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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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2
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Giudice G, Chen H, Koutsandreas T, Petsalaki E. phuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets. Mol Cell Proteomics 2024; 23:100771. [PMID: 38642805 PMCID: PMC11134849 DOI: 10.1016/j.mcpro.2024.100771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024] Open
Abstract
Signaling networks are critical for virtually all cell functions. Our current knowledge of cell signaling has been summarized in signaling pathway databases, which, while useful, are highly biased toward well-studied processes, and do not capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signaling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. While progress in methods to extract active signaling signatures from such data has been made, there are still limitations with respect to balancing bias and interpretability. Here we present phuEGO, which combines up-to-three-layer network propagation with ego network decomposition to provide small networks comprising active functional signaling modules. PhuEGO boosts the signal-to-noise ratio from global phosphoproteomics datasets, enriches the resulting networks for functional phosphosites and allows the improved comparison and integration across datasets. We applied phuEGO to five phosphoproteomics data sets from cell lines collected upon infection with SARS CoV2. PhuEGO was better able to identify common active functions across datasets and to point to a subnetwork enriched for known COVID-19 targets. Overall, phuEGO provides a flexible tool to the community for the improved functional interpretation of global phosphoproteomics datasets.
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Affiliation(s)
- Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Haoqi Chen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Thodoris Koutsandreas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom.
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3
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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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5
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Morretta E, Capuano A, D’Urso G, Voli A, Mozzicafreddo M, Di Gaetano S, Capasso D, Sala M, Scala MC, Campiglia P, Piccialli V, Casapullo A. Identification of Mortalin as the Main Interactor of Mycalin A, a Poly-Brominated C-15 Acetogenin Sponge Metabolite, by MS-Based Proteomics. Mar Drugs 2024; 22:52. [PMID: 38393023 PMCID: PMC10890321 DOI: 10.3390/md22020052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Mycalin A (MA) is a polybrominated C-15 acetogenin isolated from the marine sponge Mycale rotalis. Since this substance displays a strong antiproliferative bioactivity towards some tumour cells, we have now directed our studies towards the elucidation of the MA interactome through functional proteomic approaches, (DARTS and t-LIP-MS). DARTS experiments were performed on Hela cell lysates with the purpose of identifying MA main target protein(s); t-LiP-MS was then applied for an in-depth investigation of the MA-target protein interaction. Both these techniques exploit limited proteolysis coupled with MS analysis. To corroborate LiP data, molecular docking studies were performed on the complexes. Finally, biological and SPR analysis were conducted to explore the effect of the binding. Mortalin (GRP75) was identified as the MA's main interactor. This protein belongs to the Hsp70 family and has garnered significant attention due to its involvement in certain forms of cancer. Specifically, its overexpression in cancer cells appears to hinder the pro-apoptotic function of p53, one of its client proteins, because it becomes sequestered in the cytoplasm. Our research, therefore, has been focused on the possibility that MA might prevent this sequestration, promoting the re-localization of p53 to the nucleus and facilitating the apoptosis of tumor cells.
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Affiliation(s)
- Elva Morretta
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Alessandra Capuano
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Italy
| | - Gilda D’Urso
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Italy
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Domenica Capasso
- Department of Physics, Ettore Pancini, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy;
| | - Marina Sala
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Maria Carmina Scala
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
| | - Vincenzo Piccialli
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Agostino Casapullo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (E.M.); (A.C.); (G.D.); (A.V.); (M.S.); (M.C.S.); (P.C.)
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Goto S, Yoshida Y, Hosojima M, Kuwahara S, Kabasawa H, Aoki H, Iida T, Sawada R, Ugamura D, Yoshizawa Y, Takemoto K, Komochi K, Kobayashi R, Kaseda R, Yaoita E, Nagatoishi S, Narita I, Tsumoto K, Saito A. Megalin is involved in angiotensinogen-induced, angiotensin II-mediated ERK1/2 signaling to activate Na + -H + exchanger 3 in proximal tubules. J Hypertens 2023; 41:1831-1843. [PMID: 37682076 DOI: 10.1097/hjh.0000000000003555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
BACKGROUND Kidney angiotensin (Ang) II is produced mainly from liver-derived, glomerular-filtered angiotensinogen (AGT). Podocyte injury has been reported to increase the kidney Ang II content and induce Na + retention depending on the function of megalin, a proximal tubular endocytosis receptor. However, how megalin regulates the renal content and action of Ang II remains elusive. METHODS We used a mass spectrometry-based, parallel reaction-monitoring assay to quantitate Ang II in plasma, urine, and kidney homogenate of kidney-specific conditional megalin knockout (MegKO) and control (Ctl) mice. We also evaluated the pathophysiological changes in both mouse genotypes under the basal condition and under the condition of increased glomerular filtration of AGT induced by administration of recombinant mouse AGT (rec-mAGT). RESULTS Under the basal condition, plasma and kidney Ang II levels were comparable in the two mouse groups. Ang II was detected abundantly in fresh spot urine in conditional MegKO mice. Megalin was also found to mediate the uptake of intravenously administered fluorescent Ang II by PTECs. Administration of rec-mAGT increased kidney Ang II, exerted renal extracellular signal-regulated kinase 1/2 (ERK1/2) signaling, activated proximal tubular Na + -H + exchanger 3 (NHE3), and decreased urinary Na + excretion in Ctl mice, whereas these changes were suppressed but urinary Ang II was increased in conditional MegKO mice. CONCLUSION Increased glomerular filtration of AGT is likely to augment Ang II production in the proximal tubular lumen. Thus, megalin-dependent Ang II uptake should be involved in the ERK1/2 signaling that activates proximal tubular NHE3 in vivo , thereby causing Na + retention.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ryohei Kaseda
- Department of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata
| | | | | | - Ichiei Narita
- Department of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata
| | - Kouhei Tsumoto
- The Institute of Medical Science and Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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7
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Weber M, Sogues A, Yus E, Burgos R, Gallo C, Martínez S, Lluch‐Senar M, Serrano L. Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium. Mol Syst Biol 2023; 19:e11301. [PMID: 37642167 PMCID: PMC10568206 DOI: 10.15252/msb.202211301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.
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Affiliation(s)
- Marc Weber
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Adrià Sogues
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Eva Yus
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Raul Burgos
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Sira Martínez
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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8
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Cosarderelioglu C, Kreimer S, Plaza‐Rodriguez AI, Iglesias PA, Talbot CC, Siragy HM, Carey RM, Ubaida‐Mohien C, O'Rourke B, Ferrucci L, Bennett DA, Walston J, Abadir P. Decoding Angiotensin Receptors: TOMAHAQ-Based Detection and Quantification of Angiotensin Type-1 and Type-2 Receptors. J Am Heart Assoc 2023; 12:e030791. [PMID: 37681524 PMCID: PMC10547273 DOI: 10.1161/jaha.123.030791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023]
Abstract
Background The renin-angiotensin system plays a crucial role in human physiology, and its main hormone, angiotensin, activates 2 G-protein-coupled receptors, the angiotensin type-1 and type-2 receptors, in almost every organ. However, controversy exists about the location, distribution, and expression levels of these receptors. Concerns have been raised over the low sensitivity, low specificity, and large variability between lots of commercially available antibodies for angiotensin type-1 and type-2 receptors, which makes it difficult to reconciliate results of different studies. Here, we describe the first non-antibody-based sensitive and specific targeted quantitative mass spectrometry assay for angiotensin receptors. Methods and Results Using a technique that allows targeted analysis of multiple peptides across multiple samples in a single mass spectrometry analysis, known as TOMAHAQ (triggered by offset, multiplexed, accurate mass, high resolution, and absolute quantification), we have identified and validated specific human tryptic peptides that permit identification and quantification of angiotensin type-1 and type-2 receptors in biological samples. Several peptide sequences are conserved in rodents, making these mass spectrometry assays amenable to both preclinical and clinical studies. We have used this method to quantify angiotensin type-1 and type-2 receptors in postmortem frontal cortex samples of older adults (n=28) with Alzheimer dementia. We correlated levels of angiotensin receptors to biomarkers classically linked to renin-angiotensin system activation, including oxidative stress, inflammation, amyloid-β load, and paired helical filament-tau tangle burden. Conclusions These robust high-throughput assays will not only catalyze novel mechanistic studies in the angiotensin research field but may also help to identify patients with an unbalanced angiotensin receptor distribution who would benefit from angiotensin receptor blocker treatment.
