant evolution of influenza A viruses (IAVs) leads to the occurrence of new virus strains, which can cause epidemics and occasional pandemics. Here we compared two medically relevant IAVs, namely A/Hamburg/4/09 (H1N1pdm09) of the 2009 pandemic and the highly pathogenic avian IAV human isolate A/Thailand/1(KAN-1)/2004 (H5N1), for their ability to trigger intracellular phosphorylation patterns using a highly sensitive peptide-based kinase activity profiling approach. Virus-dependent tyrosine phosphorylations of substrate peptides largely overlap between the two viruses and are also strongly overrepresented in comparison to serine/threonine peptide phosphorylations. Both viruses trigger phosphorylations with distinct kinetics by overlapping and different kinases from which many form highly interconnected networks. As approximately half of the kinases forming a signalling hub have no known function for the IAV life cycle, we interrogated selected members of this group for their ability to interfere with IAV replication. These experiments revealed negative regulation of H1N1pdm09 and H5N1 replication by NUAK [novel (nua) kinase] kinases and by redundant ephrin A (EphA) receptor tyrosine kinases.
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Affiliation(s)
- Lu Liu
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany.,Institute of Medical Virology, Justus Liebig University Giessen, Germany
| | - Astrid Weiß
- Department of Internal Medicine, Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig-University Giessen, Germany
| | - Vera Vivian Saul
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany
| | - Ralph Theo Schermuly
- Department of Internal Medicine, Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig-University Giessen, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Germany.,German Center for Infection Research (DZIF), partner site Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany
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40
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Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizcaíno JA, Deutsch EW, Jones AR. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. J Proteome Res 2022; 21:1603-1615. [PMID: 35640880 PMCID: PMC9251759 DOI: 10.1021/acs.jproteome.1c00827] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Phosphoproteomic
methods are commonly employed to identify and
quantify phosphorylation sites on proteins. In recent years, various
tools have been developed, incorporating scores or statistics related
to whether a given phosphosite has been correctly identified or to
estimate the global false localization rate (FLR) within a given data
set for all sites reported. These scores have generally been calibrated
using synthetic datasets, and their statistical reliability on real
datasets is largely unknown, potentially leading to studies reporting
incorrectly localized phosphosites, due to inadequate statistical
control. In this work, we develop the concept of scoring modifications
on a decoy amino acid, that is, one that cannot be modified, to allow
for independent estimation of global FLR. We test a variety of amino
acids, on both synthetic and real data sets, demonstrating that the
selection can make a substantial difference to the estimated global
FLR. We conclude that while several different amino acids might be
appropriate, the most reliable FLR results were achieved using alanine
and leucine as decoys. We propose the use of a decoy amino acid to
control false reporting in the literature and in public databases
that re-distribute the data. Data are available via ProteomeXchange
with identifier PXD028840.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, U.K
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, U.K
| | - Yasset Perez Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, U.K
| | - Oscar Martin Camacho
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, U.K
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, U.K
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, U.K
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, U.K
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41
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Hunter T. A journey from phosphotyrosine to phosphohistidine and beyond. Mol Cell 2022; 82:2190-2200. [PMID: 35654043 DOI: 10.1016/j.molcel.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know about the roles of protein phosphorylation has come from studies of serine, threonine, and tyrosine phosphorylation. Much less is understood about the phosphorylation of histidine, lysine, arginine, cysteine, aspartate, and glutamate, so-called non-canonical phosphorylations. Phosphohistidine (pHis) was discovered 60 years ago as a mitochondrial enzyme intermediate; since then, evidence for the existence of histidine kinases and phosphohistidine phosphatases has emerged, together with examples where protein function is regulated by reversible histidine phosphorylation. pHis is chemically unstable and has thus been challenging to study. However, the recent development of tools for studying pHis has accelerated our understanding of the multifaceted functions of histidine phosphorylation, revealing a large number of proteins that are phosphorylated on histidine and implicating pHis in a wide range of cellular processes.
