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Parsons JD, Cocker CR, East AK, Wheatley RM, Ramachandran VK, Kaschani F, Kaiser M, Poole PS. Factors governing attachment of Rhizobium leguminosarum to legume roots at acid, neutral, and alkaline pHs. mSystems 2024:e0042224. [PMID: 39166858 DOI: 10.1128/msystems.00422-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
Rhizobial attachment to host legume roots is the first physical interaction of bacteria and plants in symbiotic nitrogen fixation. The pH-dependent primary attachment of Rhizobium leguminosarum biovar viciae 3841 to Pisum sativum (pea) roots was investigated by genome-wide insertion sequencing, luminescence-based attachment assays, and proteomic analysis. Under acid, neutral, or alkaline pH, a total of 115 genes are needed for primary attachment under one or more environmental pH, with 22 genes required for all. These include components of cell surfaces and membranes, together with enzymes that construct and modify them. Mechanisms of dealing with stress also play a part; however, exact requirements vary depending on environmental pH. RNASeq showed that knocking out the two transcriptional regulators required for attachment causes massive changes in the bacterial cell surface. Approximately half of the 54 proteins required for attachment at pH 7.0 have a role in the later stages of nodule formation. We found no evidence for a single rhicadhesin responsible for alkaline attachment, although sonicated cell surface fractions inhibited root attachment at alkaline pH. Our results demonstrate the complexity of primary root attachment and illustrate the diversity of mechanisms involved. IMPORTANCE The first step by which bacteria interact with plant roots is by attachment. In this study, we use a combination of insertion sequencing and biochemical analysis to determine how bacteria attach to pea roots and how this is influenced by pH. We identify several key adhesins, which are molecules that enable bacteria to stick to roots. This includes a novel filamentous hemagglutinin which is needed at all pHs for attachment. Overall, 115 proteins are required for attachment at one or more pHs.
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Affiliation(s)
- Jack D Parsons
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Clare R Cocker
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Alison K East
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | | | - Farnusch Kaschani
- Department of Chemical Biology, ZMB, University Duisburg-Essen, Essen, Germany
- Analytics Core Facility Essen (ACE), University Duisburg-Essen, ZMB, Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology, ZMB, University Duisburg-Essen, Essen, Germany
| | - Philip S Poole
- Department of Biology, University of Oxford, Oxford, United Kingdom
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2
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Brázdovič F, Brejová B, Siváková B, Baráth P, Kerák F, Hodorová V, Vinař T, Tomáška Ľ, Nosek J. Reduction of Ribosomal Expansion Segments in Yeast Species of the Magnusiomyces/Saprochaete Clade. Genome Biol Evol 2024; 16:evae173. [PMID: 39119893 PMCID: PMC11342254 DOI: 10.1093/gbe/evae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 06/25/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Ribosomes are ribonucleoprotein complexes highly conserved across all domains of life. The size differences of ribosomal RNAs (rRNAs) can be mainly attributed to variable regions termed expansion segments (ESs) protruding out from the ribosomal surface. The ESs were found to be involved in a range of processes including ribosome biogenesis and maturation, translation, and co-translational protein modification. Here, we analyze the rRNAs of the yeasts from the Magnusiomyces/Saprochaete clade belonging to the basal lineages of the subphylum Saccharomycotina. We find that these yeasts are missing more than 400 nt from the 25S rRNA and 150 nt from the 18S rRNAs when compared to their canonical counterparts in Saccharomyces cerevisiae. The missing regions mostly map to ESs, thus representing a shift toward a minimal rRNA structure. Despite the structural changes in rRNAs, we did not identify dramatic alterations in the ribosomal protein inventories. We also show that the size-reduced rRNAs are not limited to the species of the Magnusiomyces/Saprochaete clade, indicating that the shortening of ESs happened independently in several other lineages of the subphylum Saccharomycotina.
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Affiliation(s)
- Filip Brázdovič
- Faculty of Natural Sciences, Comenius University Bratislava, Bratislava, Slovakia
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Broňa Brejová
- Faculty of Mathematics, Physics, and Informatics, Comenius University Bratislava, Bratislava, Slovakia
| | - Barbara Siváková
- Slovak Academy of Sciences, Institute of Chemistry, Bratislava, Slovakia
| | - Peter Baráth
- Slovak Academy of Sciences, Institute of Chemistry, Bratislava, Slovakia
| | - Filip Kerák
- Faculty of Mathematics, Physics, and Informatics, Comenius University Bratislava, Bratislava, Slovakia
| | - Viktória Hodorová
- Faculty of Natural Sciences, Comenius University Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Faculty of Mathematics, Physics, and Informatics, Comenius University Bratislava, Bratislava, Slovakia
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Comenius University Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Faculty of Natural Sciences, Comenius University Bratislava, Bratislava, Slovakia
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3
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Zheng K, Lyu JC, Thomas EL, Schuster M, Sanguankiattichai N, Ninck S, Kaschani F, Kaiser M, van der Hoorn RAL. The proteome of Nicotiana benthamiana is shaped by extensive protein processing. THE NEW PHYTOLOGIST 2024; 243:1034-1049. [PMID: 38853453 DOI: 10.1111/nph.19891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/29/2024] [Indexed: 06/11/2024]
Abstract
Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant proteins in plants, yet only few processing events have been described in agroinfiltrated Nicotiana benthamiana, which has emerged as the main transient protein expression platform in plant science and molecular pharming. Here, we used in-gel digests and mass spectrometry to monitor the migration and topography of 5040 plant proteins within a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel. These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. This analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor-like kinases. Transient expression of double-tagged candidate proteins confirmed processing events in vivo. This large proteomic dataset implicates an elaborate proteolytic machinery shaping the proteome of N. benthamiana.
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Affiliation(s)
- Kaijie Zheng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Joy C Lyu
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Emma L Thomas
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Mariana Schuster
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | | | - Sabrina Ninck
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Farnusch Kaschani
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Markus Kaiser
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
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4
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Leach FE, Nagornov KO, Kozhinov AN, Tsybin YO. External Data Systems Enable Enhanced (and Sustainable) Fourier Transform Mass Spectrometry Imaging for Legacy Hybrid Linear Ion Trap-Orbitrap Platforms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39031087 DOI: 10.1021/jasms.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
Legacy Fourier transform (FT) mass spectrometers provide robust platforms for bioanalytical mass spectrometry (MS) yet lack the most modern performance capabilities. For many laboratories, the routine investment in next generation instrumentation is cost prohibitive. Field-based upgrades provide a direct path to extend the usable lifespan of MS platforms which may be considered antiquated based on performance specifications at the time of manufacture. Here we demonstrate and evaluate the performance of a hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer that has been enhanced via an external high-performance data acquisition and processing system to provide true absorption mode FT processing during an experimental acquisition. For the application to mass spectrometry imaging, several performance metrics have been improved including mass resolving power, mass accuracy, and dynamic range to provide an FTMS system comparable to current platforms. We also demonstrate, perhaps, the unexpected ability of these legacy platforms to detect usable time-domain signals up to 5 s in duration to achieve a mass resolving power 8× higher than the original platform specification.