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Affiliation(s)
- Caglar Cosarderelioglu
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
- Division of Geriatrics, Department of Internal MedicineAnkara University School of MedicineAnkaraTurkey
| | - Simion Kreimer
- The Mass Spectrometry and Proteomics FacilityJohns Hopkins University School of MedicineBaltimoreMD
| | | | - Pablo A. Iglesias
- Department of Electrical and Computer Engineering, Whiting School of EngineeringJohns Hopkins UniversityBaltimoreMD
| | - C. Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of MedicineBaltimoreMD
| | - Helmy M. Siragy
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | - Robert M. Carey
- Division of Endocrinology and Metabolism, Department of MedicineUniversity of VirginiaCharlottesvilleVA
| | | | - Brian O'Rourke
- Division of Cardiology, Department of MedicineJohns Hopkins UniversityBaltimoreMD
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of HealthBaltimoreMD
| | - David A. Bennett
- Rush Alzheimer’s Disease CenterRush University Medical CenterChicagoIL
| | - Jeremy Walston
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
| | - Peter Abadir
- Division of Geriatric Medicine and GerontologyJohns Hopkins University School of MedicineBaltimoreMD
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Gurdo N, Volke DC, McCloskey D, Nikel PI. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. N Biotechnol 2023; 74:1-15. [PMID: 36736693 DOI: 10.1016/j.nbt.2023.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
Abstract
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Douglas McCloskey
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.
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10
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Ridder MD, van den Brandeler W, Altiner M, Daran-Lapujade P, Pabst M. Proteome dynamics during transition from exponential to stationary phase under aerobic and anaerobic conditions in yeast. Mol Cell Proteomics 2023; 22:100552. [PMID: 37076048 DOI: 10.1016/j.mcpro.2023.100552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimising biosynthetic routes. Recent studies have demonstrated the potential of resource and proteomic allocation data in enhancing models for metabolic processes. However, comprehensive and accurate proteome dynamics data that can be used for such approaches are still very limited. Therefore, we performed a quantitative proteome dynamics study to comprehensively cover the transition from exponential to stationary phase for both aerobically and anaerobically grown yeast cells. The combination of highly controlled reactor experiments, biological replicates and standardised sample preparation procedures ensured reproducibility and accuracy. Additionally, we selected the CEN.PK lineage for our experiments because of its relevance for both fundamental and applied research. Together with the prototrophic, standard haploid strain CEN.PK113-7D, we also investigated an engineered strain with genetic minimisation of the glycolytic pathway, resulting in the quantitative assessment of 54 proteomes. The anaerobic cultures showed remarkably less proteome-level changes compared to the aerobic cultures, during transition from the exponential to the stationary phase as a consequence of the lack of the diauxic shift in the absence of oxygen. These results support the notion that anaerobically growing cells lack resources to adequately adapt to starvation. This proteome dynamics study constitutes an important step towards better understanding of the impact of glucose exhaustion and oxygen on the complex proteome allocation process in yeast. Finally, the established proteome dynamics data provide a valuable resource for the development of resource allocation models as well as for metabolic engineering efforts.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wiebeke van den Brandeler
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Meryem Altiner
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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11
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A critical path to producing high quality, reproducible data from quantitative western blot experiments. Sci Rep 2022; 12:17599. [PMID: 36266411 PMCID: PMC9585080 DOI: 10.1038/s41598-022-22294-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/12/2022] [Indexed: 01/13/2023] Open
Abstract
Western blotting experiments were initially performed to detect a target protein in a complex biological sample and more recently, to measure relative protein abundance. Chemiluminescence coupled with film-based detection was traditionally the gold standard for western blotting but accurate and reproducible quantification has been a major challenge from this methodology. The development of sensitive, camera-based detection technologies coupled with an updated technical approach permits the production of reproducible, quantitative data. Fluorescence reagent and detection solutions are the latest innovation in western blotting but there remains questions and debate concerning their relative sensitivity and dynamic range versus chemiluminescence. A methodology to optimize and produce excellent, quantitative western blot results with rigorous data analysis from membranes probed with both fluorescent and chemiluminescent antibodies is described. The data reveal when and how to apply these detection methods to achieve reproducible data with a stepwise approach to data processing for quantitative analysis.
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12
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Cifani P, Kentsis A. Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. J Proteome Res 2022; 21:2535-2544. [PMID: 36154077 PMCID: PMC10494574 DOI: 10.1021/acs.jproteome.2c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In spite of extensive studies of cellular signaling, many fundamental processes such as pathway integration, cross-talk, and feedback remain poorly understood. To enable integrated and quantitative measurements of cellular biochemical activities, we have developed the Quantitative Cell Proteomics Atlas (QCPA). QCPA consists of panels of targeted mass spectrometry assays to determine the abundance and stoichiometry of regulatory post-translational modifications of sentinel proteins from most known physiologic and pathogenic signaling pathways in human cells. QCPA currently profiles 1 913 peptides from 469 effectors of cell surface signaling, apoptosis, stress response, gene expression, quiescence, and proliferation. For each protein, QCPA includes triplets of isotopically labeled peptides covering known post-translational regulatory sites to determine their stoichiometries and unmodified protein regions to measure total protein abundance. The QCPA framework incorporates analytes to control for technical variability of sample preparation and mass spectrometric analysis, including TrypQuant, a synthetic substrate for accurate quantification of proteolysis efficiency for proteins containing chemically modified residues. The ability to precisely and accurately quantify most known signaling pathways should enable improved chemoproteomic approaches for the comprehensive analysis of cell signaling and clinical proteomics of diagnostic specimens. QCPA is openly available at https://qcpa.mskcc.org.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065 USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, NY, 10065 USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, NY, 10065 USA
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Alrubia S, Mao J, Chen Y, Barber J, Rostami-Hodjegan A. Altered Bioavailability and Pharmacokinetics in Crohn's Disease: Capturing Systems Parameters for PBPK to Assist with Predicting the Fate of Orally Administered Drugs. Clin Pharmacokinet 2022; 61:1365-1392. [PMID: 36056298 PMCID: PMC9553790 DOI: 10.1007/s40262-022-01169-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 12/12/2022]
Abstract
Backgrond and Objective Crohn’s disease (CD) is a chronic inflammatory bowel disease that affects a wide age range. Hence, CD patients receive a variety of drugs over their life beyond those used for CD itself. The changes to the integrity of the intestine and its drug metabolising enzymes and transporters (DMETs) can alter the oral bioavailability of drugs. However, there are other changes in systems parameters determining the fate of drugs in CD, and understanding these is essential for dose adjustment in patients with CD. Methods The current analysis gathered all the available clinical data on the kinetics of drugs in CD (by March 2021), focusing on orally administered small molecule drugs. A meta-analysis of the systems parameters affecting oral drug pharmacokinetics was conducted. The systems information gathered on intestine, liver and blood proteins and other physiological parameters was incorporated into a physiologically based pharmacokinetic (PBPK) platform to create a virtual population of CD patients, with a view for guiding dose adjustment in the absence of clinical data in CD. Results There were no uniform trends in the reported changes in reported oral bioavailability. The nature of the drug as well as the formulation affected the direction and magnitude of variation in kinetics in CD patients relative to healthy volunteers. Even for the same drug, the reported changes in exposure varied, possibly due to a lack of distinction between the activity states of CD. The highest alteration was seen with S-verapamil and midazolam, 8.7- and 5.3-fold greater exposure, respectively, in active CD patients relative to healthy volunteers. Only one report was available on liver DMETs in CD, and indicated reduced CYP3A4 activity. In a number of reports, mRNA expression of DMETs in the ileum and colon of CD patients was measured, focussing on P-glycoprotein (p-gp) transporter and CYP3A4 enzyme, and showed contradictory results. No data were available on protein expression in duodenum and jejunum despite their dominant role in oral drug absorption. Conclusion There are currently inadequate dedicated clinical or quantitative proteomic studies in CD to enable predictive PBPK models with high confidence and adequate verification. The PBPK models for CD with the available systems parameters were able to capture the major physiological influencers and the gaps to be filled by future research. Quantification of DMETs in the intestine and the liver in CD is warranted, alongside well-defined clinical drug disposition studies with a number of index drugs as biomarkers of changes in DMETs in these patients, to avoid large-scale dedicated studies for every drug to determine the effects of disease on the drug’s metabolism and disposition and the consequential safety and therapeutic concerns. Supplementary Information The online version contains supplementary material available at 10.1007/s40262-022-01169-4.
