51
|
Schira-Heinen J, Grube L, Waldera-Lupa DM, Baberg F, Langini M, Etemad-Parishanzadeh O, Poschmann G, Stühler K. Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140237. [DOI: 10.1016/j.bbapap.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
|
52
|
Monteiro F, Hubmann G, Takhaveev V, Vedelaar SR, Norder J, Hekelaar J, Saldida J, Litsios A, Wijma HJ, Schmidt A, Heinemann M. Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Mol Syst Biol 2019; 15:e9071. [PMID: 31885198 PMCID: PMC6920703 DOI: 10.15252/msb.20199071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolic heterogeneity between individual cells of a population harbors significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence require tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e., the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein design, biochemical methods, proteomics, and metabolomics, we developed a biosensor to measure glycolytic flux in single yeast cells. Therefore, drawing on the robust cell-intrinsic correlation between glycolytic flux and levels of fructose-1,6-bisphosphate (FBP), we transplanted the B. subtilis FBP-binding transcription factor CggR into yeast. With the developed biosensor, we robustly identified cell subpopulations with different FBP levels in mixed cultures, when subjected to flow cytometry and microscopy. Employing microfluidics, we were also able to assess the temporal FBP/glycolytic flux dynamics during the cell cycle. We anticipate that our biosensor will become a valuable tool to identify and study metabolic heterogeneity in cell populations.
Collapse
Affiliation(s)
- Francisca Monteiro
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
cE3c‐Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Georg Hubmann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
Laboratory of Molecular Cell BiologyDepartment of BiologyInstitute of Botany and MicrobiologyKU Leuven, & Center for Microbiology, VIBHeverlee, FlandersBelgium
| | - Vakil Takhaveev
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Silke R Vedelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Justin Norder
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Johan Hekelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Joana Saldida
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Athanasios Litsios
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Hein J Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | | | - Matthias Heinemann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| |
Collapse
|
53
|
Košec A, Novak R, Konjevoda P, Trkulja V, Bedeković V, Grgurević L. Tumor tissue hnRNP M and HSP 90α as potential predictors of disease-specific mortality in patients with early-stage cutaneous head and neck melanoma: A proteomics-based study. Oncotarget 2019; 10:6713-6722. [PMID: 31803364 PMCID: PMC6877100 DOI: 10.18632/oncotarget.27333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023] Open
Abstract
Background: Breslow tumor thickness and mitotic rate are standardly used for risk stratification of patients with malignant melanoma. However, their prognostic value is relatively limited and a need for improved prognostication has been advocated. We aimed to screen the tumor tissue proteome in a search for potentially useful prognostic factors in early-stage cutaneous head and neck melanoma. Methodology and Findings: Proteomic profiles of archival formalin-fixed tissue samples of 31 patients (age 23–90 years) with early-stage head and neck cutaneous malignant melanoma (American Joint Committee on Cancer, AJCC, stage I/II) were determined and expression intensities were compared to those of melanocytic nevi, yielding ratios used in data analysis. Medical charts were retrospectively reviewed to determine time elapsed since diagnosis to disease-specific death or censoring. In a multivariate recursive partitioning analysis (as per AJCC guidelines), higher expression levels of heterogeneous nuclear ribonucleoprotein M (hnRNP M) [n = 18, HR = 1.94 vs. the entire cohort; HR = 5.95 (95%CI 2.43–14.5) for “high” vs. “low” (n = 13)] and of heat shock protein 90 alpha (HSP 90α) [n = 17, HR = 2.09 vs. the entire cohort; HR = 4.59 (95%CI 1.87–11.2) for “high” vs. “low” (n = 14)] were each independently strongly associated with higher mortality (accounting for clinical and standard pathohistological features). Higher Breslow thickness and mitotic rate were associated with higher mortality only when proteomic data were disregarded. Conclusions and Significance: Data suggest that tumor tissue expression of hnRNP M and/or of HSP 90α deserve further investigation and clinical validation as potential novel risk stratification aids in patients with stage I-II cutaneous head and neck malignant melanoma.
Collapse
Affiliation(s)
- Andro Košec
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospital Centre Sestre Milosrdnice, Zagreb, Croatia.,These authors contributed equally to this work
| | - Ruđer Novak
- Department for Proteomics, Center for Translational and Clinical Research, School of Medicine, University of Zagreb, Zagreb, Croatia.,These authors contributed equally to this work
| | - Paško Konjevoda
- Division of Molecular Medicine, Laboratory for Epigenomics, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Vladimir Trkulja
- Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Vladimir Bedeković
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospital Centre Sestre Milosrdnice, Zagreb, Croatia
| | - Lovorka Grgurević
- Department for Proteomics, Center for Translational and Clinical Research, School of Medicine, University of Zagreb, Zagreb, Croatia.,Department of Anatomy "Drago Perović", School of Medicine, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
54
|
Abstract
While host proteins incorporated into virions during viral budding from infected cell are known to play essential roles in multiple process of the life cycle of progeny virus, these characteristics have been largely neglected in studies on rabies virus (RABV). Here, we purified the RABV virions with good purity and integrity, and analyzed their proteome by nano LC–MS/MS, followed by the confirmation with immunoblot and immuno-electronic microscopy. In addition to the 5 viral proteins, 49 cellular proteins were reproducibly identified to be incorporated into matured RABV virions. Function annotation suggested that 24 of them were likely involved in virus replication. Furthermore, cryo-EM was employed to observe the purified RABV virions, generating high-resolution pictures of the bullet-shaped virion structure of RABV. This study has provided new insights into the host proteins composition in RABV virion and shed the light for further investigation on molecular mechanisms of RABV infection, as well as the discovery of new anti-RABV therapeutics.
Collapse
|
55
|
Wu X, Yang D, Zhao F, Yang ZH, Wang D, Qiao M, Fang Y, Li W, Wu R, He P, Cong Y, Chen C, Hu L, Yan Y, Xie C, Wu Y, Han J, Zhong CQ. Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS. Mol Cell Proteomics 2019; 18:1054-1069. [PMID: 30850422 PMCID: PMC6553925 DOI: 10.1074/mcp.ra119.001380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/04/2019] [Indexed: 11/06/2022] Open
Abstract
Lipopolysaccharide (LPS)-induced macrophage activation is a prototype of innate immune response. Although key effector proteins in LPS signaling pathway have been revealed, the map of dynamic protein interactions and phosphorylation as well as the stoichiometry of protein complexes are lacking. Here we present a dynamic map of protein interactions and phosphorylation in MyD88, TRAF6 and NEMO complexes obtained by SWATH-MS. The comprehensive MS measurement leads to quantification of up to about 3,000 proteins across about 21-40 IP samples. We detected and quantified almost all known interactors of MyD88, TRAF6 and NEMO. By analyzing these quantitative data, we uncovered differential recruitment of IRAK family proteins to LPS-induced signaling complexes and determined the stoichiometry of the Myddosome complex. In addition, quantitative phosphoproteomics analysis identified a number of unreported high-confidence phosphosites on the key proteins in LPS signaling pathway. Collectively, data of dynamic protein interactions and phosphorylation presented by this study could be a resource for further study of the LPS signaling pathway.