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Affiliation(s)
- Tony Hunter
- Molecular Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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42
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Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
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Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
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43
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Kalyuzhnyy A, Eyers PA, Eyers CE, Bowler-Barnett E, Martin MJ, Sun Z, Deutsch EW, Jones AR. Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. J Proteome Res 2022; 21:1510-1524. [PMID: 35532924 PMCID: PMC9171898 DOI: 10.1021/acs.jproteome.2c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Public phosphorylation databases such as PhosphoSitePlus (PSP) and PeptideAtlas (PA) compile results from published papers or openly available mass spectrometry (MS) data. However, there is no database-level control for false discovery of sites, likely leading to the overestimation of true phosphosites. By profiling the human phosphoproteome, we estimate the false discovery rate (FDR) of phosphosites and predict a more realistic count of true identifications. We rank sites into phosphorylation likelihood sets and analyze them in terms of conservation across 100 species, sequence properties, and functional annotations. We demonstrate significant differences between the sets and develop a method for independent phosphosite FDR estimation. Remarkably, we report estimated FDRs of 84, 98, and 82% within sets of phosphoserine (pSer), phosphothreonine (pThr), and phosphotyrosine (pTyr) sites, respectively, that are supported by only a single piece of identification evidence─the majority of sites in PSP. We estimate that around 62 000 Ser, 8000 Thr, and 12 000 Tyr phosphosites in the human proteome are likely to be true, which is lower than most published estimates. Furthermore, our analysis estimates that 86 000 Ser, 50 000 Thr, and 26 000 Tyr phosphosites are likely false-positive identifications, highlighting the significant potential of false-positive data to be present in phosphorylation databases.
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Affiliation(s)
- Anton Kalyuzhnyy
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Computational Biology Facility, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Claire E Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
| | - Emily Bowler-Barnett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, U.K
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, U.K
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Andrew R Jones
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K.,Computational Biology Facility, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, U.K
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44
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Jones RD, Qian Y, Ilia K, Wang B, Laub MT, Del Vecchio D, Weiss R. Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Nat Commun 2022; 13:1720. [PMID: 35361767 PMCID: PMC8971529 DOI: 10.1038/s41467-022-29338-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Engineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
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Affiliation(s)
- Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yili Qian
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Benjamin Wang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael T Laub
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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45
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Yang X, Wang N, Ren S, Hu Y, Wang H, Ji A, Cao L, Li M, Liu J, Wang H. Phosphorylation regulation of cardiac proteins in Babesia microti infected mice in an effort to restore heart function. Parasit Vectors 2022; 15:98. [PMID: 35313969 PMCID: PMC8935697 DOI: 10.1186/s13071-022-05233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background Babesia is a common protozoan parasite that infects red blood cells. In mice infected with Babesia microti, the red blood cells were lysed, resulting in decreased oxygen-carrying capacity. To compensate for low blood oxygen levels, stress on the heart was greatly increased. Babesiosis induces a variety of pathologies; meanwhile, heart tissues initiate self-repair responses to babesiosis-induced tissue damage to restore heart function. Methods To discover the molecular mechanisms of the damage and self-repair in the heart after B. microti infection in mice, we investigated the changes in protein expression and phosphorylation modification levels in heart tissues at 0, 5, 8, 11, and 19 days post-infection using data-independent acquisition (DIA) quantitative proteomics. Results The numbers of global proteins we identified were 1934, 1966, 1984, 1989, and 1955 and of phosphopeptides were 5118, 5133, 5130, 5133, and 5140 at 0, 5, 8, 11, and 19 days, respectively, in heart cells after infection with B. microti. The results showed that after B. microti infection the differentially expressed proteins in mice mainly include fibrinogen α (Fgα), fibrinogen β (Fgβ), Serpina1b, Serpina1c, cathepsin Z, cytochrome c oxidases (COXs), RPS11, and RPS20. The proteins with phosphorylation changes mainly include 20-kDa light chain of myosin II (MLC20), myosin light chain kinase (MLCK), mitogen-activated protein kinase 14 (MAPK14), and Akt1. These proteins were mainly involved in coagulation processes, cell apoptosis, oxidative phosphorylation, and ribosomes. Conclusions The coagulation cascade-related proteins, apoptosis-related proteins, oxidative phosphorylation-related proteins, and other types of proteins are all involved in the damage and self-repair process in the heart after B. microti infection. These results offer a wealth of new targets for further exploration into the causes of heart disease induced by Babesia infection and are of great significance for novel drug development and new opportunities for targeted therapies. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05233-7.
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Affiliation(s)
- Xiaohong Yang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.,Department of Pathogenic Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ningmei Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Shuguang Ren
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.,The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yuhong Hu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.,Instrumental Analysis Center, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Han Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Aimeng Ji
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lihui Cao
- Animal Disease Control Center of Zhengding County, Shijiazhuang, Hebei, China
| | - Mengxue Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jingze Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.
| | - Hui Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.