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Affiliation(s)
- Sarah Alrubia
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester, UK.,Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jialin Mao
- Drug Metabolism and Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuan Chen
- Drug Metabolism and Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester, UK
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester, UK. .,Certara UK Ltd, Simcyp Division, Level 2-Acero, 1 Concourse Way, Sheffield, UK.
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14
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Lentil allergens identification and quantification: An update from omics perspective. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 4:100109. [PMID: 35495776 PMCID: PMC9043643 DOI: 10.1016/j.fochms.2022.100109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 02/08/2023]
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15
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Nimer RM, Sumaily KM, Almuslat A, Jabar MA, Sabi EM, Al-Muhaizea MA, Rahman AMA. Dystrophin Protein Quantification as a Duchenne Muscular Dystrophy Diagnostic Biomarker in Dried Blood Spots Using Multiple Reaction Monitoring Tandem Mass Spectrometry: A Preliminary Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123662. [PMID: 35744792 PMCID: PMC9231037 DOI: 10.3390/molecules27123662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022]
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle loss, leading to difficulties in movement. Mutations in the DMD gene that code for the protein dystrophin are responsible for the development of DMD disorder, where the synthesis of this protein is completely halted. Therefore, circulating dystrophin protein could be a promising biomarker of DMD disease. Current methods for diagnosing DMD have sensitivity, specificity, and reproducibility limitations. Herein, a quantitative liquid chromatography-tandem spectrometry (LC-MS/MS) technique in multiple reaction monitoring (MRM) mode was designed and validated for accurate dystrophin protein measurement in a dried blood spot (DBS). The method was successfully validated on the basis of international guidelines regarding calibration curves, precision, and accuracy. In addition, patients and healthy controls were used to test the amount of dystrophin protein circulating in DBS samples as a potential biomarker for DMD disorders. DMD patients were found to have considerably lower levels than controls. To the best of our knowledge, this is the first study to report dystrophin levels in DBS through LC-MS/MS as a diagnostic marker for DMD to the proposed MRM method, providing a highly specific and sensitive approach to dystrophin quantification in a DBS that can be applied in DMD screening.
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Affiliation(s)
- Refat M. Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Correspondence: (R.M.N.); (A.M.A.R.)
| | - Khalid M. Sumaily
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Arwa Almuslat
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mai Abdel Jabar
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
| | - Essa M. Sabi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Mohammad A. Al-Muhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Anas M. Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence: (R.M.N.); (A.M.A.R.)
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Yunus IS, Lee TS. Applications of targeted proteomics in metabolic engineering: advances and opportunities. Curr Opin Biotechnol 2022; 75:102709. [DOI: 10.1016/j.copbio.2022.102709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
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Kriel NL, Newton-Foot M, Bennion OT, Aldridge BB, Mehaffy C, Belisle JT, Walzl G, Warren RM, Sampson SL, Gey van Pittius NC. Localization of EccA 3 at the growing pole in Mycobacterium smegmatis. BMC Microbiol 2022; 22:140. [PMID: 35590245 PMCID: PMC9118679 DOI: 10.1186/s12866-022-02554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Bacteria require specialized secretion systems for the export of molecules into the extracellular space to modify their environment and scavenge for nutrients. The ESX-3 secretion system is required by mycobacteria for iron homeostasis. The ESX-3 operon encodes for one cytoplasmic component (EccA3) and five membrane components (EccB3 – EccE3 and MycP3). In this study we sought to identify the sub-cellular location of EccA3 of the ESX-3 secretion system in mycobacteria. Results Fluorescently tagged EccA3 localized to a single pole in the majority of Mycobacterium smegmatis cells and time-lapse fluorescent microscopy identified this pole as the growing pole. Deletion of ESX-3 did not prevent polar localization of fluorescently tagged EccA3, suggesting that EccA3 unipolar localization is independent of other ESX-3 components. Affinity purification - mass spectrometry was used to identify EccA3 associated proteins which may contribute to the localization of EccA3 at the growing pole. EccA3 co-purified with fatty acid metabolism proteins (FAS, FadA3, KasA and KasB), mycolic acid synthesis proteins (UmaA, CmaA1), cell division proteins (FtsE and FtsZ), and cell shape and cell cycle proteins (MurS, CwsA and Wag31). Secretion system related proteins Ffh, SecA1, EccA1, and EspI were also identified. Conclusions Time-lapse microscopy demonstrated that EccA3 is located at the growing pole in M. smegmatis. The co-purification of EccA3 with proteins known to be required for polar growth, mycolic acid synthesis, the Sec secretion system (SecA1), and the signal recognition particle pathway (Ffh) also suggests that EccA3 is located at the site of active cell growth. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02554-6.
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Affiliation(s)
- Nastassja L Kriel
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Mae Newton-Foot
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Owen T Bennion
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Carolina Mehaffy
- Mycobacteria Research Laboratories, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - John T Belisle
- Mycobacteria Research Laboratories, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha L Sampson
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nico C Gey van Pittius
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Reyes AV, Shrestha R, Baker PR, Chalkley RJ, Xu SL. Application of Parallel Reaction Monitoring in 15N Labeled Samples for Quantification. FRONTIERS IN PLANT SCIENCE 2022; 13:832585. [PMID: 35592564 PMCID: PMC9111532 DOI: 10.3389/fpls.2022.832585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Accurate relative quantification is critical in proteomic studies. The incorporation of stable isotope 15N to plant-expressed proteins in vivo is a powerful tool for accurate quantification with a major advantage of reducing preparative and analytical variabilities. However, 15N labeling quantification has several challenges. Less identifications are often observed in the heavy-labeled samples because of incomplete labeling, resulting in missing values in reciprocal labeling experiments. Inaccurate quantification can happen when there is contamination from co-eluting peptides or chemical noise in the MS1 survey scan. These drawbacks in quantification can be more pronounced in less abundant but biologically interesting proteins, which often have very few identified peptides. Here, we demonstrate the application of parallel reaction monitoring (PRM) to 15N labeled samples on a high resolution, high mass accuracy Orbitrap mass spectrometer to achieve reliable quantification even of low abundance proteins in samples.