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Affiliation(s)
- Franklin E Leach
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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5
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Müller J, Boubaker G, Müller N, Uldry AC, Braga-Lagache S, Heller M, Hemphill A. Investigating Antiprotozoal Chemotherapies with Novel Proteomic Tools-Chances and Limitations: A Critical Review. Int J Mol Sci 2024; 25:6903. [PMID: 39000012 PMCID: PMC11241152 DOI: 10.3390/ijms25136903] [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: 05/31/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Identification of drug targets and biochemical investigations on mechanisms of action are major issues in modern drug development. The present article is a critical review of the classical "one drug"-"one target" paradigm. In fact, novel methods for target deconvolution and for investigation of resistant strains based on protein mass spectrometry have shown that multiple gene products and adaptation mechanisms are involved in the responses of pathogens to xenobiotics rather than one single gene or gene product. Resistance to drugs may be linked to differential expression of other proteins than those interacting with the drug in protein binding studies and result in complex cell physiological adaptation. Consequently, the unraveling of mechanisms of action needs approaches beyond proteomics. This review is focused on protozoan pathogens. The conclusions can, however, be extended to chemotherapies against other pathogens or cancer.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Ghalia Boubaker
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
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6
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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7
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Font-Farre M, Brown D, Toth R, Mahadevan C, Brazier-Hicks M, Morimoto K, Kaschani F, Sinclair J, Dale R, Hall S, Morris M, Kaiser M, Wright AT, Burton J, van der Hoorn RAL. Discovery of active mouse, plant and fungal cytochrome P450s in endogenous proteomes and upon expression in planta. Sci Rep 2024; 14:10091. [PMID: 38698065 PMCID: PMC11066006 DOI: 10.1038/s41598-024-60333-x] [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: 08/01/2023] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Eukaryotes produce a large number of cytochrome P450s that mediate the synthesis and degradation of diverse endogenous and exogenous metabolites. Yet, most of these P450s are uncharacterized and global tools to study these challenging, membrane-resident enzymes remain to be exploited. Here, we applied activity profiling of plant, mouse and fungal P450s with chemical probes that become reactive when oxidized by P450 enzymes. Identification by mass spectrometry revealed labeling of a wide range of active P450s, including six plant P450s, 40 mouse P450s and 13 P450s of the fungal wheat pathogen Zymoseptoria tritici. We next used transient expression of GFP-tagged P450s by agroinfiltration to show ER-targeting and NADPH-dependent, activity-based labeling of plant, mouse and fungal P450s. Both global profiling and transient expression can be used to detect a broad range of active P450s to study e.g. their regulation and discover selective inhibitors.
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Affiliation(s)
- Maria Font-Farre
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Daniel Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Reka Toth
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - John Sinclair
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Richard Dale
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Samantha Hall
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Melloney Morris
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Jonathan Burton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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8
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Kunová N, Ondrovičová G, Bauer JA, Krajčovičová V, Pinkas M, Stojkovičová B, Havalová H, Lukáčová V, Kohútová L, Košťan J, Martináková L, Baráth P, Nováček J, Zoll S, Kereϊche S, Kutejová E, Pevala V. Polyphosphate and tyrosine phosphorylation in the N-terminal domain of the human mitochondrial Lon protease disrupts its functions. Sci Rep 2024; 14:9923. [PMID: 38688959 PMCID: PMC11061198 DOI: 10.1038/s41598-024-60030-9] [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: 12/18/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Phosphorylation plays a crucial role in the regulation of many fundamental cellular processes. Phosphorylation levels are increased in many cancer cells where they may promote changes in mitochondrial homeostasis. Proteomic studies on various types of cancer identified 17 phosphorylation sites within the human ATP-dependent protease Lon, which degrades misfolded, unassembled and oxidatively damaged proteins in mitochondria. Most of these sites were found in Lon's N-terminal (NTD) and ATPase domains, though little is known about the effects on their function. By combining the biochemical and cryo-electron microscopy studies, we show the effect of Tyr186 and Tyr394 phosphorylations in Lon's NTD, which greatly reduce all Lon activities without affecting its ability to bind substrates or perturbing its tertiary structure. A substantial reduction in Lon's activities is also observed in the presence of polyphosphate, whose amount significantly increases in cancer cells. Our study thus provides an insight into the possible fine-tuning of Lon activities in human diseases, which highlights Lon's importance in maintaining proteostasis in mitochondria.
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Grants
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- BIOMEDIRES - II. stage, ITMS: 313011W428 European Regional Development Fund
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
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Affiliation(s)
- Nina Kunová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gabriela Ondrovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Veronika Krajčovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Laboratory of Clinical and Molecular Genetics, National Institute of Children's Diseases, Limbová 1, 833 40, Bratislava, Slovakia
| | - Matyáš Pinkas
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Barbora Stojkovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Henrieta Havalová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Július Košťan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna, Biocenter 5, 1030, Vienna, Austria
| | - Lucia Martináková
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Peter Baráth
- Medirex Group Academy, Nitra, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Nováček
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereϊche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic.
| | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
| | - Vladimír Pevala
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
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9
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Stewart H, Grinfeld D, Petzoldt J, Hagedorn B, Skoblin M, Makarov A, Hock C. Crowd control of ions in the Astral analyzer. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5006. [PMID: 38501497 DOI: 10.1002/jms.5006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/20/2024]
Abstract
Space charge effects are the Achilles' heel of all high-resolution ion optical devices. In time-of-flight mass analyzers, these may manifest as reduction of resolving power, mass measurement shift, peak coalescence, and/or transmission losses, while highly sensitive modern ion sources and injection devices ensure that such limits are easily exceeded. Space charge effects have been investigated, by experiment and simulation study, for the astral multi-reflection analyzer, incorporating ion focusing via a pair of converging ion mirrors, and fed by a pulsed extraction ion trap. Major factors were identified as the resonant effect between ~103 ions of similar m/z in-flight and the expansion of trapped packets of ~104-5 ions prior to extraction. Optimum operation and compensated ion mirror calibration strategies were then generated and described based on these findings.