Collapse
Affiliation(s)
- Xiurong Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Daowei Yang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Fu Zhao
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Zhang-Hua Yang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Dazheng Wang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Muzhen Qiao
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yuan Fang
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Wanyun Li
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Rui Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Peng He
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yu Cong
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Chang'an Chen
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Lichen Hu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yihua Yan
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Changchuan Xie
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Yaying Wu
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Jiahuai Han
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| | - Chuan-Qi Zhong
- From the ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life Sciences, Xiamen University
| |
Collapse
|
56
|
Kovacs-Simon A, Hemsley CM, Scott AE, Prior JL, Titball RW. Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages. BMC Microbiol 2019; 19:97. [PMID: 31092204 PMCID: PMC6521459 DOI: 10.1186/s12866-019-1469-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/30/2019] [Indexed: 02/02/2023] Open
Abstract
Background Burkholderia pseudomallei is a human pathogen causing severe infections in tropical and subtropical regions and is classified as a bio-threat agent. B. thailandensis strain E264 has been proposed as less pathogenic surrogate for understanding the interactions of B. pseudomallei with host cells. Results We show that, unlike B. thailandensis strain E264, the pattern of growth of B. thailandensis strain E555 in macrophages is similar to that of B. pseudomallei. We have genome sequenced B. thailandensis strain E555 and using the annotated sequence identified genes and proteins up-regulated during infection. Changes in gene expression identified more of the known B. pseudomallei virulence factors than changes in protein levels and used together we identified 16% of the currently known B. pseudomallei virulence factors. These findings demonstrate the utility of B. thailandensis strain E555 to study virulence of B. pseudomallei. Conclusions A weakness of studies using B. thailandensis as a surrogate for B. pseudomallei is that the strains used replicate at a slower rate in infected cells. We show that the pattern of growth of B. thailandensis strain E555 in macrophages closely mirrors that of B. pseudomallei. Using this infection model we have shown that virulence factors of B. pseudomallei can be identified as genes or proteins whose expression is elevated on the infection of macrophages. This finding confirms the utility of B. thailandensis strain E555 as a surrogate for B. pseudomallei and this strain should be used for future studies on virulence mechanisms. Electronic supplementary material The online version of this article (10.1186/s12866-019-1469-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- A Kovacs-Simon
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - C M Hemsley
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - A E Scott
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - J L Prior
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.,CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - R W Titball
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| |
Collapse
|
57
|
Clark DJ, Hu Y, Schnaubelt M, Fu Y, Ponce S, Chen SY, Zhou Y, Shah P, Zhang H. Simple Tip-Based Sample Processing Method for Urinary Proteomic Analysis. Anal Chem 2019; 91:5517-5522. [PMID: 30924636 PMCID: PMC6512789 DOI: 10.1021/acs.analchem.8b05234] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mass spectrometry-based urinary proteomics is one of the most attractive strategies to discover proteins for diagnosis, prognosis, monitoring, or prediction of therapeutic responses of urological diseases involving the kidney, prostate, and bladder; however, interfering compounds found in urine necessitate sample preparation strategies that are currently not suitable for urinary proteomics in the clinical setting. Herein, we describe the C4-tip method, comprising a simple, automated strategy utilizing a reverse-phase resin tip-based format and "on-tip" digestion to examine the urine proteome. We first determined the optimal conditions for protein isolation and protease digestion on the C4-tip using the standard protein bovine fetuin. Next, we applied the C4-tip method to urinary proteomics, identifying a total of 813 protein groups using LC-MS/MS, with identified proteins from the C4-tip method displaying a similar distribution of gene ontology (GO) cellular component assignments compared to identified proteins from an ultrafiltration preparation method. Finally, we assessed the reproducibility of the C4-tip method, revealing a high Spearman correlation R-value for shared proteins identified across all tips. Together, we have shown the C4-tip method to be a simple, robust method for high-throughput analysis of the urinary proteome by mass spectrometry in the clinical setting.
Collapse
Affiliation(s)
- David J. Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Yi Fu
- The Bradley Department of Electrical and Computer Engineering Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Shao-Yung Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Yangying Zhou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Punit Shah
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| |
Collapse
|
58
|
Moritz CP, Mühlhaus T, Tenzer S, Schulenborg T, Friauf E. Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause. J Neurochem 2019; 149:582-604. [PMID: 30664243 DOI: 10.1111/jnc.14664] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 01/02/2019] [Indexed: 01/02/2023]
Abstract
Transcription, translation, and turnover of transcripts and proteins are essential for cellular function. The contribution of those factors to protein levels is under debate, as transcript levels and cognate protein levels do not necessarily correlate due to regulation of translation and protein turnover. Here we propose neuronal polarity as a third factor that is particularly evident in the CNS, leading to considerable distances between somata and axon terminals. Consequently, transcript levels may negatively correlate with cognate protein levels in CNS regions, i.e., transcript and protein levels behave reciprocally. To test this hypothesis, we performed an integrative inter-omics study and analyzed three interconnected rat auditory brainstem regions (cochlear nuclear complex, CN; superior olivary complex, SOC; inferior colliculus, IC) and the rest of the brain as a reference. We obtained transcript and protein sets in these regions of interest (ROIs) by DNA microarrays and label-free mass spectrometry, and performed principal component and correlation analyses. We found 508 transcript|protein pairs and detected poor to moderate transcript|protein correlation in all ROIs, as evidenced by coefficients of determination from 0.34 to 0.54. We identified 57-80 negatively correlating gene products in the ROIs and intensively analyzed four of them for which the correlation was poorest. Three cognate proteins (Slc6a11, Syngr1, Tppp) were synaptic and hence candidates for a negative correlation because of protein transport into axon terminals. Thus, we systematically analyzed the negatively correlating gene products. Gene ontology analyses revealed overrepresented transport/synapse-related proteins, supporting our hypothesis. We present 30 synapse/transport-related proteins with poor transcript|protein correlation. In conclusion, our analyses support that protein transport in polar cells is a third factor that influences the protein level and, thereby, the transcript|protein correlation. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* and *Open Data* because it provided all relevant information to reproduce the study in the manuscript and because it made the data publicly available. The data can be accessed at https://osf.io/ha28n/. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
Collapse
Affiliation(s)
- Christian P Moritz
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Synaptopathies and Autoantibodies, Institut NeuroMyoGène INSERM U1217/ CNRS, UMR 5310, Faculty of Medicine, University Jean Monnet, Saint-Étienne, France
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Schulenborg
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.,Division of Allergology, Paul-Ehrlich-Institut, Langen, Germany
| | - Eckhard Friauf
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
59
|
Zhu J, Garrigues L, Van den Toorn H, Stahl B, Heck AJR. Discovery and Quantification of Nonhuman Proteins in Human Milk. J Proteome Res 2019; 18:225-238. [PMID: 30489082 PMCID: PMC6326037 DOI: 10.1021/acs.jproteome.8b00550] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 01/11/2023]
Abstract
The question whether and which nonhuman peptides or proteins are present in human milk was raised many decades ago. However, due to cross-reactivity or nonspecific antibody recognition, the accuracy of detection by immunochemical methods has been a concern. Additionally, the relative low-abundance of nonhuman peptides/proteins in the complex milk sample makes them a challenging target to detect. Here, by deep proteome profiling, we detected several nonhuman peptides, which could be grouped as nonhuman proteins. We next estimated their concentration in human milk by combining data-dependent shotgun proteomics and parallel reaction monitoring. First, we fractionated human milk at the protein level and were able to detect 1577 human proteins. Additionally, we identified 109 nonhuman peptides, of which 71 were grouped into 36 nonhuman proteins. In the next step, we targeted 37 nonhuman peptides and nine of them could be repeatedly quantified in human milk samples. Peptides/proteins originating from bovine milk products were the dominant nonhuman proteins observed, notably bovine caseins (α-S1-, α-S2-, β-, κ-caseins) and β-lactoglobulin. The method we present here can be expanded to investigate more about nonhuman peptides and proteins in human milk and give a better understanding of how human milk plays a role in allergy prevention.