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Affiliation(s)
- Andres V. Reyes
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Peter R. Baker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Robert J. Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA, United States
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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Schmidt A, Schreiner D. Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry. Methods Mol Biol 2022; 2537:231-246. [PMID: 35895268 DOI: 10.1007/978-1-0716-2521-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular diversification of the cellular proteome through alternative splicing has emerged as an important biological principle. However, the lack of tools to specifically detect and quantify proteoforms (Smith et al., Nat Methods 10:186-187, 2013) is a major impediment to functional studies. Recently, biological mass spectrometry (MS) has undergone impressive advances (Mann, Nat Rev Mol Cell Biol 17:678, 2016), including the generation of a highly diverse set of biological applications (Aebersold and Mann, Nature 537:347-355, 2016), and has demonstrated to be an essential tool to address many biological questions (Savitski et al., Science 346:1255784, 2014; Rinner et al., Nat Methods 5:315-318, 2008). In particular, targeted LC-MS, with its high selectivity and specificity, is ideally suited for the precise and sensitive quantification of specific proteins and their proteoforms (Picotti and Aebersold, Nat Methods 9:555-566, 2012). We describe in detail the application of this workflow applied to dissect the molecular diversity of the synaptic adhesion proteins and their splicing-derived proteoforms (Schreiner et al., Elife 4:e07794, 2015).
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21
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Cifani P, Kentsis A. Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods Mol Biol 2022; 2393:207-224. [PMID: 34837181 PMCID: PMC10320743 DOI: 10.1007/978-1-0716-1803-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent advances in nanoscale separations and high-resolution mass spectrometry permit highly sensitive and accurate analyses of complex protein mixtures. Here, we describe improved methods for nanoscale multidimensional chromatography coupled to targeted mass spectrometry (tMS) to achieve ultrasensitive quantification of peptides in complex proteomes. The presented chromatographic system consists of capillary strong-cation exchange (SCX) chromatography column, from which peptides are eluted directly onto high-resolution reversed-phase (RP) analytical columns and nanoelectrospray ion source. SCX prefractionation is used to separate phosphorylated peptides, permitting their ultrasensitive quantification. Resolution and robustness of this chromatographic system, together with the orthogonality of SCX and RP separations, permit scheduling of large panels of targeted MS assays. This design also enables seamless scaling to three-dimensional separations, thereby enabling large-scale, ultrasensitive quantitative proteomics.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Trahan C, Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods Mol Biol 2022; 2477:195-223. [PMID: 35524119 DOI: 10.1007/978-1-0716-2257-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to get a comprehensive picture of cellular behavior and to understand biological systems. In the past two decades, affinity purification coupled to mass spectrometry has become a powerful tool to comprehensively study interaction networks and their assemblies. To overcome initial limitations of the approach, in particular, the effect of protein and RNA degradation, loss of transient interactors, and poor overall yield of intact complexes from cell lysates, various modifications to affinity purification protocols have been devised over the years. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol as described here has been optimized for the yeast S. cerevisiae.
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Affiliation(s)
- Christian Trahan
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- RNP Biochemistry Laboratory, Center for Genetic and Neurological Diseases, Institut de recherches cliniques de Montréal, Montréal, QC, Canada.
- Département de biochimie et médicine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada.
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Kumari M, Pradhan UK, Joshi R, Punia A, Shankar R, Kumar R. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC PLANT BIOLOGY 2021; 21:604. [PMID: 34937558 PMCID: PMC8693493 DOI: 10.1186/s12870-021-03394-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. RESULTS We were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. CONCLUSIONS This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.
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Affiliation(s)
- Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upendra Kumar Pradhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
- Present address: ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, 110012, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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van Bentum M, Selbach M. An Introduction to Advanced Targeted Acquisition Methods. Mol Cell Proteomics 2021; 20:100165. [PMID: 34673283 PMCID: PMC8600983 DOI: 10.1016/j.mcpro.2021.100165] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
Targeted proteomics via selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) enables fast and sensitive detection of a preselected set of target peptides. However, the number of peptides that can be monitored in conventional targeting methods is usually rather small. Recently, a series of methods has been described that employ intelligent acquisition strategies to increase the efficiency of mass spectrometers to detect target peptides. These methods are based on one of two strategies. First, retention time adjustment-based methods enable intelligent scheduling of target peptide retention times. These include Picky, iRT, as well as spike-in free real-time adjustment methods such as MaxQuant.Live. Second, in spike-in triggered acquisition methods such as SureQuant, Pseudo-PRM, TOMAHAQ, and Scout-MRM, targeted scans are initiated by abundant labeled synthetic peptides added to samples before the run. Both strategies enable the mass spectrometer to better focus data acquisition time on target peptides. This either enables more sensitive detection or a higher number of targets per run. Here, we provide an overview of available advanced targeting methods and highlight their intrinsic strengths and weaknesses and compatibility with specific experimental setups. Our goal is to provide a basic introduction to advanced targeting methods for people starting to work in this field. Advanced acquisition methods improve focus of mass spectrometers on target peptides. This review discusses existing methods based on two strategies. Retention time adjustment-based methods enable intelligent scheduling of peptide RTs. In spike-in triggered acquisition methods targeted scans are initiated by spike-ins.
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Affiliation(s)
- Mirjam van Bentum
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
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25
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Wang Q. Building Personalized Cancer Therapeutics through Multi-Omics Assays and Bacteriophage-Eukaryotic Cell Interactions. Int J Mol Sci 2021; 22:ijms22189712. [PMID: 34575870 PMCID: PMC8468737 DOI: 10.3390/ijms22189712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage-eukaryotic cell interaction provides the biological foundation of Phage Display technology, which has been widely adopted in studies involving protein-protein and protein-peptide interactions, and it provides a direct link between the proteins and the DNA encoding them. Phage display has also facilitated the development of new therapeutic agents targeting personalized cancer mutations. Proteins encoded by mutant genes in cancers can be processed and presented on the tumor cell surface by human leukocyte antigen (HLA) molecules, and such mutant peptides are called Neoantigens. Neoantigens are naturally existing tumor markers presented on the cell surface. In clinical settings, the T-cell recognition of neoantigens is the foundation of cancer immunotherapeutics. This year, we utilized phage display to successfully develop the 1st antibody-based neoantigen targeting approach for next-generation personalized cancer therapeutics. In this article, we discussed the strategies for identifying neoantigens, followed by using phage display to create personalized cancer therapeutics-a complete pipeline for personalized cancer treatment.
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Affiliation(s)
- Qing Wang
- Complete Omics Inc., 1448 S. Rolling Rd, Baltimore, MD 21227, USA
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26
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Melby JA, Roberts DS, Larson EJ, Brown KA, Bayne EF, Jin S, Ge Y. Novel Strategies to Address the Challenges in Top-Down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1278-1294. [PMID: 33983025 PMCID: PMC8310706 DOI: 10.1021/jasms.1c00099] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, including the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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27
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Cirksena K, Hütte HJ, Shcherbakova A, Thumberger T, Sakson R, Weiss S, Jensen LR, Friedrich A, Todt D, Kuss AW, Ruppert T, Wittbrodt J, Bakker H, Buettner FFR. The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development. Mol Cell Proteomics 2021; 20:100092. [PMID: 33975020 PMCID: PMC8256286 DOI: 10.1016/j.mcpro.2021.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
C-mannosylation is a modification of tryptophan residues with a single mannose and can affect protein folding, secretion, and/or function. To date, only a few proteins have been demonstrated to be C-mannosylated, and studies that globally assess protein C-mannosylation are scarce. To interrogate the C-mannosylome of human induced pluripotent stem cells, we compared the secretomes of CRISPR–Cas9 mutants lacking either the C-mannosyltransferase DPY19L1 or DPY19L3 to WT human induced pluripotent stem cells using MS-based quantitative proteomics. The secretion of numerous proteins was reduced in these mutants, including that of A Disintegrin And Metalloproteinase with ThromboSpondin Motifs 16 (ADAMTS16), an extracellular protease that was previously reported to be essential for optic fissure fusion in zebrafish eye development. To test the functional relevance of this observation, we targeted dpy19l1 or dpy19l3 in embryos of the Japanese rice fish medaka (Oryzias latipes) by CRISPR–Cas9. We observed that targeting of dpy19l3 partially caused defects in optic fissure fusion, called coloboma. We further showed in a cellular model that DPY19L1 and DPY19L3 mediate C-mannosylation of a recombinantly expressed thrombospondin type 1 repeat of ADAMTS16 and thereby support its secretion. Taken together, our findings imply that DPY19L3-mediated C-mannosylation is involved in eye development by assisting secretion of the extracellular protease ADAMTS16. TSR1 of ADAMTS16 can be C-mannosylated. Deletion of DPY19L1 or DPY19L3 in hiPSCs caused reduced secretion of ADAMTS16. Targeting of dpy19l3 in medaka occasionally led to coloboma.