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46
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Abstract
![]()
Protein post-translational
modifications (PTMs) enable cells to
rapidly change in response to biological stimuli. With hundreds of
different PTMs, understanding these control mechanisms is complex.
To date, efforts have focused on investigating the effect of a single
PTM on protein function. Yet, many proteins contain multiple PTMs.
Moreover, one PTM can alter the prevalence of another, a phenomenon
termed PTM crosstalk. Understanding PTM crosstalk is critical; however,
its detection is challenging since PTMs occur substoichiometrically.
Here, we develop an enrichment-free, label-free proteomics method
that utilizes high-field asymmetric ion mobility spectrometry (FAIMS)
to enhance the detection of PTM crosstalk. We show that by searching
for multiple combinations of dynamic PTMs on peptide sequences, a
6-fold increase in candidate PTM crosstalk sites is identified compared
with that of standard liquid chromatography-tandem mass spectrometry
(LC-MS/MS) workflows. Additionally, by cycling through FAIMS compensation
voltages within a single LC-FAIMS-MS/MS run, we show that our LC-FAIMS-MS/MS
workflow can increase multi-PTM-containing peptide identifications
without additional increases in run times. With 159 novel candidate
crosstalk sites identified, we envisage LC-FAIMS-MS/MS to play an
important role in expanding the repertoire of multi-PTM identifications.
Moreover, it is only by detecting PTM crosstalk that we can “see”
the full picture of how proteins are regulated.
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Affiliation(s)
- Kish R Adoni
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Debbie L Cunningham
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - John K Heath
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Aneika C Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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47
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Zn(II)-DPA functionalized graphene oxide two-dimensional nanocomposites for N-phosphoproteins enrichment. Talanta 2022; 243:123384. [DOI: 10.1016/j.talanta.2022.123384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/15/2022]
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48
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Su W, Qiu T, Zhang M, Hao C, Zeng P, Huang Z, Du W, Yun T, Xuan Y, Zhang L, Guo Y, Jiao W. Systems biomarker characteristics of circulating alkaline phosphatase activities for 48 types of human diseases. Curr Med Res Opin 2022; 38:201-209. [PMID: 34719310 DOI: 10.1080/03007995.2021.2000715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most human diseases are accompanied by systems changes. Systems biomarkers should reflect such changes. The phosphorylation and dephosphorylation of biomolecules maintain human homeostasis. However, the systems biomarker characteristics of circulating alkaline phosphatase, a routine blood test conducted for many human diseases, have never been investigated. METHOD This study retrieved the circulating alkaline phosphatase (ALP) activities from patients with 48 clinically confirmed diseases and healthy individuals from the database of our hospital during the past five years. A detailed analysis of the statistical characteristics of ALP was conducted, including quantiles, receiving operator curve (ROC), and principal component analysis. RESULTS Among the 48 diseases, 45 had increased, and three had decreased median levels of ALP activities compared to the healthy control. Preeclampsia, hepatic encephalopathy, pancreatic cancer, and liver cancer had the highest median values, whereas nephrotic syndrome, lupus erythematosus, and nephritis had decreased median values compared to the healthy control. Further, area under curve (AUC) values were ranged between 0.61 and 0.87 for 19 diseases, and the ALP activities were the best systems biomarker for preeclampsia (AUC 0.87), hepatic encephalopathy (AUC 0.87), liver cancer (AUC 0.81), and pancreatic cancer (AUC 0.81). CONCLUSIONS Alkaline phosphatase was a decent systems biomarker for 19 different types of human diseases. Understanding the molecular mechanisms of over-up-and-down-regulation of ALP activities might be the key to understanding the whole-body systems' reactions during specific disease progression.