Collapse
Affiliation(s)
- Jing Zhu
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Luc Garrigues
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Henk Van den Toorn
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Bernd Stahl
- Danone
Nutricia Research, 3584
CT Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
60
|
Panatala R, Barbato S, Kozai T, Luo J, Kapinos LE, Lim RYH. Nuclear Pore Membrane Proteins Self-Assemble into Nanopores. Biochemistry 2019; 58:484-488. [DOI: 10.1021/acs.biochem.8b01179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Radhakrishnan Panatala
- Biozentrum and Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Suncica Barbato
- Biozentrum and Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Toshiya Kozai
- Biozentrum and Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Jinghui Luo
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Larisa E. Kapinos
- Biozentrum and Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Roderick Y. H. Lim
- Biozentrum and Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
61
|
Torres-Gutiérrez E, Pérez-Cervera Y, Camoin L, Zenteno E, Aquino-Gil MO, Lefebvre T, Cabrera-Bravo M, Reynoso-Ducoing O, Bucio-Torres MI, Salazar-Schettino PM. Identification of O-Glcnacylated Proteins in Trypanosoma cruzi. Front Endocrinol (Lausanne) 2019; 10:199. [PMID: 30984116 PMCID: PMC6449728 DOI: 10.3389/fendo.2019.00199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/11/2019] [Indexed: 01/16/2023] Open
Abstract
Originally an anthropozoonosis in the Americas, Chagas disease has spread from its previous borders through migration. It is caused by the protozoan Trypanosoma cruzi. Differences in disease severity have been attributed to a natural pleomorphism in T. cruzi. Several post-translational modifications (PTMs) have been studied in T. cruzi, but to date no work has focused on O-GlcNAcylation, a highly conserved monosaccharide-PTM of serine and threonine residues mainly found in nucleus, cytoplasm, and mitochondrion proteins. O-GlcNAcylation is thought to regulate protein function analogously to protein phosphorylation; indeed, crosstalk between both PTMs allows the cell to regulate its functions in response to nutrient levels and stress. Herein, we demonstrate O-GlcNAcylation in T. cruzi epimastigotes by three methods: by using specific antibodies against the modification in lysates and whole parasites, by click chemistry labeling, and by proteomics. In total, 1,271 putative O-GlcNAcylated proteins and six modification sequences were identified by mass spectrometry (data available via ProteomeXchange, ID PXD010285). Most of these proteins have structural and metabolic functions that are essential for parasite survival and evolution. Furthermore, O-GlcNAcylation pattern variations were observed by antibody detection under glucose deprivation and heat stress conditions, supporting their possible role in the adaptive response. Given the numerous biological processes in which O-GlcNAcylated proteins participate, its identification in T. cruzi proteins opens a new research field in the biology of Trypanosomatids, improve our understanding of infection processes and may allow us to identify new therapeutic targets.
Collapse
Affiliation(s)
- Elia Torres-Gutiérrez
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yobana Pérez-Cervera
- Centro de Investigación Facultad de Medicina-UNAM and Facultad de Odontología, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, Mexico
| | - Luc Camoin
- INSERM, Institut Paoli-Calmetes, CRCM, Marseille Protéomique, Aix-Marseille Univ, Marseille, France
| | - Edgar Zenteno
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Moyira Osny Aquino-Gil
- Centro de Investigación Facultad de Medicina-UNAM and Facultad de Odontología, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, Mexico
- Instituto Tecnológico de Oaxaca, Tecnológico Nacional de Mexico, Oaxaca, Mexico
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Lille, France
| | - Tony Lefebvre
- CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Lille, France
| | | | | | - Martha Irene Bucio-Torres
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Martha Irene Bucio-Torres
| | - Paz María Salazar-Schettino
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Paz María Salazar-Schettino
| |
Collapse
|
62
|
Mass Spectrometry-Based Biomarkers in Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:435-449. [PMID: 31347063 DOI: 10.1007/978-3-030-15950-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increases the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
Collapse
|
63
|
Chanda A, Kalita B, Patra A, Senevirathne WDST, Mukherjee AK. Proteomic analysis and antivenomics study of Western India Naja naja venom: correlation between venom composition and clinical manifestations of cobra bite in this region. Expert Rev Proteomics 2018; 16:171-184. [DOI: 10.1080/14789450.2019.1559735] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Abhishek Chanda
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Bhargab Kalita
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Aparup Patra
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Wanigasingha. D. Sandani T. Senevirathne
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
- Deptartment of Rabies and Vaccine Quality Control, Medical Research Institute, Colombo, Sri Lanka
| | - Ashis K. Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| |
Collapse
|
64
|
Buchs N, Braga-Lagache S, Uldry AC, Brodard J, Debonneville C, Reynard JS, Heller M. Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1735. [PMID: 30555495 PMCID: PMC6281998 DOI: 10.3389/fpls.2018.01735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/08/2018] [Indexed: 05/17/2023]
Abstract
Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the United States, vector transmission, and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it has yet not been possible to isolate or visualize viral particles from GRBV-infected plants, thereby hampering the development of a serological assay that would facilitate GRBV detection in grapevine. In this work, mass spectrometry approaches were applied in order to quantify GRBV in infected plants and identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in petioles was determined to be in the range of 100-900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. In leaves on the other hand, the V1 copy number per unit wet tissue weight appeared to be about six times lower than in petioles, and about 300 times lower in terms of protein concentration in the extractable protein mass, albeit these estimations could only be made with one reference peptide detectable in leaf extracts. Moreover, we found in leaf and petiole extracts of GRBV-infected plants a consistent upregulation of several enzymes involved in flavonoid biosynthesis by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for Grapevine leafroll-associated virus infection on the transcriptome level. Finally and importantly, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting-associated virus.
Collapse
Affiliation(s)
- Natasha Buchs
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Justine Brodard
- Institute for Plant Production Science, Agroscope, Nyon, Switzerland
| | | | | | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| |
Collapse
|
65
|
Prechtl RM, Janßen D, Behr J, Ludwig C, Küster B, Vogel RF, Jakob F. Sucrose-Induced Proteomic Response and Carbohydrate Utilization of Lactobacillus sakei TMW 1.411 During Dextran Formation. Front Microbiol 2018; 9:2796. [PMID: 30532743 PMCID: PMC6265474 DOI: 10.3389/fmicb.2018.02796] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/31/2018] [Indexed: 01/10/2023] Open
Abstract
Lactobacillus (L.) sakei belongs to the dominating lactic acid bacteria in indigenous meat fermentations, while diverse strains of this species have also been isolated from plant fermentations. We could recently show, that L. sakei TMW 1.411 produces a high molecular weight dextran from sucrose, indicating its potential use as a dextran forming starter culture. However, the general physiological response of L. sakei to sucrose as carbohydrate source has not been investigated yet, especially upon simultaneous dextran formation. To address this lack of knowledge, we sequenced the genome of L. sakei TMW 1.411 and performed a label-free, quantitative proteomics approach to investigate the sucrose-induced changes in the proteomic profile of this strain in comparison to its proteomic response to glucose. In total, 21 proteins were found to be differentially expressed at the applied significance criteria (FDR ≤ 0.01). Among these, 14 were associated with the carbohydrate metabolism including several enzymes, which enable sucrose and fructose uptake, as well as, their subsequent intracellular metabolization, respectively. The plasmid-encoded, extracellular dextransucrase of L. sakei TMW 1.411 was expressed at high levels irrespective of the present carbohydrate and was predominantly responsible for sucrose consumption in growth experiments using sucrose as sole carbohydrate source, while the released fructose from the dextransucrase reaction was more preferably taken up and intracellularly metabolized than sucrose. Genomic comparisons revealed, that operons coding for uptake and intracellular metabolism of sucrose and fructose are chromosomally conserved among L. sakei, while plasmid-located dextransucrase genes are present only in few strains. In accordance with these findings, all 59 different L. sakei strains of our strain collection were able to grow on sucrose as sole carbohydrate source, while eight of them exhibited a mucous phenotype on agar plates indicating dextran formation from sucrose. Our study therefore highlights the intrinsic adaption of L. sakei to plant environments, where sucrose is abundant, and provides fundamental knowledge regarding the use of L. sakei as starter culture for sucrose-based food fermentation processes with in-situ dextran formation.