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Affiliation(s)
- Karsten Cirksena
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hermann J Hütte
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | | | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Riff Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alina Friedrich
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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28
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Lozančić M, Žunar B, Hrestak D, Lopandić K, Teparić R, Mrša V. Systematic Comparison of Cell Wall-Related Proteins of Different Yeasts. J Fungi (Basel) 2021; 7:jof7020128. [PMID: 33572482 PMCID: PMC7916363 DOI: 10.3390/jof7020128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 11/16/2022] Open
Abstract
Yeast cell walls have two major roles, to preserve physical integrity of the cell, and to ensure communication with surrounding molecules and cells. While the first function requires evolutionary conserved polysaccharide network synthesis, the second needs to be flexible and provide adaptability to different habitats and lifestyles. In this study, the comparative in silico analysis of proteins required for cell wall biosynthesis and functions containing 187 proteins of 92 different yeasts was performed in order to assess which proteins were broadly conserved among yeasts and which were more species specific. Proteins were divided into several groups according to their role and localization. As expected, many Saccharomyces cerevisiae proteins involved in protein glycosylation, glycosylphosphatidylinositol (GPI) synthesis and the synthesis of wall polysaccharides had orthologues in most other yeasts. Similarly, a group of GPI anchored proteins involved in cell wall biosynthesis (Gas proteins and Dfg5p/Dcw1p) and other non-GPI anchored cell wall proteins involved in the wall synthesis and remodeling were highly conserved. However, GPI anchored proteins involved in flocculation, aggregation, cell separation, and those of still unknown functions were not highly conserved. The proteins localized in the cell walls of various yeast species were also analyzed by protein biotinylation and blotting. Pronounced differences were found both in the patterns, as well as in the overall amounts of different groups of proteins. The amount of GPI-anchored proteins correlated with the mannan to glucan ratio of the wall. Changes of the wall proteome upon temperature shift to 42 °C were detected.
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Affiliation(s)
- Mateja Lozančić
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.L.); (B.Ž.); (D.H.); (R.T.)
| | - Bojan Žunar
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.L.); (B.Ž.); (D.H.); (R.T.)
| | - Dora Hrestak
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.L.); (B.Ž.); (D.H.); (R.T.)
| | - Ksenija Lopandić
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences, 1180 Vienna, Austria;
| | - Renata Teparić
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.L.); (B.Ž.); (D.H.); (R.T.)
| | - Vladimir Mrša
- Laboratory of Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.L.); (B.Ž.); (D.H.); (R.T.)
- Correspondence:
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29
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Kim Y, Yeo I, Huh I, Kim J, Han D, Jang JY, Kim Y. Development and Multiple Validation of the Protein Multi-marker Panel for Diagnosis of Pancreatic Cancer. Clin Cancer Res 2021; 27:2236-2245. [PMID: 33504556 DOI: 10.1158/1078-0432.ccr-20-3929] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE To develop and validate a protein-based, multi-marker panel that provides superior pancreatic ductal adenocarcinoma (PDAC) detection abilities with sufficient diagnostic performance. EXPERIMENTAL DESIGN A total of 959 plasma samples from patients at multiple medical centers were used. To construct an optimal, diagnostic, multi-marker panel, we applied data preprocessing procedure to biomarker candidates. The multi-marker panel was developed using a training set comprised of 261 PDAC cases and 290 controls. Subsequent evaluations were performed in a validation set comprised of 65 PDAC cases and 72 controls. Further validation was performed in an independent set comprised of 75 PDAC cases and 47 controls. RESULTS A multi-marker panel containing 14 proteins was developed. The multi-marker panel achieved AUCs of 0.977 and 0.953 for the training set and validation set, respectively. In an independent validation set, the multi-marker panel yielded an AUC of 0.928. The diagnostic performance of the multi-marker panel showed significant improvements compared with carbohydrate antigen (CA) 19-9 alone (training set AUC = 0.977 vs. 0.872, P < 0.001; validation set AUC = 0.953 vs. 0.832, P < 0.01; independent validation set AUC = 0.928 vs. 0.771, P < 0.001). When the multi-marker panel and CA 19-9 were combined, the diagnostic performance of the combined panel was improved for all sets. CONCLUSIONS This multi-marker panel and the combined panel showed statistically significant improvements in diagnostic performance compared with CA 19-9 alone and has the potential to complement CA 19-9 as a diagnostic marker in clinical practice.
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Affiliation(s)
- Yoseop Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, College of Engineering, Seoul, Republic of South Korea
| | - Injoon Yeo
- Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of South Korea
| | - Iksoo Huh
- College of Nursing and Research Institute of Nursing Science, Seoul National University, Seoul, Republic of South Korea
| | - Jaenyeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, College of Engineering, Seoul, Republic of South Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of South Korea
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of South Korea.
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, College of Engineering, Seoul, Republic of South Korea. .,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of South Korea.,Institute of Bioengineering, Seoul National University, Seoul, Republic of South Korea
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30
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Gao Y, Ping L, Duong D, Zhang C, Dammer EB, Li Y, Chen P, Chang L, Gao H, Wu J, Xu P. Mass-Spectrometry-Based Near-Complete Draft of the Saccharomyces cerevisiae Proteome. J Proteome Res 2021; 20:1328-1340. [PMID: 33443437 DOI: 10.1021/acs.jproteome.0c00721] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proteomics approaches designed to catalogue all open reading frames (ORFs) under a defined set of growth conditions of an organism have flourished in recent years. However, no proteome has been sequenced completely so far. Here, we generate the largest yeast proteome data set, including 5610 identified proteins, using a strategy based on optimized sample preparation and high-resolution mass spectrometry. Among the 5610 identified proteins, 94.1% are core proteins, which achieves near-complete coverage of the yeast ORFs. Comprehensive analysis of missing proteins showed that proteins are missed mainly due to physical properties. A review of protein abundance shows that our proteome encompasses a uniquely broad dynamic range. Additionally, these values highly correlate with mRNA abundance, implying a high level of accuracy, sensitivity, and precision. We present examples of how the data could be used, including reannotating gene localization, providing expression evidence of pseudogenes. Our near-complete yeast proteome data set will be a useful and important resource for further systematic studies.
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Affiliation(s)
- Yuan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Lingyan Ping
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Duc Duong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Chengpu Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Eric B Dammer
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,Center for Neurodegenerative Diseases, Emory Proteomics Service Center, and Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Peiru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Junzhu Wu
- School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, School of Medicine, Wuhan University, Wuhan 430072, P. R. China.,Anhui Medical University, Hefei 230032, P. R. China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
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31
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Karayel O, Michaelis AC, Mann M, Schulman BA, Langlois CR. DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift. Proc Natl Acad Sci U S A 2020; 117:32806-32815. [PMID: 33288721 PMCID: PMC7768684 DOI: 10.1073/pnas.2020197117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome-based readouts can serve as comprehensive systems-level assays in all cellular systems.