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Affiliation(s)
- Wenhao Su
- Systems Biology & Medicine Center for Complex Diseases, Center for Clinical Research, Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tong Qiu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meng Zhang
- Systems Biology & Medicine Center for Complex Diseases, Center for Clinical Research, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cui Hao
- Systems Biology & Medicine Center for Complex Diseases, Center for Clinical Research, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Pengjiao Zeng
- Systems Biology & Medicine Center for Complex Diseases, Center for Clinical Research, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhangfeng Huang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenxing Du
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tianxiang Yun
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yunpeng Xuan
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lijuan Zhang
- Systems Biology & Medicine Center for Complex Diseases, Center for Clinical Research, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yachong Guo
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
- Institute Theory of Polymers, Leibniz-Institut für Polymerforschung Dresden, Dresden, Germany
| | - Wenjie Jiao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
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49
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Garrido A, Santamaría E, Fernández-Irigoyen J, Soto M, Simonet C, Fernández M, Obiang D, Tolosa E, Martí MJ, Padmanabhan S, Malagelada C, Ezquerra M, Fernández-Santiago R. Differential Phospho-Signatures in Blood Cells Identify LRRK2 G2019S Carriers in Parkinson's Disease. Mov Disord 2022; 37:1004-1015. [PMID: 35049090 PMCID: PMC9306798 DOI: 10.1002/mds.28927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Background The clinicopathological phenotype of G2019S LRRK2‐associated Parkinson's disease (L2PD) is similar to idiopathic Parkinson's disease (iPD), and G2019S LRRK2 nonmanifesting carriers (L2NMCs) are at increased risk for development of PD. With various therapeutic strategies in the clinical and preclinical pipeline, there is an urgent need to identify biomarkers that can aid early diagnosis and patient enrichment for ongoing and future LRRK2‐targeted trials. Objective The objective of this work was to investigate differential protein and phospho‐protein changes related to G2019S mutant LRRK2 in peripheral blood mononuclear cells from G2019S L2PD patients and G2019S L2NMCs, identify specific phospho‐protein changes associated with the G2019S mutation and with disease status, and compare findings with patients with iPD. Methods We performed an unbiased phospho‐proteomic study by isobaric label–based mass spectrometry using peripheral blood mononuclear cell group pools from a LRRK2 cohort from Spain encompassing patients with G2019S L2PD (n = 20), G2019S L2NMCs (n = 20), healthy control subjects (n = 30), patients with iPD (n = 15), patients with R1441G L2PD (n = 5), and R1441G L2NMCs (n = 3) (total N = 93). Results Comparing G2019S carriers with healthy controls, we identified phospho‐protein changes associated with the G2019S mutation. Moreover, we uncovered a specific G2019S phospho‐signature that changes with disease status and can discriminate patients with G2019S L2PD, G2019S L2NMCs, and healthy controls. Although patients with iPD showed a differential phospho‐proteomic profile, biological enrichment analyses revealed similar changes in deregulated pathways across the three groups. Conclusions We found a differential phospho‐signature associated with LRRK2 G2019S for which, consistent with disease status, the phospho‐profile from PD at‐risk G2019S L2NMCs was more similar to healthy controls than patients with G2019S L2PD with the manifested disease. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
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Affiliation(s)
- Alicia Garrido
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Enrique Santamaría
- Proteored-ISCIII, Proteomics Platform, Clinical Neuroproteomics Unit, Navarrabiomed, Departamento de Salud, UPNA, IdiSNA, Pamplona, Navarra, Spain
| | - Joaquín Fernández-Irigoyen
- Proteored-ISCIII, Proteomics Platform, Clinical Neuroproteomics Unit, Navarrabiomed, Departamento de Salud, UPNA, IdiSNA, Pamplona, Navarra, Spain
| | - Marta Soto
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Cristina Simonet
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Manel Fernández
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain.,Parkinson's Disease and Movement Disorders Group of the Institut de Neurociències (Universitat de Barcelona), Barcelona, Catalonia, Spain
| | - Donina Obiang
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Eduardo Tolosa
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - María-José Martí
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, New York, New York, USA
| | - Cristina Malagelada
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain.,Department of Biomedicine, Faculty of Medicine, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Mario Ezquerra
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain
| | - Rubén Fernández-Santiago
- Parkinson Disease and Movement Disorders Unit, Neurology Service, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, Barcelona, Catalonia, Spain.,Lab of Parkinson Disease & Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII), Barcelona, Catalonia, Spain.,Histology Unit, Department of Biomedicine, Faculty of Medicine, Universitat de Barcelona, Barcelona, Catalonia, Spain
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Melo-Braga MND, Moreira RDS, Gervásio JHDB, Felicori LF. Overview of protein posttranslational modifications in Arthropoda venoms. J Venom Anim Toxins Incl Trop Dis 2022; 28:e20210047. [PMID: 35519418 PMCID: PMC9036706 DOI: 10.1590/1678-9199-jvatitd-2021-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022] Open
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