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10
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Guzman UH, Martinez-Val A, Ye Z, Damoc E, Arrey TN, Pashkova A, Renuse S, Denisov E, Petzoldt J, Peterson AC, Harking F, Østergaard O, Rydbirk R, Aznar S, Stewart H, Xuan Y, Hermanson D, Horning S, Hock C, Makarov A, Zabrouskov V, Olsen JV. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nat Biotechnol 2024:10.1038/s41587-023-02099-7. [PMID: 38302753 DOI: 10.1038/s41587-023-02099-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th isolation windows, dissolving the differences between data-dependent and -independent methods. This is achieved by pairing a quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Eugen Damoc
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | - Anna Pashkova
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | - Florian Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Rydbirk
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susana Aznar
- Centre for Neuroscience and Stereology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Yue Xuan
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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11
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McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571320. [PMID: 38168169 PMCID: PMC10759996 DOI: 10.1101/2023.12.12.571320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performed in vivo PPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
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12
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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13
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Gautam SS, Singh SP. Immunopurification Reagents and Their Application in Biologics and Biomarker Quantitation Using LC-MS/MS in Drug Discovery. J Chromatogr Sci 2023; 61:799-805. [PMID: 36469494 DOI: 10.1093/chromsci/bmac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 10/01/2023]
Abstract
The LC-MS/MS technology is one of the most utilized bio-analytical tools owing to its advantage of selectivity, sensitivity and multitasking. The advent of novel biological therapies and increasing demand for protein biomarker identification and quantitation have put the LC-MS/MS technology at the forefront. The questions which are been posed to the LC-MS/MS scientist are complex. The complexity of the question increases further with the matrices in which these questions need to be answered. To bring down the complexity of the analysis, LC-MS/MS technology is utilizing the immunopurification (IP) technique as the new sample preparation technique. The IP reagents are the most common reagents which are used to decrease the matrices' complexity and allow the LC-MS/MS system to reach greater sensitivity. The utilization of these reagents is increasing every day, but the proper utilization of these reagents is still unknown to the common analyst in drug discovery. The present review throws light on the utilization aspect of these reagents, as we have classified these reagents on basis of their utilization, which will allow the readers to gain an understanding of these reagents. This review will also talk about the merits and the demerits of each approach and the current understanding of utilizing these reagents.
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Affiliation(s)
- Shashyendra Singh Gautam
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
- Biocon-Bristol-Myers Squibb Research Centre, Syngene International Ltd, Bangalore 560100, India
| | - Sheelendra Pratap Singh
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
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14
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Divisekara T, Schum S, Mazzoleni L. Ultrahigh performance LC/FT-MS non-targeted screening for biomass burning organic aerosol with MZmine2 and MFAssignR. CHEMOSPHERE 2023; 338:139403. [PMID: 37422220 DOI: 10.1016/j.chemosphere.2023.139403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
In recent years, ultrahigh performance liquid chromatography Fourier transform mass spectrometry (LC/FT-MS) based non-targeted screening (NTS) methods have become increasingly popular for comprehensive analysis of complex organic mixtures. However, applying these methods for environmental complex mixture analysis is challenging due to the extreme complexity of natural samples and a lack of standard samples or surrogates for environmental complex mixtures. Furthermore, limited molecular markers in the databases and insufficient data processing software workflows make the application of these methods more challenging for environmental complex mixtures. In this work, we implement a new NTS data processing workflow to process data collected from ultrahigh performance liquid chromatography and Fourier transform Orbitrap Elite Mass Spectrometry (LC/FT-MS) by combining MZmine2 and MFAssignR, two opensource data processing tools and commercial Mesquite liquid smoke as a surrogate for biomass burning organic aerosol. MZmine2.53 data extraction followed MFAssignR molecular formula assignment offered noise free and highly accurate 1733 individual molecular formulas presented in liquid smoke with 4906 molecular species, including isomers. The results of this new approach were consistent with the results of direct infusion FT-MS analysis confirming its reliability. Over 90% of the molecular formulas presented in mesquite liquid smoke were matched with the molecular formulas of ambient biomass burning organic aerosol. This suggests the potential use of commercial liquid smoke is an acceptable surrogate for biomass burning organic aerosol research. The presented method significantly improves the identification of the molecular composition of biomass burning organic aerosol by successfully addressing some of the limitations related to the data analysis and giving a semi quantitative insight into the analysis.
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Affiliation(s)
- Thusitha Divisekara
- Department of Chemistry, Michigan Technological University, Houghton, MI, USA
| | - Simeon Schum
- Department of Chemistry, Michigan Technological University, Houghton, MI, USA; Chemical Advanced Resolution Methods Laboratory, Michigan Technological University, Houghton, MI, USA
| | - Lynn Mazzoleni
- Department of Chemistry, Michigan Technological University, Houghton, MI, USA.
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15
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Pernis M, Salaj T, Bellová J, Danchenko M, Baráth P, Klubicová K. Secretome analysis revealed that cell wall remodeling and starch catabolism underlie the early stages of somatic embryogenesis in Pinus nigra. FRONTIERS IN PLANT SCIENCE 2023; 14:1225424. [PMID: 37600183 PMCID: PMC10436561 DOI: 10.3389/fpls.2023.1225424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Somatic embryogenesis is an efficient mean for rapid micropropagation and preservation of the germplasm of valuable coniferous trees. Little is known about how the composition of secretome tracks down the level of embryogenic capacity. Unlike embryogenic tissue on solid medium, suspension cell cultures enable the study of extracellular proteins secreted into a liquid cultivation medium, avoiding contamination from destructured cells. Here, we present proteomic data of the secretome of Pinus nigra cell lines with contrasting embryogenic capacity, accounting for variability between genotypes. Our results showed that cell wall-related and carbohydrate-acting proteins were the most differentially accumulated. Peroxidases, extensin, α-amylase, plant basic secretory family protein (BSP), and basic secretory protease (S) were more abundant in the medium from the lines with high embryogenic capacity. In contrast, the medium from the low embryogenic capacity cell lines contained a higher amount of polygalacturonases, hothead protein, and expansin, which are generally associated with cell wall loosening or softening. These results corroborated the microscopic findings in cell lines with low embryogenic capacity-long suspensor cells without proper assembly. Furthermore, proteomic data were subsequently validated by peroxidase and α-amylase activity assays, and hence, we conclude that both tested enzyme activities can be considered potential markers of high embryogenic capacity.
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Affiliation(s)
- Miroslav Pernis
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Terézia Salaj
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jana Bellová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Klubicová
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
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16
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Poljovka A, Musil M, Bednář D, Chovanová K, Bauerová-Hlinková V, Bellová J, Kohútová L, Baráth P, Zámocký M. Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties. Antioxidants (Basel) 2023; 12:1382. [PMID: 37507921 PMCID: PMC10376177 DOI: 10.3390/antiox12071382] [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: 05/31/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
Catalase-peroxidases (KatGs) are unique bifunctional oxidoreductases that contain heme in their active centers allowing both the peroxidatic and catalatic reaction modes. These originally bacterial enzymes are broadly distributed among various fungi allowing them to cope with reactive oxygen species present in the environment or inside the cells. We used various biophysical, biochemical, and bioinformatics methods to investigate differences between catalase-peroxidases originating in thermophilic and mesophilic fungi from different habitats. Our results indicate that the architecture of the active center with a specific post-translational modification is highly similar in mesophilic and thermophilic KatG and also the peroxidatic acitivity with ABTS, guaiacol, and L-DOPA. However, only the thermophilic variant CthedisKatG reveals increased manganese peroxidase activity at elevated temperatures. The catalatic activity releasing molecular oxygen is comparable between CthedisKatG and mesophilic MagKatG1 over a broad temperature range. Two constructed point mutations in the active center were performed selectively blocking the formation of described post-translational modification in the active center. They exhibited a total loss of catalatic activity and changes in the peroxidatic activity. Our results indicate the capacity of bifunctional heme enzymes in the variable reactivity for potential biotech applications.