Collapse
Affiliation(s)
- Roman M Prechtl
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Dorothee Janßen
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Jürgen Behr
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Bernhard Küster
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Frank Jakob
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| |
Collapse
|
66
|
Dehecq M, Decourty L, Namane A, Proux C, Kanaan J, Le Hir H, Jacquier A, Saveanu C. Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes. EMBO J 2018; 37:embj.201899278. [PMID: 30275269 DOI: 10.15252/embj.201899278] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to characterize the composition and dynamics of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Upf1-23 (Upf1, Upf2, Upf3) and Upf1-decapping Upf1-decapping contained the mRNA decapping enzyme, together with Nmd4 and Ebs1, two proteins that globally affected NMD and were critical for RNA degradation mediated by the Upf1 C-terminal helicase region. The fact that Nmd4 association with RNA was partially dependent on Upf1-23 components and the similarity between Nmd4/Ebs1 and mammalian Smg5-7 proteins suggest that NMD operates through conserved, successive Upf1-23 and Upf1-decapping complexes. This model can be extended to accommodate steps that are missing in yeast, to serve for further mechanistic studies of NMD in eukaryotes.
Collapse
Affiliation(s)
- Marine Dehecq
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Laurence Decourty
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France
| | - Caroline Proux
- Transcriptome and Epigenome, CITECH, Institut Pasteur, Paris, France
| | - Joanne Kanaan
- Expression des ARN Messagers Eucaryotes, Biology Department, CNRS UMR8197, Inserm U1024, Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
| | - Hervé Le Hir
- Expression des ARN Messagers Eucaryotes, Biology Department, CNRS UMR8197, Inserm U1024, Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
| | - Alain Jacquier
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France
| | - Cosmin Saveanu
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France
| |
Collapse
|
67
|
mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. Sci Rep 2018; 8:12502. [PMID: 30131517 PMCID: PMC6104027 DOI: 10.1038/s41598-018-30332-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/20/2018] [Indexed: 12/02/2022] Open
Abstract
Regulation of gene expression at the translational level allows rapid adaptation of cellular proteomes to quickly changing environmental conditions and is thus central for prokaryotic organisms. Small non-coding RNAs (sRNAs) have been reported to effectively orchestrate translation control in bacteria and archaea mainly by targeting mRNAs by partial base complementarity. Here we report an unprecedented mechanism how sRNAs are capable of modulating protein biosynthesis in the halophilic archaeon Haloferax volcanii. By analyzing the ribosome-associated ncRNAs (rancRNAs) under different stress conditions we identified an intergenic sRNA, termed rancRNA_s194, that is primarily expressed during exponential growth under all tested conditions. By interaction with the ribosome rancRNA_s194 inhibits peptide bond formation and protein synthesis in vitro but appears to target a specific mRNA in vivo. The respective knock-out strain shows a reduced lag phase in media containing xylose as sole carbon source and outcompetes the wildtype cells under these conditions. Mass spectrometry, polysome profiling and mRNA binding competition experiments suggest that rancRNA_s194 prevents the cstA mRNA from being efficiently translated by H. volcanii ribosomes. These findings enlarge the regulatory repertoire of archaeal sRNAs in modulating post-transcriptional gene expression.
Collapse
|
68
|
Saltzman AB, Leng M, Bhatt B, Singh P, Chan DW, Dobrolecki L, Chandrasekaran H, Choi JM, Jain A, Jung SY, Lewis MT, Ellis MJ, Malovannaya A. gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data. Mol Cell Proteomics 2018; 17:2270-2283. [PMID: 30093420 DOI: 10.1074/mcp.tir118.000850] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
In quantitative mass spectrometry, the method by which peptides are grouped into proteins can have dramatic effects on downstream analyses. Here we describe gpGrouper, an inference and quantitation algorithm that offers an alternative method for assignment of protein groups by gene locus and improves pseudo-absolute iBAQ quantitation by weighted distribution of shared peptide areas. We experimentally show that distributing shared peptide quantities based on unique peptide peak ratios improves quantitation accuracy compared with conventional winner-take-all scenarios. Furthermore, gpGrouper seamlessly handles two-species samples such as patient-derived xenografts (PDXs) without ignoring the host species or species-shared peptides. This is a critical capability for proper evaluation of proteomics data from PDX samples, where stromal infiltration varies across individual tumors. Finally, gpGrouper calculates peptide peak area (MS1) based expression estimates from multiplexed isobaric data, producing iBAQ results that are directly comparable across label-free, isotopic, and isobaric proteomics approaches.
Collapse
Affiliation(s)
- Alexander B Saltzman
- From the ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | - Mei Leng
- From the ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | - Bhoomi Bhatt
- From the ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | - Purba Singh
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030
| | - Doug W Chan
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030
| | - Lacey Dobrolecki
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030.,**Patient-Derived Xenograft and Advanced In Vivo Models Core
| | | | | | | | - Sung Y Jung
- From the ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology.,¶Mass Spectrometry Proteomics Core
| | - Michael T Lewis
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030.,‖Dan L Duncan Comprehensive Cancer Center.,**Patient-Derived Xenograft and Advanced In Vivo Models Core.,‡‡Department of Molecular and Cellular Biology
| | - Matthew J Ellis
- §Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030.,‖Dan L Duncan Comprehensive Cancer Center.,‡‡Department of Molecular and Cellular Biology
| | - Anna Malovannaya
- From the ‡Verna and Marrs McLean Department of Biochemistry and Molecular Biology; .,‡‡Department of Molecular and Cellular Biology.,¶Mass Spectrometry Proteomics Core.,‖Dan L Duncan Comprehensive Cancer Center
| |
Collapse
|
69
|
Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018; 17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Werner Liesack
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
| | | |
Collapse
|
70
|
Heissel S, Bunkenborg J, Kristiansen MP, Holmbjerg AF, Grimstrup M, Mørtz E, Kofoed T, Højrup P. Evaluation of spectral libraries and sample preparation for DIA-LC-MS analysis of host cell proteins: A case study of a bacterially expressed recombinant biopharmaceutical protein. Protein Expr Purif 2018. [DOI: 10.1016/j.pep.2018.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
71
|
Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
72
|
Lee PY, Chin SF, Low TY, Jamal R. Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. J Proteomics 2018; 187:93-105. [PMID: 29953962 DOI: 10.1016/j.jprot.2018.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.
Collapse
Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia.
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| |
Collapse
|
73
|
Ankney JA, Muneer A, Chen X. Relative and Absolute Quantitation in Mass Spectrometry-Based Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:49-77. [PMID: 29894226 DOI: 10.1146/annurev-anchem-061516-045357] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.
Collapse
Affiliation(s)
- J Astor Ankney
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Adil Muneer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
74
|
Kramer DA, Quiroga AD, Lian J, Fahlman RP, Lehner R. Fasting and refeeding induces changes in the mouse hepatic lipid droplet proteome. J Proteomics 2018; 181:213-224. [DOI: 10.1016/j.jprot.2018.04.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/10/2018] [Accepted: 04/14/2018] [Indexed: 12/29/2022]
|
75
|
Alimonti JB, Ribecco-Lutkiewicz M, Sodja C, Jezierski A, Stanimirovic DB, Liu Q, Haqqani AS, Conlan W, Bani-Yaghoub M. Zika virus crosses an in vitro human blood brain barrier model. Fluids Barriers CNS 2018; 15:15. [PMID: 29759080 PMCID: PMC5952854 DOI: 10.1186/s12987-018-0100-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Zika virus (ZIKV) is a flavivirus that is highly neurotropic causing congenital abnormalities and neurological damage to the central nervous systems (CNS). In this study, we used a human induced pluripotent stem cell (iPSC)-derived blood brain barrier (BBB) model to demonstrate that ZIKV can infect brain endothelial cells (i-BECs) without compromising the BBB barrier integrity or permeability. Although no disruption to the BBB was observed post-infection, ZIKV particles were released on the abluminal side of the BBB model and infected underlying iPSC-derived neural progenitor cells (i-NPs). AXL, a putative ZIKV cellular entry receptor, was also highly expressed in ZIKV-susceptible i-BEC and i-NPs. This iPSC-derived BBB model can help elucidate the mechanism by which ZIKV can infect BECs, cross the BBB and gain access to the CNS.