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - André C Michaelis
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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32
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Kosaka Y, Aoki W, Mori M, Aburaya S, Ohtani Y, Minakuchi H, Ueda M. Selected reaction monitoring for the quantification of Escherichia coli ribosomal proteins. PLoS One 2020; 15:e0236850. [PMID: 33315868 PMCID: PMC7735604 DOI: 10.1371/journal.pone.0236850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022] Open
Abstract
Ribosomes are the sophisticated machinery that is responsible for protein synthesis in a cell. Recently, quantitative mass spectrometry (qMS) have been successfully applied for understanding the dynamics of protein complexes. Here, we developed a highly specific and reproducible method to quantify all ribosomal proteins (r-proteins) by combining selected reaction monitoring (SRM) and isotope labeling. We optimized the SRM methods using purified ribosomes and Escherichia coli lysates and verified this approach as detecting 41 of the 54 r-proteins separately synthesized in E. coli S30 extracts. The SRM methods will enable us to utilize qMS as a highly specific analytical tool in the research of E. coli ribosomes, and this methodology have potential to accelerate the understanding of ribosome biogenesis, function, and the development of engineered ribosomes with additional functions.
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Affiliation(s)
- Yuishin Kosaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, Kyoto, Japan
- * E-mail:
| | - Megumi Mori
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, Kyoto, Japan
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33
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Gao Y, Fillmore TL, Munoz N, Bentley GJ, Johnson CW, Kim J, Meadows JA, Zucker JD, Burnet MC, Lipton AK, Bilbao A, Orton DJ, Kim YM, Moore RJ, Robinson EW, Baker SE, Webb-Robertson BJM, Guss AM, Gladden JM, Beckham GT, Magnuson JK, Burnum-Johnson KE. High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2020; 8:603488. [PMID: 33425868 PMCID: PMC7793925 DOI: 10.3389/fbioe.2020.603488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/10/2020] [Indexed: 11/13/2022] Open
Abstract
Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As a key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme and pathway identification and design in metabolic engineering. To fulfill the increasing need for analyzing large sample sets with faster turnaround time in systems biology, high-throughput LC-SRM is greatly needed. Even though nanoflow LC-SRM has better sensitivity, it lacks the speed offered by microflow LC-SRM. Recent advancements in mass spectrometry instrumentation significantly enhance the scan speed and sensitivity of LC-SRM, thereby creating opportunities for applying the high speed of microflow LC-SRM without losing peptide multiplexing power or sacrificing sensitivity. Here, we studied the performance of microflow LC-SRM relative to nanoflow LC-SRM by monitoring 339 peptides representing 132 enzymes in Pseudomonas putida KT2440 grown on various carbon sources. The results from the two LC-SRM platforms are highly correlated. In addition, the response curve study of 248 peptides demonstrates that microflow LC-SRM has comparable sensitivity for the majority of detected peptides and better mass spectrometry signal and chromatography stability than nanoflow LC-SRM.
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Affiliation(s)
- Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Gayle J Bentley
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Christopher W Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jamie A Meadows
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Jeremy D Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C Burnet
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna K Lipton
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aivett Bilbao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Errol W Robinson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Bobbie-Jo M Webb-Robertson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam M Guss
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Jon K Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
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Sperk M, van Domselaar R, Rodriguez JE, Mikaeloff F, Sá Vinhas B, Saccon E, Sönnerborg A, Singh K, Gupta S, Végvári Á, Neogi U. Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses. J Proteome Res 2020; 19:4259-4274. [PMID: 33095583 PMCID: PMC7640957 DOI: 10.1021/acs.jproteome.0c00380] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Emerging and re-emerging infectious diseases due to RNA viruses cause major negative consequences for the quality of life, public health, and overall economic development. Most of the RNA viruses causing illnesses in humans are of zoonotic origin. Zoonotic viruses can directly be transferred from animals to humans through adaptation, followed by human-to-human transmission, such as in human immunodeficiency virus (HIV), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and, more recently, SARS coronavirus 2 (SARS-CoV-2), or they can be transferred through insects or vectors, as in the case of Crimean-Congo hemorrhagic fever virus (CCHFV), Zika virus (ZIKV), and dengue virus (DENV). At the present, there are no vaccines or antiviral compounds against most of these viruses. Because proteins possess a vast array of functions in all known biological systems, proteomics-based strategies can provide important insights into the investigation of disease pathogenesis and the identification of promising antiviral drug targets during an epidemic or pandemic. Mass spectrometry technology has provided the capacity required for the precise identification and the sensitive and high-throughput analysis of proteins on a large scale and has contributed greatly to unravelling key protein-protein interactions, discovering signaling networks, and understanding disease mechanisms. In this Review, we present an account of quantitative proteomics and its application in some prominent recent examples of emerging and re-emerging RNA virus diseases like HIV-1, CCHFV, ZIKV, and DENV, with more detail with respect to coronaviruses (MERS-CoV and SARS-CoV) as well as the recent SARS-CoV-2 pandemic.
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Affiliation(s)
- Maike Sperk
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Robert van Domselaar
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Jimmy Esneider Rodriguez
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Flora Mikaeloff
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Beatriz Sá Vinhas
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Elisa Saccon
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Anders Sönnerborg
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Division
of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Kamal Singh
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Soham Gupta
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
| | - Ákos Végvári
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 14152 Sweden
| | - Ujjwal Neogi
- Division
of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Campus Flemingsberg, Stockholm 14152, Sweden
- Department
of Molecular Microbiology and Immunology and the Bond Life Science
Center, University of Missouri, Columbia, Missouri 65211, United States
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35
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Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis. Molecules 2020; 25:molecules25163582. [PMID: 32781706 PMCID: PMC7466104 DOI: 10.3390/molecules25163582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The photosynthetic apparatus and metabolic enzymes of cyanobacteria are subject to various controls, such as transcriptional regulation and post-translational modifications, to ensure that the entire cellular system functions optimally. In particular, phosphorylation plays key roles in many cellular controls such as enzyme activity, signal transduction, and photosynthetic apparatus restructuring. Therefore, elucidating the governing functions of phosphorylation is crucial to understanding the regulatory mechanisms underlying metabolism and photosynthesis. In this study, we determined protein content and phosphorylation levels to reveal the regulation of intracellular metabolism and photosynthesis in Synechocystis sp. PCC 6803; for this, we obtained quantitative data of proteins and their phosphorylated forms involved in photosynthesis and metabolism under various growth conditions (photoautotrophic, mixotrophic, heterotrophic, dark, and nitrogen-deprived conditions) using targeted proteomic and phosphoproteomic analyses with nano-liquid chromatography-triple quadrupole mass spectrometry. The results indicated that in addition to the regulation of protein expression, the regulation of phosphorylation levels of cyanobacterial photosynthetic apparatus and metabolic enzymes was pivotal for adapting to changing environmental conditions. Furthermore, reduced protein levels of CpcC and altered phosphorylation levels of CpcB, ApcA, OCP, and PsbV contributed to the cellular response of the photosynthesis apparatus to nitrogen deficiency.
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36
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Preparation of Tissue Samples for Large-scale Quantitative Mass Spectrometric Analysis. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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37
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Erickson BK, Schweppe DK, Yu Q, Rad R, Haas W, McAlister GC, Gygi SP. Parallel Notched Gas-Phase Enrichment for Improved Proteome Identification and Quantification with Fast Spectral Acquisition Rates. J Proteome Res 2020; 19:2750-2757. [PMID: 31990573 PMCID: PMC7334078 DOI: 10.1021/acs.jproteome.9b00715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gas-phase fractionation enables better quantitative accuracy, improves signal-to-noise ratios, and increases sensitivity in proteomic analyses. However, traditional gas-phase enrichment, which relies upon a large continuous bin, results in suboptimal enrichment, as most chromatographic separations are not 100% orthogonal relative to the first MS dimension (MS1m/z). As such, ions with similar m/z values tend to elute at the same retention time, which prevents the partitioning of narrow precursor m/z distributions into a few large continuous gas-phase enrichment bins. To overcome this issue, we developed and tested the use of notched isolation waveforms, which simultaneously isolate multiple discrete m/z windows in parallel (e.g., 650-700 m/z and 800-850 m/z). By comparison to a canonical gas-phase fractionation method, notched waveforms do not require bin optimization via in silico digestion or wasteful sample injections to isolate multiple precursor windows. Importantly, the collection of all m/z bins simultaneously using the isolation waveform does not suffer from the sensitivity and duty cycle pitfalls inherent to sequential collection of multiple m/z bins. Applying a notched injection waveform provided consistent enrichment of precursor ions, which resulted in improved proteome depth with greater coverage of low-abundance proteins. Finally, using a reductive dimethyl labeling approach, we show that notched isolation waveforms increase the number of quantified peptides with improved accuracy and precision across a wider dynamic range.