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Affiliation(s)
- Andrej Poljovka
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Miloš Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
- International Clinical Research Centre, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200 Brno, Czech Republic
| | - David Bednář
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
- International Clinical Research Centre, St. Anne's University Hospital Brno, 65691 Brno, Czech Republic
| | - Katarína Chovanová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Jana Bellová
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84538 Bratislava, Slovakia
| | - Lenka Kohútová
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84538 Bratislava, Slovakia
| | - Peter Baráth
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84538 Bratislava, Slovakia
| | - Marcel Zámocký
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
- Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
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17
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Cadang L, Tam CYJ, Moore BN, Fichtl J, Yang F. A Highly Efficient Workflow for Detecting and Identifying Sequence Variants in Therapeutic Proteins with a High Resolution LC-MS/MS Method. Molecules 2023; 28:molecules28083392. [PMID: 37110623 PMCID: PMC10144261 DOI: 10.3390/molecules28083392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Large molecule protein therapeutics have steadily grown and now represent a significant portion of the overall pharmaceutical market. These complex therapies are commonly manufactured using cell culture technology. Sequence variants (SVs) are undesired minor variants that may arise from the cell culture biomanufacturing process that can potentially affect the safety and efficacy of a protein therapeutic. SVs have unintended amino acid substitutions and can come from genetic mutations or translation errors. These SVs can either be detected using genetic screening methods or by mass spectrometry (MS). Recent advances in Next-generation Sequencing (NGS) technology have made genetic testing cheaper, faster, and more convenient compared to time-consuming low-resolution tandem MS and Mascot Error Tolerant Search (ETS)-based workflows which often require ~6 to 8 weeks data turnaround time. However, NGS still cannot detect non-genetic derived SVs while MS analysis can do both. Here, we report a highly efficient Sequence Variant Analysis (SVA) workflow using high-resolution MS and tandem mass spectrometry combined with improved software to greatly reduce the time and resource cost associated with MS SVA workflows. Method development was performed to optimize the high-resolution tandem MS and software score cutoff for both SV identification and quantitation. We discovered that a feature of the Fusion Lumos caused significant relative under-quantitation of low-level peptides and turned it off. A comparison of common Orbitrap platforms showed that similar quantitation values were obtained on a spiked-in sample. With this new workflow, the amount of false positive SVs was decreased by up to 93%, and SVA turnaround time by LC-MS/MS was shortened to 2 weeks, comparable to NGS analysis speed and making LC-MS/MS the top choice for SVA workflow.
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Affiliation(s)
- Lance Cadang
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| | - Chi Yan Janet Tam
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| | | | - Juergen Fichtl
- Pharma Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Feng Yang
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
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18
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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19
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Yan H, Li D, Xu W. A high resolution Fourier transform ion trap enabled by image current splicing: a theoretical study. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1345-1354. [PMID: 36815265 DOI: 10.1039/d2ay02034c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The relatively high work pressure within an ion trap has limited the implementation of the Fourier transform technique for high resolution mass analysis. The main reason is that high buffer gas pressure will cause the rapid decay of ion oscillations. In this study, an image current splicing method based on the filter diagonalization method (FDM) and the Hilbert transform was developed to increase the resolving power of nondestructive mass analysis in a linear ion trap. First, multiple repeated experiments (or ion trajectory simulations) were performed to collect multiple sets of data. Using the FDM, the frequency component distribution was extracted from short image current transients collected from each experiment. The Hilbert transform was then applied to calculate and normalize the decay envelope of each transient. The relative abundance was calculated by counting the envelopes. Finally, image current transients collected from these multiple experiments were spliced and merged into a whole signal with much longer duration and continuous phase. This splicing method could effectively increase the duration of the image current, and thus improve the mass resolution of the ion trap mass analyzer. The mass resolution (m/Δm) was improved from 183.5 to 5.8 × 103, and the average relative difference was 2.8%. The proposed method resolved 3 adjacent peaks which originally could not be resolved from the raw signal by the fast Fourier transform (FFT). Besides simulated data, this method was also applied to the experimental data collected from a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The influence of electronic noise on the proposed method was also discussed in this study.
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Affiliation(s)
- Haoqiang Yan
- College of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China.
| | - Dayu Li
- College of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China.
| | - Wei Xu
- State Key Laboratory of Explosion Science and Technology, School of Life Science, Beijing Institute of Technology, Haidian, Beijing 100081, China.
- Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, 100081, China
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20
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Ivanova B, Spiteller M. Stochastic dynamic ultraviolet photofragmentation and high collision energy dissociation mass spectrometric kinetics of triadimenol and sucralose. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:32348-32370. [PMID: 36462070 DOI: 10.1007/s11356-022-24259-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
The major goal of the paper is to provide empirical proof of view that innovative stochastic dynamic mass spectrometric equation D″SD = 2.6388·10-17·(< I2 > - < I > 2) determines the exact analyte concentration in solution via quantifying experimental variable intensity (I) of an analyte ion per any short span of scan time of any measurement, which also appears applicable to quantify laser-induced ultraviolet photofragmentation and high energy collision dissociation mass spectrometric processes. Triadimenol (1) and sucralose (2) using positive and negative polarity are examined. Laser irradiation energy λex = 213 nm is utilized. The issue is of central importance for monitoring organic micro-pollutants in surface, ground, and drinking water as well as tasks of risk assessment for environment and human health from contamination with organics. Despite the significant importance of the topic, answering the question of functional kinetic relations of such processes is by no means straightforward, so far, due to a lack of in-depth knowledge of mechanistic aspects of fragment paths of analytes in environment and foods as well as kinetics of processes under ultraviolet laser irradiation. Although there is truth in the classical theory of first-order reaction kinetics, it does not describe all kinetic data on analytes (1) and (2). A new damped sine wave functional response to a large amount of kinetics is presented. High-resolution mass spectrometric data and chemometrics are used. The study provides empirical evidence for claim that temporal behavior of mass spectrometric variable intensity under negative polarity obeys a certain scientific law written by means of equation above. It is the same for positive and negative soft-ionization mass spectrometric conditions.