Collapse
Affiliation(s)
- Judie B. Alimonti
- Human Health Therapeutics Research Center, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON Canada
| | - Maria Ribecco-Lutkiewicz
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| | - Caroline Sodja
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| | - Anna Jezierski
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| | - Danica B. Stanimirovic
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| | - Qing Liu
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| | - Arsalan S. Haqqani
- Human Health Therapeutics Research Center, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON Canada
| | - Wayne Conlan
- Human Health Therapeutics Research Center, National Research Council of Canada, 100 Sussex Dr., Ottawa, ON Canada
| | - Mahmud Bani-Yaghoub
- Human Health Therapeutics Research Center, National Research Council of Canada, Bldg M54-1200 Montreal Rd., Ottawa, ON K1A 0R6 Canada
| |
Collapse
|
76
|
Schada von Borzyskowski L, Carrillo M, Leupold S, Glatter T, Kiefer P, Weishaupt R, Heinemann M, Erb TJ. An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metab Eng 2018; 47:423-433. [DOI: 10.1016/j.ymben.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
|
77
|
Chevreux G, Tilly N, Bihoreau N. Quantification of proteins by data independent acquisition: Performance assessment of the Hi3 methodology. Anal Biochem 2018; 549:184-187. [DOI: 10.1016/j.ab.2018.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 10/17/2022]
|
78
|
Karlsson CAQ, Järnum S, Winstedt L, Kjellman C, Björck L, Linder A, Malmström JA. Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS. Mol Cell Proteomics 2018; 17:1097-1111. [PMID: 29511047 PMCID: PMC5986240 DOI: 10.1074/mcp.ra117.000525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/16/2018] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a combined mass spectrometry-based proteomics strategy to investigate how the human proteome is transiently modified by the pathogen Streptococcus pyogenes, with a particular focus on bacterial cleavage of IgG in vivo. In invasive diseases, S. pyogenes evokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG. S. pyogenes produces IdeS, a protease cleaving IgG in the lower hinge region and we find highly effective IdeS-cleavage of IgG in samples from local IgG poor microenvironments. The results show that IdeS contributes to the adaptation of S. pyogenes to its normal ecological niches. Additionally, the work identifies novel clinical opportunities for in vivo pathogen detection.
Collapse
Affiliation(s)
- Christofer A Q Karlsson
- From the ‡Lund University, Division of Infection Medicine, Department of Clinical Sciences, Solvegatan 19, BMC, Lund, 221 84 Lund, Sweden
| | - Sofia Järnum
- §Hansa Medical AB, Scheelevägen 22, 223 63 Lund, Sweden
| | - Lena Winstedt
- §Hansa Medical AB, Scheelevägen 22, 223 63 Lund, Sweden
| | | | - Lars Björck
- From the ‡Lund University, Division of Infection Medicine, Department of Clinical Sciences, Solvegatan 19, BMC, Lund, 221 84 Lund, Sweden
| | - Adam Linder
- From the ‡Lund University, Division of Infection Medicine, Department of Clinical Sciences, Solvegatan 19, BMC, Lund, 221 84 Lund, Sweden
| | - Johan A Malmström
- From the ‡Lund University, Division of Infection Medicine, Department of Clinical Sciences, Solvegatan 19, BMC, Lund, 221 84 Lund, Sweden;
| |
Collapse
|
79
|
Abstract
A comprehensive reference map of protein abundances in budding yeast is generated by combining the 21 largest quantitative proteome datasets currently available for this model organism.
Collapse
|
80
|
Ho B, Baryshnikova A, Brown GW. Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. Cell Syst 2018; 6:192-205.e3. [PMID: 29361465 DOI: 10.1016/j.cels.2017.12.004] [Citation(s) in RCA: 252] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/10/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022]
Abstract
Protein activity is the ultimate arbiter of function in most cellular pathways, and protein concentration is fundamentally connected to protein action. While the proteome of yeast has been subjected to the most comprehensive analysis of any eukaryote, existing datasets are difficult to compare, and there is no consensus abundance value for each protein. We evaluated 21 quantitative analyses of the S. cerevisiae proteome, normalizing and converting all measurements of protein abundance into the intuitive measurement of absolute molecules per cell. We estimate the cellular abundance of 92% of the proteins in the yeast proteome and assess the variation in each abundance measurement. Using our protein abundance dataset, we find that a global response to diverse environmental stresses is not detected at the level of protein abundance, we find that protein tags have only a modest effect on protein abundance, and we identify proteins that are differentially regulated at the mRNA abundance, mRNA translation, and protein abundance levels.
Collapse
Affiliation(s)
- Brandon Ho
- Department of Biochemistry and Donnelly Center, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Grant W Brown
- Department of Biochemistry and Donnelly Center, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
81
|
Li JJ, Chew GL, Biggin MD. Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res 2017; 45:11821-11836. [PMID: 29040683 PMCID: PMC5714229 DOI: 10.1093/nar/gkx898] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/25/2017] [Indexed: 11/17/2022] Open
Abstract
Translation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an ‘amplification exponent’. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels. We show that in Saccharomyces cerevisiae TRmD represents ∼20% of the variance in translation and directs an amplification exponent of 1.20 with a 95% confidence interval [1.14, 1.26]. TRmIND constitutes the remaining ∼80% of the variance in translation and explains ∼5% of the variance in protein expression. We also find that TRmD and TRmIND are preferentially determined by different mRNA sequence features: TRmIND by the length of the open reading frame and TRmD both by a ∼60 nucleotide element that spans the initiating AUG and by codon and amino acid frequency. Our work provides more appropriate estimates of translational control and implies that TRmIND is under different evolutionary selective pressures than TRmD.
Collapse
Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Guo-Liang Chew
- Computational Biology Program, Public Health Sciences and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark D Biggin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94708, USA
| |
Collapse
|
82
|
Klotz C, O'Flaherty S, Goh YJ, Barrangou R. Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics. Front Microbiol 2017; 8:2174. [PMID: 29167661 PMCID: PMC5682318 DOI: 10.3389/fmicb.2017.02174] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/23/2017] [Indexed: 01/17/2023] Open
Abstract
Bacterial surface-layers (S-layers) are semi-porous crystalline arrays that self-assemble to form the outermost layer of some cell envelopes. S-layers have been shown to act as scaffolding structures for the display of auxiliary proteins externally. These S-layer associated proteins have recently gained attention in probiotics due to their direct physical contact with the intestinal mucosa and potential role in cell proliferation, adhesion, and immunomodulation. A number of studies have attempted to catalog the S-layer associated proteome of Lactobacillus acidophilus NCFM under a single condition. However, due to the versatility of the cell surface, we chose to employ a multiplexing-based approach with the intention of accurately contrasting multiple conditions. In this study, a previously described lithium chloride isolation protocol was used to release proteins bound to the L. acidophilus S-layer during logarithmic and early stationary growth phases. Protein quantification values were obtained via TMT (tandem mass tag) labeling combined with a triple-stage mass spectrometry (MS3) method. Results showed significant growth stage-dependent alterations to the surface-associated proteome while simultaneously highlighting the sensitivity and reproducibility of the technology. Thus, this study establishes a framework for quantifying condition-dependent changes to cell surface proteins that can easily be applied to other S-layer forming bacteria.