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Affiliation(s)
- Brian K Erickson
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Ramin Rad
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Wilhem Haas
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Graeme C McAlister
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, Massachusetts 02115, United States
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38
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He J, Meng L, Ruppel J, Yang J, Kaur S, Xu K. Automated, Generic Reagent and Ultratargeted 2D-LC-MS/MS Enabling Quantification of Biotherapeutics and Soluble Targets down to pg/mL Range in Serum. Anal Chem 2020; 92:9412-9420. [PMID: 32510921 DOI: 10.1021/acs.analchem.0c01910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry has recently emerged as a powerful analytical tool for the assessment of pharmacokinetics and biomarkers in drug development. Compared with ligand binding assays, a major advantage of mass spectrometry-based assays is that they are less dependent on high quality binding reagents, while a key limitation is the relatively lower sensitivity. To address the sensitivity issue, we have developed a generic reagent, ultratargeted two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) method which combines commercially available protein A affinity capture, targeted analyte isolation by 2D-LC, and targeted detection by multiple reaction monitoring (MRM). A targeted-2D-with-dilution configuration was designed to automate 2D-LC-MS/MS. This method was systematically evaluated using an anti-CD22 monoclonal antibody spiked into monkey and human serum, where lower limits of quantification (LLOQ) of 0.78 and 1.56 ng/mL were achieved, respectively. This represents an over 100-fold improvement in assay sensitivity compared to the conventional LC-MS/MS method. The performance of the method was further confirmed by analyzing another monoclonal antibody, bevacizumab, as well as a soluble antigen, circulating PD-L1. The results indicate that our method enables quantification of antibody therapeutics and antigen biomarkers in both clinical and nonclinical samples in the pg/mL to low ng/mL range. Protein A affinity capture was employed as a universal sample preparation procedure applicable to both full-length antibody therapeutics and antibody-antigen complexes. This novel method is also fully automated and proven to be highly robust for routine bioanalysis in drug development.
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Affiliation(s)
- Jintang He
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lingyao Meng
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jane Ruppel
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jie Yang
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Surinder Kaur
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Keyang Xu
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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39
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Achour B, Al-Majdoub ZM, Rostami-Hodjegan A, Barber J. Mass Spectrometry of Human Transporters. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:223-247. [PMID: 32084322 DOI: 10.1146/annurev-anchem-091719-024553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
- Certara, Princeton, New Jersey 08540, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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40
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Radko S, Ptitsyn K, Novikova S, Kiseleva Y, Moysa A, Kurbatov L, Mannanova M, Zgoda V, Ponomarenko E, Lisitsa A, Archakov A. Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma. Biomedicines 2020; 8:E133. [PMID: 32456365 PMCID: PMC7277749 DOI: 10.3390/biomedicines8050133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma.
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Affiliation(s)
- Sergey Radko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Svetlana Novikova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Yana Kiseleva
- Russian Scientific Center of Roentgenoradiology, Moscow 117485, Russia;
| | - Alexander Moysa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Maria Mannanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Alexander Archakov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
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41
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Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. MASS SPECTROMETRY REVIEWS 2020; 39:229-244. [PMID: 28691345 PMCID: PMC5799042 DOI: 10.1002/mas.21540] [Citation(s) in RCA: 393] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/01/2017] [Indexed: 05/03/2023]
Abstract
Skyline is a freely available, open-source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers the informatics encompassed by the Skyline ecosystem, from computationally assisted targeted mass spectrometry method development, to raw acquisition file data processing, and quantitative analysis and results sharing.
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Affiliation(s)
- Lindsay K Pino
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brian C Searle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - James G Bollinger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brook Nunn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington
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42
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Effects of mutations of GID protein–coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:4971-4983. [DOI: 10.1007/s00253-020-10573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/27/2020] [Accepted: 03/22/2020] [Indexed: 02/03/2023]
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43
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Hentschel A, Ahrends R. Developing a Robust Assay to Monitor and Quantify Key Players of Metabolic Pathways during Adipogenesis by Targeted Proteomics. Proteomics 2020; 20:e1900141. [PMID: 32196961 DOI: 10.1002/pmic.201900141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Targeted data acquisition using nano liquid chromatrography (nano-LC) coupled mass spectrometry is an emerging approach when there is a need to quantify proteins with high accuracy, sensitivity, and reproducibility. Nevertheless, creating assays meeting all those criteria still remains a laborious task, especially when investigating low abundant proteins and small concentration changes. In this work a targeted data acquisition workflow is developed reducing time and effort to target and investigate key players of metabolic pathways during the process of adipocyte differentiation. This leads to accurate and sensitive quantification of proteins involved in the synthesis of fatty acids, glycerolipids, glycerophospholipids, sphingolipids, the production of energy and reduction equivalents. Additionally low abundant signaling molecules part of the peroxisome proliferator-activated receptor gamma (PPARγ) and insulin signaling pathway with ≈400 for the insulin receptor substrate and 1100 copies per cell for PPARγ are determined.
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Affiliation(s)
- Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bioanalytics, Standartisation, Otto-Hahn-Straße 6b, Dortmund, D-44227, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bioanalytics, Standartisation, Otto-Hahn-Straße 6b, Dortmund, D-44227, Germany.,Institute of Analytical Chemistry, University of Vienna, Währinger str. 38, Vienna, A-1090, Austria
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44
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Chen Z, Gao Y, Zhong D. Technologies to improve the sensitivity of existing chromatographic methods used for bioanalytical studies. Biomed Chromatogr 2020; 34:e4798. [PMID: 31994210 DOI: 10.1002/bmc.4798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
Chromatographic method has long been recognized as the most widely used separation method in bioanalytical research. However, the relatively low sensitivity of existing chromatographic methods remains a significant challenge, as the requirements for experimental procedures become more demanding. This review discusses the main causes for the low sensitivity of chromatographic methods and aims to introduce different technologies for enhancing their sensitivity in the following aspects: (i) different pretreatment methods for improving clean-up efficiency and recovery; (ii) derivatization step for altering the chromatographic behavior of analytes and enhancing MS ionization efficiency; (iii) optimal LC-MS conditions and appropriate separation mechanism; and (iv) applications of other chromatographic methods, including miniaturized LC, 2D-LC, 2D-GC, and supercritical fluid chromatography. Altogether, this review is devoted to summarizing the recent technologies reported in the literature and providing new strategies for the detection of bioanalytes.
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Affiliation(s)
- Zhendong Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiong Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dafang Zhong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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45
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Abstract
Mass spectrometry based proteomics approaches are routinely used to discover candidate biomarkers. These studies often use small number of samples to discover candidate proteins that are later validated on a large cohort of samples. Targeted proteomics has emerged as a powerful method for quantification of multiple proteins in complex biological matrix. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) are two main methods of choice for quantifying and validating proteins across hundreds to thousands of samples. Over the years, many software tools have become available that enable the users to carry out the analysis. In this chapter, we describe selection of proteotypic peptides, sample preparation, generating a response curve, data acquisition and analysis of PRM data using Skyline software for targeted proteomics to quantify candidate markers in urine.