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl Für Analytische Chemie, Institut Für Umweltforschung, Fakultät Für Chemie Und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Nordrhein-Westfalen, Germany.
| | - Michael Spiteller
- Lehrstuhl Für Analytische Chemie, Institut Für Umweltforschung, Fakultät Für Chemie Und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Nordrhein-Westfalen, Germany
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21
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Deschamps E, Calabrese V, Schmitz I, Hubert-Roux M, Castagnos D, Afonso C. Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis. Molecules 2023; 28:2061. [PMID: 36903305 PMCID: PMC10003995 DOI: 10.3390/molecules28052061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Pharmaceutical analysis refers to an area of analytical chemistry that deals with active compounds either by themselves (drug substance) or when formulated with excipients (drug product). In a less simplistic way, it can be defined as a complex science involving various disciplines, e.g., drug development, pharmacokinetics, drug metabolism, tissue distribution studies, and environmental contamination analyses. As such, the pharmaceutical analysis covers drug development to its impact on health and the environment. Moreover, due to the need for safe and effective medications, the pharmaceutical industry is one of the most heavily regulated sectors of the global economy. For this reason, powerful analytical instrumentation and efficient methods are required. In the last decades, mass spectrometry has been increasingly used in pharmaceutical analysis both for research aims and routine quality controls. Among different instrumental setups, ultra-high-resolution mass spectrometry with Fourier transform instruments, i.e., Fourier transform ion cyclotron resonance (FTICR) and Orbitrap, gives access to valuable molecular information for pharmaceutical analysis. In fact, thanks to their high resolving power, mass accuracy, and dynamic range, reliable molecular formula assignments or trace analysis in complex mixtures can be obtained. This review summarizes the principles of the two main types of Fourier transform mass spectrometers, and it highlights applications, developments, and future perspectives in pharmaceutical analysis.
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Affiliation(s)
- Estelle Deschamps
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100 Villeurbanne, France
| | - Isabelle Schmitz
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Marie Hubert-Roux
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
| | - Denis Castagnos
- ORIL Industrie, Servier Group, 13 r Auguste Desgenétais, 76210 Bolbec, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnières, CEDEX, 76821 Mont-Saint-Aignan, France
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22
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Barakat A, Birkeland E, Jørstad MD, El Hajj M, Marijani M, Døskeland A, Mjaavatten O, Berven FS, Mustafa T. Proteomic analysis of peripheral blood mononuclear cells isolated from patients with pulmonary tuberculosis: A pilot study from Zanzibar, Tanzania. PLoS One 2023; 18:e0281757. [PMID: 36787336 PMCID: PMC9928017 DOI: 10.1371/journal.pone.0281757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
This study aimed at exploring the proteomic profile of PBMCs to predict treatment response in pulmonary tuberculosis (PTB). This was a pilot study conducted among 8 adult patients from Zanzibar, Tanzania with confirmed PTB. Blood samples were collected at baseline, at 2 months of treatment, and at the end of treatment at 6 months. Proteins were extracted from PBMCs and analyzed using LC-MS/MS based label free quantitative proteomics. Overall, 3,530 proteins were quantified across the samples, and 12 differentially expressed proteins were identified at both 2 months of treatment and at treatment completion, which were involved in cellular and metabolic processes, as well as binding and catalytic activity. Seven were downregulated proteins (HSPA1B/HSPA1A, HSPH1, HSP90AA1, lipopolysaccharide-binding protein, complement component 9, calcyclin-binding protein, and protein transport protein Sec31A), and 5 proteins were upregulated (SEC14 domain and spectrin repeat-containing protein 1, leucine-rich repeat-containing 8 VRAC subunit D, homogentisate 1,2-dioxygenase, NEDD8-activating enzyme E1 regulatory subunit, and N-acetylserotonin O-methyltransferase-like protein). The results showed that proteome analysis of PBMCs can be used as a novel technique to identify protein abundance change with anti-tuberculosis treatment. The novel proteins elucidated in this work may provide new insights for understanding PTB pathogenesis, treatment, and prognosis.
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Affiliation(s)
- Ahmed Barakat
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Even Birkeland
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Melissa D. Jørstad
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Magalie El Hajj
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Medical Affairs, Partner 4 Health, Paris, France
| | - Msafiri Marijani
- Department of Diagnostic Services, Mnazi Mmoja Hospital, Zanzibar, The United Republic of Tanzania
| | - Anne Døskeland
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Mjaavatten
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Tehmina Mustafa
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
- * E-mail:
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23
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Taspase1 Facilitates Topoisomerase IIβ-Mediated DNA Double-Strand Breaks Driving Estrogen-Induced Transcription. Cells 2023; 12:cells12030363. [PMID: 36766705 PMCID: PMC9913075 DOI: 10.3390/cells12030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The human protease Taspase1 plays a pivotal role in developmental processes and cancerous diseases by processing critical regulators, such as the leukemia proto-oncoprotein MLL. Despite almost two decades of intense research, Taspase1's biology is, however, still poorly understood, and so far its cellular function was not assigned to a superordinate biological pathway or a specific signaling cascade. Our data, gained by methods such as co-immunoprecipitation, LC-MS/MS and Topoisomerase II DNA cleavage assays, now functionally link Taspase1 and hormone-induced, Topoisomerase IIβ-mediated transient DNA double-strand breaks, leading to active transcription. The specific interaction with Topoisomerase IIα enhances the formation of DNA double-strand breaks that are a key prerequisite for stimulus-driven gene transcription. Moreover, Taspase1 alters the H3K4 epigenetic signature upon estrogen-stimulation by cleaving the chromatin-modifying enzyme MLL. As estrogen-driven transcription and MLL-derived epigenetic labelling are reduced upon Taspase1 siRNA-mediated knockdown, we finally characterize Taspase1 as a multifunctional co-activator of estrogen-stimulated transcription.
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24
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Kellie JF, Schneck NA, Causon JC, Baba T, Mehl JT, Pohl KI. Top-Down Characterization and Intact Mass Quantitation of a Monoclonal Antibody Drug from Serum by Use of a Quadrupole TOF MS System Equipped with Electron-Activated Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:17-26. [PMID: 36459688 DOI: 10.1021/jasms.2c00206] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Time-of-flight MS systems for biopharmaceutical and protein characterization applications may play an even more pivotal role in the future as biotherapeutics increase in drug pipelines and as top-down MS approaches increase in use. Here, a recently developed TOF MS system is examined for monoclonal antibody (mAb) characterization from serum samples. After immunocapture, purified drug material spiked into monkey serum or dosed for an in-life study is analyzed by top-down MS. While characterization aspects are a distinct advantage of the MS platform, MS system and software capabilities are also shown regarding intact protein quantitation. Such applications are demonstrated to help enable comprehensive protein molecule quantitation and characterization by use of TOF MS instrumentation.