Collapse
Affiliation(s)
- Courtney Klotz
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Sarah O'Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States.,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
83
|
Liao Y, Weber D, Xu W, Durbin-Johnson BP, Phinney BS, Lönnerdal B. Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation. J Proteome Res 2017; 16:4113-4121. [PMID: 28925267 DOI: 10.1021/acs.jproteome.7b00486] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of α-casein, β-casein, and κ-casein in human milk samples (n = 88) collected between day 1 and day 360 postpartum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37 ± 3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (α-), 0.04 to 4.42 g/L (β-), and 0.10 to 1.72 g/L (α-), with β-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, β-casein, κ-casein, total casein, and a significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.
Collapse
Affiliation(s)
- Yalin Liao
- Department of Nutrition, University of California , Davis, 95616, United States.,School of Veterinary & Life Sciences, Murdoch University , Murdoch, WA 6150, Australia
| | - Darren Weber
- Genome Center Proteomics Core Facility, University of California , Davis, 95616, United States
| | - Wei Xu
- School of Veterinary & Life Sciences, Murdoch University , Murdoch, WA 6150, Australia
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California , Davis, 95616, United States
| | - Brett S Phinney
- Genome Center Proteomics Core Facility, University of California , Davis, 95616, United States
| | - Bo Lönnerdal
- Department of Nutrition, University of California , Davis, 95616, United States
| |
Collapse
|
84
|
Kim M, Eetemadi A, Tagkopoulos I. DeepPep: Deep proteome inference from peptide profiles. PLoS Comput Biol 2017; 13:e1005661. [PMID: 28873403 PMCID: PMC5600403 DOI: 10.1371/journal.pcbi.1005661] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 09/15/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
Protein inference, the identification of the protein set that is the origin of a given peptide profile, is a fundamental challenge in proteomics. We present DeepPep, a deep-convolutional neural network framework that predicts the protein set from a proteomics mixture, given the sequence universe of possible proteins and a target peptide profile. In its core, DeepPep quantifies the change in probabilistic score of peptide-spectrum matches in the presence or absence of a specific protein, hence selecting as candidate proteins with the largest impact to the peptide profile. Application of the method across datasets argues for its competitive predictive ability (AUC of 0.80±0.18, AUPR of 0.84±0.28) in inferring proteins without need of peptide detectability on which the most competitive methods rely. We find that the convolutional neural network architecture outperforms the traditional artificial neural network architectures without convolution layers in protein inference. We expect that similar deep learning architectures that allow learning nonlinear patterns can be further extended to problems in metagenome profiling and cell type inference. The source code of DeepPep and the benchmark datasets used in this study are available at https://deeppep.github.io/DeepPep/. The accurate identification of proteins in a proteomics sample, called the protein inference problem, is a fundamental challenge in biomedical sciences. Current approaches are based on applications of traditional neural networks, linear optimization and Bayesian techniques. We here present DeepPep, a deep-convolutional neural network framework that predicts the protein set from a standard proteomics mixture, given all protein sequences and a peptide profile. Comparison to leading methods shows that DeepPep has most robust performance with various instruments and datasets. Our results provide evidence that using sequence-level location information of a peptide in the context of proteome sequence can result in more accurate and robust protein inference. We conclude that Deep Learning on protein sequence leads to superior platforms for protein inference that can be further refined with additional features and extended for far reaching applications.
Collapse
Affiliation(s)
- Minseung Kim
- Department of Computer Science, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ameen Eetemadi
- Department of Computer Science, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ilias Tagkopoulos
- Department of Computer Science, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
- * E-mail:
| |
Collapse
|
85
|
He X, Cao X, He Y, Bhattarai K, Rogers J, Hartson S, Jiang H. Hemolymph proteins of Anopheles gambiae larvae infected by Escherichia coli. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 74:110-124. [PMID: 28431895 PMCID: PMC5531190 DOI: 10.1016/j.dci.2017.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 06/07/2023]
Abstract
Anopheles gambiae is a major vector of human malaria and its immune system in part determines the fate of ingested parasites. Proteins, hemocytes and fat body in hemolymph are critical components of this system, mediating both humoral and cellular defenses. Here we assessed differences in the hemolymph proteomes of water- and E. coli-pricked mosquito larvae by a gel-LC-MS approach. Among the 1756 proteins identified, 603 contained a signal peptide but accounted for two-third of the total protein amount on the quantitative basis. The sequence homology search indicated that 233 of the 1756 may be related to defense. In general, we did not detect substantial differences between the control and induced plasma samples in terms of protein numbers or levels. Protein distributions in the gel slices suggested post-translational modifications (e.g. proteolysis) and formation of serpin-protease complexes and high Mr immune complexes. Based on the twenty-five most abundant proteins, we further suggest that major functions of the larval hemolymph are storage, transport, and immunity. In summary, this study provided first data on constitution, levels, and possible functions of hemolymph proteins in the mosquito larvae, reflecting complex changes occurring in the fight against E. coli infection.
Collapse
Affiliation(s)
- Xuesong He
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA; Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yan He
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Krishna Bhattarai
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA; Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steve Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA; Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| |
Collapse
|
86
|
Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T. Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma. Proteomics Clin Appl 2017. [PMID: 28626882 DOI: 10.1002/prca.201700014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is the most common primary malignant liver tumor and a leading cause of cancer-related deaths worldwide. Cirrhosis induced by hepatitis-C virus (HCV) infection is the most critical risk factor for HCC. However, the mechanism of HCV-induced carcinogenesis is not fully understood. Plasma microparticles (PMP) contribute to numerous physiological and pathological processes and contain proteins whose composition correlates to the respective pathophysiological conditions. EXPERIMENTAL DESIGN We analyzed PMP from 22 HCV-induced cirrhosis patients, 16 HCV-positive HCC patients with underlying cirrhosis and 18 healthy controls. PMP were isolated using ultracentrifugation and analyzed via label-free LC-MS/MS. RESULTS We identified 840 protein groups and quantified 507 proteins. 159 proteins were found differentially abundant between the three experimental groups. PMP in both disease entities displayed remarkable differences in the proteome composition compared to healthy controls. Conversely, the proteome difference between both diseases was minimal. GO analysis revealed that PMP isolated from both diseases were significantly enriched in proteins involved in complement activation, while endopeptidase activity was downregulated exclusively in HCC patients. CONCLUSION This study reports for the first time a quantitative proteome analysis for PMP from patients with HCV-induced cirrhosis and HCC. Data are available via ProteomeXchange with identifier PXD005777.
Collapse
Affiliation(s)
- Raghda Saad Zaghloul Taleb
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.,Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Pacint Moez
- Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Doreen Younan
- Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Matthias Tenbusch
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| |
Collapse
|
87
|
In-depth PtdIns(3,4,5)P 3 signalosome analysis identifies DAPP1 as a negative regulator of GPVI-driven platelet function. Blood Adv 2017; 1:918-932. [PMID: 29242851 DOI: 10.1182/bloodadvances.2017005173] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The class I phosphoinositide 3-kinase (PI3K) isoforms play important roles in platelet priming, activation, and stable thrombus formation. Class I PI3Ks predominantly regulate cell function through their catalytic product, the signaling phospholipid phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3], which coordinates the localization and/or activity of a diverse range of binding proteins. Notably, the complete repertoire of these class I PI3K effectors in platelets remains unknown, limiting mechanistic understanding of class I PI3K-mediated control of platelet function. We measured robust agonist-driven PtdIns (3,4,5)P3 generation in human platelets by lipidomic mass spectrometry (MS), and then used affinity-capture coupled to high-resolution proteomic MS to identify the targets of PtdIns (3,4,5)P3 in these cells. We reveal for the first time a diverse platelet PtdIns(3,4,5)P3 interactome, including kinases, signaling adaptors, and regulators of small GTPases, many of which are previously uncharacterized in this cell type. Of these, we show dual adaptor for phosphotyrosine and 3-phosphoinositides (DAPP1) to be regulated by Src-family kinases and PI3K, while platelets from DAPP1-deficient mice display enhanced thrombus formation on collagen in vitro. This was associated with enhanced platelet α/δ granule secretion and αIIbβ3 integrin activation downstream of the collagen receptor glycoprotein VI. Thus, we present the first comprehensive analysis of the PtdIns(3,4,5)P3 signalosome of human platelets and identify DAPP1 as a novel negative regulator of platelet function. This work provides important new insights into how class I PI3Ks shape platelet function.