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46
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Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM. Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5775554. [PMID: 32128557 PMCID: PMC7054198 DOI: 10.1093/database/baaa008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The identification and accurate quantitation of protein abundance has been a major objective of proteomics research. Abundance studies have the potential to provide users with data that can be used to gain a deeper understanding of protein function and regulation and can also help identify cellular pathways and modules that operate under various environmental stress conditions. One of the central missions of the Saccharomyces Genome Database (SGD; https://www.yeastgenome.org) is to work with researchers to identify and incorporate datasets of interest to the wider scientific community, thereby enabling hypothesis-driven research. A large number of studies have detailed efforts to generate proteome-wide abundance data, but deeper analyses of these data have been hampered by the inability to compare results between studies. Recently, a unified protein abundance dataset was generated through the evaluation of more than 20 abundance datasets, which were normalized and converted to common measurement units, in this case molecules per cell. We have incorporated these normalized protein abundance data and associated metadata into the SGD database, as well as the SGD YeastMine data warehouse, resulting in the addition of 56 487 values for untreated cells grown in either rich or defined media and 28 335 values for cells treated with environmental stressors. Abundance data for protein-coding genes are displayed in a sortable, filterable table on Protein pages, available through Locus Summary pages. A median abundance value was incorporated, and a median absolute deviation was calculated for each protein-coding gene and incorporated into SGD. These values are displayed in the Protein section of the Locus Summary page. The inclusion of these data has enhanced the quality and quantity of protein experimental information presented at SGD and provides opportunities for researchers to access and utilize the data to further their research.
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Affiliation(s)
- Robert S Nash
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
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47
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Hart-Smith G. Combining Targeted and Untargeted Data Acquisition to Enhance Quantitative Plant Proteomics Experiments. Methods Mol Biol 2020; 2139:169-178. [PMID: 32462586 DOI: 10.1007/978-1-0716-0528-8_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Most quantitative proteomics experiments either target a limited number of selected proteins for quantification or quantify proteins on a broad scale in an untargeted manner. However, we recently demonstrated that experiments that have both targeted and untargeted components can be particularly advantageous. Using a combined targeted and untargeted liquid chromatography-tandem mass spectrometry data acquisition strategy termed TDA/DDA (shorthand for targeted data acquisition/data-dependent acquisition), which we applied to a model quantitative plant proteomics experiment performed on Arabidopsis, we demonstrated improved quantification of both targeted and untargeted proteins relative to purely untargeted experiments performed using conventional data-dependent acquisition (Hart-Smith et al. Front Plant Sci 8:1669, 2017). This suggests that many quantitative proteomics datasets earmarked for collection using data-dependent acquisition are likely to benefit from the use of TDA/DDA instead.This chapter describes how TDA/DDA liquid chromatography-tandem mass spectrometry methods can be created on commonly used mass spectrometric instrument platforms. It described how, using freely available software, tandem mass spectrometry inclusion lists designed to target proteins of hypothesized interest can be generated. Best practice implementation of these inclusion lists in TDA/DDA strategies is then described. Relative to conventional data-dependent acquisition, the liquid chromatography-tandem mass spectrometry methods created using these guidelines increase the chances of quantifying targeted proteins and can produce widespread improvements in the reproducibility of untargeted protein quantification, without compromising the total numbers of proteins quantified. They are compatible with different quantitative proteomics methodologies, including metabolic labeling, chemical labeling and label-free approaches, and can be used to create tailored assay libraries to aid the interpretation of quantitative proteomics data collected using data-independent acquisition.
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Affiliation(s)
- Gene Hart-Smith
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
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48
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Genereux JC. Mass spectrometric approaches for profiling protein folding and stability. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:111-144. [PMID: 31928723 DOI: 10.1016/bs.apcsb.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Mass spectrometry has rapidly become a preferred technology for identifying and quantifying proteins. As such, it has been increasingly incorporated into methodologies for interrogating protein stability and folding. Although no single technology can satisfy all desired applications, several emerging approaches have shown outstanding success at providing biological insight into the stability of the proteome. This chapter outlines some of these recent emerging technologies.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA, United States
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49
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Lodens S, Roelants SLKW, Ciesielska K, Geys R, Derynck E, Maes K, Pattyn F, Van Renterghem L, Mottet L, Dierickx S, Vanhaecke L, Devreese B, De Maeseneire SL, Soetaert W. Unraveling and resolving inefficient glucolipid biosurfactants production through quantitative multiomics analyses of Starmerella bombicola strains. Biotechnol Bioeng 2019; 117:453-465. [PMID: 31612987 DOI: 10.1002/bit.27191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/20/2019] [Accepted: 10/10/2019] [Indexed: 01/18/2023]
Abstract
Glucolipids (GLs) are glycolipid biosurfactants with promising properties. These GLs are composed of glucose attached to a hydroxy fatty acid through a ω and/or ω-1 glycosidic linkage. Up until today these interesting molecules could only be produced using an engineered Starmerella bombicola strain (∆ugtB1::URA3 G9) producing GLs instead of sophorolipids, albeit with a very low average productivity (0.01 g·L-1 ·h-1 ). In this study, we investigated the reason(s) for this via reverse-transcription quantitative polymerase chain reaction and Liquid chromatography-multireaction monitoring-mass spectrometry. We found that all glycolipid biosynthetic genes and enzymes were downregulated in the ∆ugtB1 G9 strain in comparison to the wild type. The underlying reason for this downregulation was further investigated by performing quantitative metabolome comparison of the ∆ugtB1 G9 strain with the wild type and two other engineered strains also tinkered in their glycolipid biosynthetic gene cluster. This analysis revealed a clear distortion of the entire metabolism of the ∆ugtB1 G9 strain compared to all the other strains. Because the parental strain of the former was a spontaneous ∆ura3 mutant potentially containing other "hidden" mutations, a new GL production strain was generated based on a rationally engineered ∆ura3 mutant (PT36). Indeed, a 50-fold GL productivity increase (0.51 g·L-1 ·h-1 ) was obtained with the new ∆ugtB1::URA3 PT36 strain compared with the G9-based strain (0.01 g·L-1 ·h-1 ) in a 10 L bioreactor experiment, yielding 118 g/L GLs instead of 8.39 g/L. Purification was investigated and basic properties of the purified GLs were determined. This study forms the base for further development and optimization of S. bombicola as a production platform strain for (new) biochemicals.
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Affiliation(s)
- Sofie Lodens
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sophie L K W Roelants
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Bio Base Europe Pilot Plant, Desteldonk, Belgium
| | | | - Robin Geys
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | - Filip Pattyn
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Lisa Van Renterghem
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Sven Dierickx
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bart Devreese
- L-Probe, Department of Sciences, Ghent University, Ghent, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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50
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Li Y, Lammi C, Boschin G, Arnoldi A, Aiello G. Recent Advances in Microalgae Peptides: Cardiovascular Health Benefits and Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11825-11838. [PMID: 31588750 DOI: 10.1021/acs.jafc.9b03566] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There is now great interest in food protein hydrolysates and food-derived peptides, because they may provide numerous health benefits. Among other foodstuffs, microalgae appear to be sustainable sources of proteins and bioactive peptides that can be exploited in foods and functional formulations. This review considers protein hydrolysates and individual peptides that may be relevant in cardiovascular disease prevention because they mimic the functions of mediators involved in pathologic processes that represent relevant risk factors for cardiovascular disease development, such as hypercholesterolemia, hypertension, diabetes, inflammation, and oxidative status. Some of these peptides are also multifunctional (i.e., they offer more than one benefit). Moreover, the most efficient techniques for protein extraction and hydrolyzation are commented on, as well as the best methodologies for high-throughput detection and quantification. Finally, current challenges and critical issues are discussed.
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Affiliation(s)
- Yuchen Li
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Carmen Lammi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Giovanna Boschin
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Anna Arnoldi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Gilda Aiello
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
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