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Affiliation(s)
- John F Kellie
- GSK, Collegeville, Pennsylvania 19426, United States
| | | | | | | | - John T Mehl
- GSK, Collegeville, Pennsylvania 19426, United States
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25
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Contributions of vibrational spectroscopy to virology: A review. CLINICAL SPECTROSCOPY 2022; 4:100022. [PMCID: PMC9093054 DOI: 10.1016/j.clispe.2022.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/17/2023]
Abstract
Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970 s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review considers the history of the application of vibrational spectroscopic techniques to the characterisation of the morphology and chemical compositions of viruses, their attachment to, uptake by and replication in cells, and their potential for the detection of viruses in population screening, and in infection response monitoring applications. Particular consideration is devoted to recent efforts in the detection of severe acute respiratory syndrome coronavirus 2, and monitoring COVID-19.
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26
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Orsburn BC, Yuan Y, Bumpus NN. Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry. Nat Commun 2022; 13:7246. [PMID: 36433961 PMCID: PMC9700839 DOI: 10.1038/s41467-022-34919-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022] Open
Abstract
Single cell proteomics is a powerful tool with potential for markedly enhancing understanding of cellular processes. Here we report the development and application of multiplexed single cell proteomics using trapped ion mobility time-of-flight mass spectrometry. When employing a carrier channel to improve peptide signal, this method allows over 40,000 tandem mass spectra to be acquired in 30 min. Using a KRASG12C model human-derived cell line, we demonstrate the quantification of over 1200 proteins per cell with high relative sequence coverage permitting the detection of multiple classes of post-translational modifications in single cells. When cells were treated with a KRASG12C covalent inhibitor, this approach revealed cell-to-cell variability in the impact of the drug, providing insight missed by traditional proteomics. We provide multiple resources necessary for the application of single cell proteomics to drug treatment studies including tools to reduce cell cycle linked proteomic effects from masking pharmacological phenotypes.
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Affiliation(s)
- Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, 21205, Baltimore, MD, USA.
| | - Yuting Yuan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, 21205, Baltimore, MD, USA
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, 21205, Baltimore, MD, USA.
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27
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Selicky T, Jurcik M, Mikolaskova B, Pitelova A, Mayerova N, Kretova M, Osadska M, Jurcik J, Holic R, Kohutova L, Bellova J, Benko Z, Gregan J, Bagelova Polakova S, Barath P, Cipak L, Cipakova I. Defining the Functional Interactome of Spliceosome-Associated G-Patch Protein Gpl1 in the Fission Yeast Schizosaccharomyces pombe. Int J Mol Sci 2022; 23:12800. [PMID: 36361590 PMCID: PMC9658070 DOI: 10.3390/ijms232112800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 08/31/2023] Open
Abstract
Pre-mRNA splicing plays a fundamental role in securing protein diversity by generating multiple transcript isoforms from a single gene. Recently, it has been shown that specific G-patch domain-containing proteins are critical cofactors involved in the regulation of splicing processes. In this study, using the knock-out strategy, affinity purification and the yeast-two-hybrid assay, we demonstrated that the spliceosome-associated G-patch protein Gpl1 of the fission yeast S. pombe mediates interactions between putative RNA helicase Gih35 (SPAC20H4.09) and WD repeat protein Wdr83, and ensures their binding to the spliceosome. Furthermore, RT-qPCR analysis of the splicing efficiency of deletion mutants indicated that the absence of any of the components of the Gpl1-Gih35-Wdr83 complex leads to defective splicing of fet5 and pwi1, the reference genes whose unspliced isoforms harboring premature stop codons are targeted for degradation by the nonsense-mediated decay (NMD) pathway. Together, our results shed more light on the functional interactome of G-patch protein Gpl1 and revealed that the Gpl1-Gih35-Wdr83 complex plays an important role in the regulation of pre-mRNA splicing in S. pombe.
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Affiliation(s)
- Tomas Selicky
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Matus Jurcik
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Barbora Mikolaskova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, 840 05 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Miroslava Kretova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Michaela Osadska
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Jan Jurcik
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Roman Holic
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, 840 05 Bratislava, Slovakia
| | - Lenka Kohutova
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
| | - Jana Bellova
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
| | - Zsigmond Benko
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Egyetem tér 1, H4032 Debrecen, Hungary
| | - Juraj Gregan
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 24, 3430 Tulln an der Donau, Austria
| | - Silvia Bagelova Polakova
- Department of Membrane Biochemistry, Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska cesta 9, 840 05 Bratislava, Slovakia
| | - Peter Barath
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia
- Medirex Group Academy, Novozamocka 67, 949 05 Nitra, Slovakia
| | - Lubos Cipak
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Ingrid Cipakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
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28
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Zhang Y, Dreyer B, Govorukhina N, Heberle AM, Končarević S, Krisp C, Opitz CA, Pfänder P, Bischoff R, Schlüter H, Kwiatkowski M, Thedieck K, Horvatovich PL. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Anal Chem 2022; 94:10893-10906. [PMID: 35880733 PMCID: PMC9366746 DOI: 10.1021/acs.analchem.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
With increasing sensitivity and accuracy in mass spectrometry,
the tumor phosphoproteome is getting into reach. However, the selection
of quantitation techniques best-suited to the biomedical question
and diagnostic requirements remains a trial and error decision as
no study has directly compared their performance for tumor tissue
phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC
(stable isotope labeling by amino acids in cell culture), and tandem
mass tag (TMT) isobaric tandem mass tags technology for quantitative
phosphosite profiling in tumor tissue. Compared to the classic SILAC
method, spike-in-SILAC is not limited to cell culture analysis, making
it suitable for quantitative analysis of tumor tissue samples. TMT
offered the lowest accuracy and the highest precision and robustness
toward different phosphosite abundances and matrices. Spike-in-SILAC
offered the best compromise between these features but suffered from
a low phosphosite coverage. LFQ offered the lowest precision but the
highest number of identifications. Both spike-in-SILAC and LFQ presented
susceptibility to matrix effects. Match between run (MBR)-based analysis
enhanced the phosphosite coverage across technical replicates in LFQ
and spike-in-SILAC but further reduced the precision and robustness
of quantification. The choice of quantitative methodology is critical
for both study design such as sample size in sample groups and quantified
phosphosites and comparison of published cancer phosphoproteomes.
Using ovarian cancer tissue as an example, our study builds a resource
for the design and analysis of quantitative phosphoproteomic studies
in cancer research and diagnostics.