Collapse
|
88
|
Quantitative proteomics: challenges and opportunities in basic and applied research. Nat Protoc 2017; 12:1289-1294. [DOI: 10.1038/nprot.2017.040] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
89
|
Bauernfeind AL, Babbitt CC. The predictive nature of transcript expression levels on protein expression in adult human brain. BMC Genomics 2017; 18:322. [PMID: 28438116 PMCID: PMC5402646 DOI: 10.1186/s12864-017-3674-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/01/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. RESULTS Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell. Although most categories of transcripts have extremely weak predictive value for the expression of their associated proteins (R2 values of < 10%), transcripts coding for protein kinases and membrane-associated proteins, including those that are part of receptors or ion transporters, are among those that are most predictive of downstream protein expression levels. CONCLUSIONS The predictive value of transcript expression for corresponding proteins is variable in human brain samples, reflecting the complex regulation of protein expression. However, we found that transcriptomic analyses are appropriate for assessing the expression levels of certain classes of proteins, including those that modify proteins, such as kinases and phosphatases, regulate metabolic and synaptic activity, or are associated with a cellular membrane. These findings can be used to guide the interpretation of gene expression results from primate brain samples.
Collapse
Affiliation(s)
- Amy L Bauernfeind
- Department of Neuroscience, Washington University Medical School, St. Louis, MO, 63110, USA. .,Department of Anthropology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| |
Collapse
|
90
|
Goeminne LJE, Gevaert K, Clement L. Experimental design and data-analysis in label-free quantitative LC/MS proteomics: A tutorial with MSqRob. J Proteomics 2017; 171:23-36. [PMID: 28391044 DOI: 10.1016/j.jprot.2017.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 12/14/2022]
Abstract
Label-free shotgun proteomics is routinely used to assess proteomes. However, extracting relevant information from the massive amounts of generated data remains difficult. This tutorial provides a strong foundation on analysis of quantitative proteomics data. We provide key statistical concepts that help researchers to design proteomics experiments and we showcase how to analyze quantitative proteomics data using our recent free and open-source R package MSqRob, which was developed to implement the peptide-level robust ridge regression method for relative protein quantification described by Goeminne et al. MSqRob can handle virtually any experimental proteomics design and outputs proteins ordered by statistical significance. Moreover, its graphical user interface and interactive diagnostic plots provide easy inspection and also detection of anomalies in the data and flaws in the data analysis, allowing deeper assessment of the validity of results and a critical review of the experimental design. Our tutorial discusses interactive preprocessing, data analysis and visualization of label-free MS-based quantitative proteomics experiments with simple and more complex designs. We provide well-documented scripts to run analyses in bash mode on GitHub, enabling the integration of MSqRob in automated pipelines on cluster environments (https://github.com/statOmics/MSqRob). SIGNIFICANCE The concepts outlined in this tutorial aid in designing better experiments and analyzing the resulting data more appropriately. The two case studies using the MSqRob graphical user interface will contribute to a wider adaptation of advanced peptide-based models, resulting in higher quality data analysis workflows and more reproducible results in the proteomics community. We also provide well-documented scripts for experienced users that aim at automating MSqRob on cluster environments.
Collapse
Affiliation(s)
- Ludger J E Goeminne
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Belgium; Department of Biochemistry, Ghent University, Belgium; Bioinformatics Institute Ghent, Ghent University, Belgium.
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, VIB, Belgium; Department of Biochemistry, Ghent University, Belgium; Bioinformatics Institute Ghent, Ghent University, Belgium.
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium; Bioinformatics Institute Ghent, Ghent University, Belgium.
| |
Collapse
|
91
|
Cho JY, Lee HJ, Jeong SK, Paik YK. Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification. J Proteome Res 2017; 16:4435-4445. [DOI: 10.1021/acs.jproteome.6b01019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
92
|
Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W. Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance. J Proteome Res 2017; 16:1410-1424. [PMID: 28217993 DOI: 10.1021/acs.jproteome.6b00645] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the intersample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant, and Progenesis QIP, was benchmarked using their default parameters and some modified settings. Beyond this, the intersample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession. The technical component was considerably higher than the biological intersample variability, suggesting an effect on the degree and validity of reported biological changes in protein abundance. Surprisingly, the biological variability, protein abundance estimates, and protein fold changes were recorded differently by the software used to quantify the proteins, warranting caution in the comparison of discovery proteomics results. As expected, ∼99% of the proteome was invariant in the isogenic plants in the absence of environmental factors; however, few proteins showed substantial quantitative variability. This naturally occurring variation between individual organisms can have an impact on the causality of reported protein fold changes.
Collapse
Affiliation(s)
- Mhd Rami Al Shweiki
- Research Group Proteome Analytics, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany
| | - Susann Mönchgesang
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany
| | - Petra Majovsky
- Research Group Proteome Analytics, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany
| | - Domenika Thieme
- Research Group Proteome Analytics, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany
| | - Diana Trutschel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen , Stockumer Straße. 12, 58453 Witten, Germany.,Martin-Luther-University Halle-Wittenberg , Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Research Group Proteome Analytics, Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle (Saale), Germany
| |
Collapse
|
93
|
Simicevic J, Deplancke B. Transcription factor proteomics-Tools, applications, and challenges. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600317] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/18/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Jovan Simicevic
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics; Lausanne Switzerland
- LimmaTech Biologics AG; Schlieren Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics; Lausanne Switzerland
| |
Collapse
|
94
|
Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Bréhélin C. Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions. FRONTIERS IN PLANT SCIENCE 2017; 8:894. [PMID: 28611809 PMCID: PMC5447075 DOI: 10.3389/fpls.2017.00894] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/12/2017] [Indexed: 05/18/2023]
Abstract
Lipid droplets (LDs) are cell compartments specialized for oil storage. Although their role and biogenesis are relatively well documented in seeds, little is known about their composition, structure and function in senescing leaves where they also accumulate. Here, we used a label free quantitative mass spectrometry approach to define the LD proteome of aging Arabidopsis leaves. We found that its composition is highly different from that of seed/cotyledon and identified 28 proteins including 9 enzymes of the secondary metabolism pathways involved in plant defense response. With the exception of the TRIGALACTOSYLDIACYLGLYCEROL2 protein, we did not identify enzymes implicated in lipid metabolism, suggesting that growth of leaf LDs does not occur by local lipid synthesis but rather through contact sites with the endoplasmic reticulum (ER) or other membranes. The two most abundant proteins of the leaf LDs are the CALEOSIN3 and the SMALL RUBBER PARTICLE1 (AtSRP1); both proteins have structural functions and participate in plant response to stress. CALEOSIN3 and AtSRP1 are part of larger protein families, yet no other members were enriched in the LD proteome suggesting a specific role of both proteins in aging leaves. We thus examined the function of AtSRP1 at this developmental stage and found that AtSRP1 modulates the expression of CALEOSIN3 in aging leaves. Furthermore, AtSRP1 overexpression induces the accumulation of triacylglycerol with an unusual composition compared to wild-type. We demonstrate that, although AtSRP1 expression is naturally increased in wild type senescing leaves, its overexpression in senescent transgenic lines induces an over-accumulation of LDs organized in clusters at restricted sites of the ER. Conversely, atsrp1 knock-down mutants displayed fewer but larger LDs. Together our results reveal that the abundancy of AtSRP1 regulates the neo-formation of LDs during senescence. Using electron tomography, we further provide evidence that LDs in leaves share tenuous physical continuity as well as numerous contact sites with the ER membrane. Thus, our data suggest that leaf LDs are functionally distinct from seed LDs and that their biogenesis is strictly controlled by AtSRP1 at restricted sites of the ER.