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Affiliation(s)
- Yang Zhang
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.,Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Benjamin Dreyer
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alexander M Heberle
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Saša Končarević
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt/Main, Germany
| | - Christoph Krisp
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christiane A Opitz
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neurology, National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Pauline Pfänder
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Bioscience, Heidelberg University, 69117 Heidelberg, Germany
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen 9700 AD, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen 9700 AD, The Netherlands
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.,Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Peter L Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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29
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Walz A, Stoiber K, Huettig A, Schlichting H, Barth JV. Navigate Flying Molecular Elephants Safely to the Ground: Mass-Selective Soft Landing up to the Mega-Dalton Range by Electrospray Controlled Ion-Beam Deposition. Anal Chem 2022; 94:7767-7778. [PMID: 35609119 PMCID: PMC9178560 DOI: 10.1021/acs.analchem.1c04495] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to Ttotal = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.
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Affiliation(s)
- Andreas Walz
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Karolina Stoiber
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Annette Huettig
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Hartmut Schlichting
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
| | - Johannes V Barth
- Physics Department E20, Technical University of Munich, 85748 Garching, Germany
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30
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Chauvistré H, Shannan B, Daignault-Mill SM, Ju RJ, Picard D, Egetemaier S, Váraljai R, Gibhardt CS, Sechi A, Kaschani F, Keminer O, Stehbens SJ, Liu Q, Yin X, Jeyakumar K, Vogel FCE, Krepler C, Rebecca VW, Kubat L, Lueong SS, Forster J, Horn S, Remke M, Ehrmann M, Paschen A, Becker JC, Helfrich I, Rauh D, Kaiser M, Gul S, Herlyn M, Bogeski I, Rodríguez-López JN, Haass NK, Schadendorf D, Roesch A. Persister state-directed transitioning and vulnerability in melanoma. Nat Commun 2022; 13:3055. [PMID: 35650266 PMCID: PMC9160289 DOI: 10.1038/s41467-022-30641-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/10/2022] [Indexed: 12/30/2022] Open
Abstract
Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. Melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhigh cells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhigh persister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine 2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor plasticity and primes melanoma cells towards lineage-specific elimination.
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Affiliation(s)
- Heike Chauvistré
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Batool Shannan
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Sheena M Daignault-Mill
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Robert J Ju
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Picard
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Egetemaier
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Renáta Váraljai
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Christine S Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Antonio Sechi
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Farnusch Kaschani
- Department of Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Samantha J Stehbens
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Qin Liu
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Kirujan Jeyakumar
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Felix C E Vogel
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | - Linda Kubat
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, 45141, Essen, Germany
| | - Smiths S Lueong
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, 45122, Essen, Germany
| | - Jan Forster
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Department of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Susanne Horn
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Marc Remke
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Ehrmann
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
- Department of Microbiology, University of Duisburg-Essen, Universitätsstraße 2, 45117, Essen, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Jürgen C Becker
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, 45141, Essen, Germany
| | - Iris Helfrich
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Markus Kaiser
- Department of Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | | | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - José Neptuno Rodríguez-López
- GENZ-Group of Research on Enzymology, Department of Biochemistry and Molecular Biology-A, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Murcia, Spain
| | - Nikolas K Haass
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Alexander Roesch
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany.
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany.
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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31
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Wang Z, Ge Y, Bi S, Liang Y, Shi Q. Molecular characterization of organic aerosol in winter from Beijing using UHPLC-Orbitrap MS. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151507. [PMID: 34762951 DOI: 10.1016/j.scitotenv.2021.151507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The urban organic aerosol (OA) may pose a serious threat to human health and ecological environment. In order to understand the molecular characteristics of organic compounds in aerosols, atmospheric PM2.5 samples were collected in Beijing and the extracts were analyzed by liquid chromatography-Orbitrap mass spectrometry combined with negative-ion electrospray ionization, positive-ion electrospray ionization, and positive-ion atmospheric pressure photoionization sources. The combination of multiple ionization sources realized the comprehensive molecular characterization of organic compounds in OA, and 1976 (+APPI), 3038 (-ESI), and 4376 (+ESI) molecular formulas were identified in this study. Significant differences in the species, abundance, and number of subgroups (CHO, CHN, CHON, CHONS, CHOS, and CH compounds) were clarified. Chemical fingerprinting of organics in the PM2.5 extract were investigated by high-throughput non-target compound analytical methods. Structure induction of organic compounds was realized through fragmentation prediction of MS/MS spectra with Sirius software. Furthermore, a total of 50 nitroaromatic formulas, 285 organosulfates (OS) formulas, 57 nitrooxy-OS formulas, 228 CHO- formulas with carboxyl groups, and 36 monoketone formulas were determined based on diagnostic fragmentation filtering. Our results provide important insights into the molecular composition and structural characteristics of OA, and establish foundation for exploring the interaction between composition and physicochemical properties.
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Affiliation(s)
- Zhiheng Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China
| | - Yafen Ge
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China
| | - Shasha Bi
- Food and Drug Fiber Quality Supervision and Testing Center, Changzhou 213000, PR China
| | - Yongmei Liang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China.
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, PR China
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Cillingová A, Tóth R, Mojáková A, Zeman I, Vrzoňová R, Siváková B, Baráth P, Neboháčová M, Klepcová Z, Brázdovič F, Lichancová H, Hodorová V, Brejová B, Vinař T, Mutalová S, Vozáriková V, Mutti G, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J. Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PLoS Genet 2022; 18:e1009815. [PMID: 35255079 PMCID: PMC8929692 DOI: 10.1371/journal.pgen.1009815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/17/2022] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in β-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates.
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Affiliation(s)
- Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Renáta Tóth
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Anna Mojáková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Igor Zeman
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Romana Vrzoňová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Zuzana Klepcová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Brázdovič
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Lichancová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sofia Mutalová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Giacomo Mutti
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Atilla Gácser
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- * E-mail:
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Gabay O, Shoshan Y, Kopel E, Ben-Zvi U, Mann TD, Bressler N, Cohen-Fultheim R, Schaffer AA, Roth SH, Tzur Z, Levanon EY, Eisenberg E. Landscape of adenosine-to-inosine RNA recoding across human tissues. Nat Commun 2022; 13:1184. [PMID: 35246538 PMCID: PMC8897444 DOI: 10.1038/s41467-022-28841-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/27/2022] [Indexed: 12/18/2022] Open
Abstract
RNA editing by adenosine deaminases changes the information encoded in the mRNA from its genomic blueprint. Editing of protein-coding sequences can introduce novel, functionally distinct, protein isoforms and diversify the proteome. The functional importance of a few recoding sites has been appreciated for decades. However, systematic methods to uncover these sites perform poorly, and the full repertoire of recoding in human and other mammals is unknown. Here we present a new detection approach, and analyze 9125 GTEx RNA-seq samples, to produce a highly-accurate atlas of 1517 editing sites within the coding region and their editing levels across human tissues. Single-cell RNA-seq data shows protein recoding contributes to the variability across cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation. This comprehensive set can facilitate understanding of the role of recoding in human physiology and diseases. Gabay et al. provide a highly-accurate atlas of recoding by A-to-I RNA editing in human, profiled across tissues and cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation.