Collapse
Affiliation(s)
- Lysiane Brocard
- Plant Imaging Platform, Bordeaux Imaging Center, UMS 3420 Centre National de la Recherche Scientifique, US4 Institut National de la Santé et de la Recherche Médicale, University of BordeauxBordeaux, France
| | - Françoise Immel
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Denis Coulon
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
- Bordeaux INPTalence, France
| | - Nicolas Esnay
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Karine Tuphile
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Stéphanie Pascal
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Stéphane Claverol
- Proteome Platform, Functional Genomic Center of Bordeaux, University of BordeauxBordeaux, France
| | - Laëtitia Fouillen
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Jean-Jacques Bessoule
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
| | - Claire Bréhélin
- Laboratory of Membrane Biogenesis, Centre National de la Recherche Scientifique, UMR 5200Villenave d'Ornon, France
- Laboratory of Membrane Biogenesis, University of Bordeaux, UMR 5200Villenave d'Ornon, France
- *Correspondence: Claire Bréhélin
| |
Collapse
|
95
|
Wiśniewski JR. Label-Free and Standard-Free Absolute Quantitative Proteomics Using the "Total Protein" and "Proteomic Ruler" Approaches. Methods Enzymol 2016; 585:49-60. [PMID: 28109442 DOI: 10.1016/bs.mie.2016.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample. The method offers an easy way to quantify thousands of protein per sample. A related method, the "Proteomic Ruler," enables conversion of the protein abundance data calculated by TPA to compute numbers of protein copies per cell. TPA and the Proteomic Ruler are powerful tools for studying dynamics of cell architecture.
Collapse
Affiliation(s)
- J R Wiśniewski
- Biochemical Proteomics Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
96
|
Sialana FJ, Gulyassy P, Májek P, Sjöstedt E, Kis V, Müller AC, Rudashevskaya EL, Mulder J, Bennett KL, Lubec G. Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels. Proteomics 2016; 16:2911-2920. [DOI: 10.1002/pmic.201600234] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/26/2016] [Accepted: 10/17/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Fernando J. Sialana
- Department of Pharmaceutical Chemistry; University of Vienna; Vienna Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Peter Gulyassy
- Laboratory of Proteomics; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Evelina Sjöstedt
- Science for Life Laboratory; School of Biotechnology; KTH-Royal Institute of Technology; Stockholm Sweden
- Science for Life Laboratory; Department of Immunology; Genetics and Pathology; Uppsala University; Uppsala Sweden
| | - Viktor Kis
- Department of Anatomy; Cell and Developmental Biology; Eötvös Loránd University; Budapest Hungary
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | | | - Jan Mulder
- Science for Life Laboratory; Department of Neuroscience; Uppsala University; Uppsala Sweden
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry; University of Vienna; Vienna Austria
| |
Collapse
|
97
|
Laursen T, Borch J, Knudsen C, Bavishi K, Torta F, Martens HJ, Silvestro D, Hatzakis NS, Wenk MR, Dafforn TR, Olsen CE, Motawia MS, Hamberger B, Møller BL, Bassard JE. Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum. Science 2016; 354:890-893. [PMID: 27856908 DOI: 10.1126/science.aag2347] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2023]
Abstract
Metabolic highways may be orchestrated by the assembly of sequential enzymes into protein complexes, or metabolons, to facilitate efficient channeling of intermediates and to prevent undesired metabolic cross-talk while maintaining metabolic flexibility. Here we report the isolation of the dynamic metabolon that catalyzes the formation of the cyanogenic glucoside dhurrin, a defense compound produced in sorghum plants. The metabolon was reconstituted in liposomes, which demonstrated the importance of membrane surface charge and the presence of the glucosyltransferase for metabolic channeling. We used in planta fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy to study functional and structural characteristics of the metabolon. Understanding the regulation of biosynthetic metabolons offers opportunities to optimize synthetic biology approaches for efficient production of high-value products in heterologous hosts.
Collapse
Affiliation(s)
- Tomas Laursen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Jonas Borch
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Center For Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Helle Juel Martens
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Daniele Silvestro
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Nikos S Hatzakis
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- Department of Chemistry, Nano-Science Center, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Business, Energy and Industrial Strategy, Her Majesty's Government, UK
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Carlsberg Research Laboratory, DK-1799 Copenhagen V, Denmark
| | - Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- bioSYNergy, Center for Synthetic Biology, DK-1871 Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| |
Collapse
|
98
|
Edfors F, Danielsson F, Hallström BM, Käll L, Lundberg E, Pontén F, Forsström B, Uhlén M. Gene-specific correlation of RNA and protein levels in human cells and tissues. Mol Syst Biol 2016; 12:883. [PMID: 27951527 PMCID: PMC5081484 DOI: 10.15252/msb.20167144] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/05/2016] [Accepted: 09/15/2016] [Indexed: 02/02/2023] Open
Abstract
An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.
Collapse
Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Frida Danielsson
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| |
Collapse
|
99
|
Braga-Lagache S, Buchs N, Iacovache MI, Zuber B, Jackson CB, Heller M. Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins. Mol Cell Proteomics 2016; 15:3640-3652. [PMID: 27738094 DOI: 10.1074/mcp.m116.060491] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 10/04/2016] [Indexed: 11/06/2022] Open
Abstract
Cells of the vascular system release spherical vesicles, called microparticles, in the size range of 0.1-1 μm induced by a variety of stress factors resulting in variable concentrations between health and disease. Furthermore, microparticles have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today's most used analytical technology for microparticle characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past.We propose the use of nano-liquid chromatography two-stage mass spectrometry as a nonbiased tool for quantitative MP proteome analysis.For this, we developed an improved microparticle isolation protocol and quantified the microparticle protein composition of twelve healthy volunteers with a label-free, data-dependent and independent proteomics approach on a quadrupole orbitrap instrument.Using aliquots of 250 μl platelet-free plasma from one individual donor, we achieved excellent reproducibility with an interassay coefficient of variation of 2.7 ± 1.7% (mean ± 1 standard deviation) on individual peptide intensities across 27 acquisitions performed over a period of 3.5 months. We show that the microparticle proteome between twelve healthy volunteers were remarkably similar, and that it is clearly distinguishable from whole cell and platelet lysates. We propose the use of the proteome profile shown in this work as a quality criterion for microparticle purity in proteomics studies. Furthermore, one freeze thaw cycle damaged the microparticle integrity, articulated by a loss of cytoplasm proteins, encompassing a specific set of proteins involved in regulating dynamic structures of the cytoskeleton, and thrombin activation leading to MP clotting. On the other hand, plasma membrane protein composition was unaffected. Finally, we show that multiplexed data-independent acquisition can be used for relative quantification of target proteins using Skyline software. Mass spectrometry data are available via ProteomeXchange (identifier PXD003935) and panoramaweb.org (https://panoramaweb.org/labkey/N1OHMk.url).
Collapse
Affiliation(s)
| | | | | | - Benoît Zuber
- §Experimental Morphology at the Institute of Anatomy, and
| | | | | |
Collapse
|
100
|
Bauer M, Cubizolles F, Schmidt A, Nigg EA. Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. EMBO J 2016; 35:2152-2166. [PMID: 27539480 PMCID: PMC5048348 DOI: 10.15252/embj.201694462] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022] Open
Abstract
Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas-6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosomes is presently known. Here, we have used two complementary approaches, targeted proteomics and EGFP-tagging of centrosomal proteins at endogenous loci, to measure protein abundance in cultured human cells and purified centrosomes. Our results provide a first assessment of the absolute and relative amounts of major components of the human centrosome. Specifically, they predict that human centriolar cartwheels comprise up to 16 stacked hubs and 1 molecule of STIL for every dimer of Sas-6. This type of quantitative information will help guide future studies of the molecular basis of centrosome assembly and function.
Collapse
Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|