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Affiliation(s)
- Orshay Gabay
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yoav Shoshan
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Udi Ben-Zvi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Tomer D Mann
- Tel Aviv Sourasky Medical Center and Sackler school of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Bressler
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Roni Cohen-Fultheim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Amos A Schaffer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ziv Tzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel. .,The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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34
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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35
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Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
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Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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36
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Ahamad N, Gupta S, Parashar D. Using Omics to Study Leprosy, Tuberculosis, and Other Mycobacterial Diseases. Front Cell Infect Microbiol 2022; 12:792617. [PMID: 35281437 PMCID: PMC8908319 DOI: 10.3389/fcimb.2022.792617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Mycobacteria are members of the Actinomycetales order, and they are classified into one family, Mycobacteriaceae. More than 20 mycobacterial species cause disease in humans. The Mycobacterium group, called the Mycobacterium tuberculosis complex (MTBC), has nine closely related species that cause tuberculosis in animals and humans. TB can be detected worldwide and one-fourth of the world's population is contaminated with tuberculosis. According to the WHO, about two million dies from it, and more than nine million people are newly infected with TB each year. Mycobacterium tuberculosis (M. tuberculosis) is the most potential causative agent of tuberculosis and prompts enormous mortality and morbidity worldwide due to the incompletely understood pathogenesis of human tuberculosis. Moreover, modern diagnostic approaches for human tuberculosis are inefficient and have many lacks, while MTBC species can modulate host immune response and escape host immune attacks to sustain in the human body. "Multi-omics" strategies such as genomics, transcriptomics, proteomics, metabolomics, and deep sequencing technologies could be a comprehensive strategy to investigate the pathogenesis of mycobacterial species in humans and offer significant discovery to find out biomarkers at the early stage of disease in the host. Thus, in this review, we attempt to understand an overview of the mission of "omics" approaches in mycobacterial pathogenesis, including tuberculosis, leprosy, and other mycobacterial diseases.
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Affiliation(s)
- Naseem Ahamad
- Department of Oral and Maxillofacial Diagnostic Sciences, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, India
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, United States
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37
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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38
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Škodová-Sveráková I, Záhonová K, Juricová V, Danchenko M, Moos M, Baráth P, Prokopchuk G, Butenko A, Lukáčová V, Kohútová L, Bučková B, Horák A, Faktorová D, Horváth A, Šimek P, Lukeš J. Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum. BMC Biol 2021; 19:251. [PMID: 34819072 PMCID: PMC8611851 DOI: 10.1186/s12915-021-01186-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown. RESULTS We designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes. CONCLUSIONS The identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Valéria Juricová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Medirex Group Academy n.o., Trnava, Slovakia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Barbora Bučková
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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39
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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Xue W, Zhang H, Liu M, Chen X, He S, Chu Y. Metabolomics-based screening analysis of PPCPs in water pretreated with five different SPE columns. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4594-4603. [PMID: 34580678 DOI: 10.1039/d1ay01313k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The selection of solid phase extraction (SPE) columns in the pretreatment process plays a decisive role in the screening and quantification of pharmaceutical and personal care products (PPCPs). As growing PPCPs have frequently been detected in the aquatic environment, it is a burdensome task through one-by-one recovery comparison to judge which column presents relatively ideal pretreatment results for PPCPs. In view of this, we developed a novel metabolomics-based screening method based on ultrahigh-performance liquid chromatography-tandem mass spectrometer (UHPLC-MS/MS) results to accurately, rapidly and comprehensively choose a suitable column from 5 different kinds to handle 64 PPCPs in two water environments (50 μg L-1/pH ≅ 7.0/pure water and 1 μg L-1/pH ≅ 7.0/reservoir water) through seeking 'biomarkers', for which multivariate and univariate analyses were adopted. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) play a crucial role in multivariate analysis, and the pairwise t-test and fold change judgement in univariate analysis. Each column group was fully separated from the other 4 groups in PCA and OPLS-DA plots, laying a foundation to distinguish 'biomarkers' between groups. The S-Plot, permutation and variable importance in projection (VIP) in OPLS-DA were employed to screen and identify 'biomarkers', which were further verified by a pairwise t-test and fold change judgement. Eventually, the 64 PPCPs as 'biomarkers' were divided into 5 groups, which correspond to 5 column groups, consistent with the findings of traditional PPCP recovery comparison, proving the validity of the metabolomics-based screening method. This novel method will exhibit greater superiority in choosing suitable SPE columns to handle a growing and larger number of PPCPs in water environments and beyond.
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Affiliation(s)
- Weifeng Xue
- Technical Center of Dalian Customs, Dalian 116000, China.
| | - Haiqin Zhang
- School of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Mengyao Liu
- Technical Center of Dalian Customs, Dalian 116000, China.
| | - Xi Chen
- Technical Center of Dalian Customs, Dalian 116000, China.
| | - Shuwen He
- Technical Center of Dalian Customs, Dalian 116000, China.
| | - Yingqian Chu
- Technical Center of Dalian Customs, Dalian 116000, China.
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The yeast mitochondrial succinylome: Implications for regulation of mitochondrial nucleoids. J Biol Chem 2021; 297:101155. [PMID: 34480900 PMCID: PMC8477199 DOI: 10.1016/j.jbc.2021.101155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022] Open
Abstract
Acylation modifications, such as the succinylation of lysine, are post-translational modifications and a powerful means of regulating protein activity. Some acylations occur nonenzymatically, driven by an increase in the concentration of acyl group donors. Lysine succinylation has a profound effect on the corresponding site within the protein, as it dramatically changes the charge of the residue. In eukaryotes, it predominantly affects mitochondrial proteins because the donor of succinate, succinyl-CoA, is primarily generated in the tricarboxylic acid cycle. Although numerous succinylated mitochondrial proteins have been identified in Saccharomyces cerevisiae, a more detailed characterization of the yeast mitochondrial succinylome is still lacking. Here, we performed a proteomic MS analysis of purified yeast mitochondria and detected 314 succinylated mitochondrial proteins with 1763 novel succinylation sites. The mitochondrial nucleoid, a complex of mitochondrial DNA and mitochondrial proteins, is one of the structures whose protein components are affected by succinylation. We found that Abf2p, the principal component of mitochondrial nucleoids responsible for compacting mitochondrial DNA in S. cerevisiae, can be succinylated in vivo on at least thirteen lysine residues. Abf2p succinylation in vitro inhibits its DNA-binding activity and reduces its sensitivity to digestion by the ATP-dependent ScLon protease. We conclude that changes in the metabolic state of a cell resulting in an increase in the concentration of tricarboxylic acid intermediates may affect mitochondrial functions.
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DePriest BP, Vieira N, Bidgoli A, Paczesny S. An overview of multiplexed analyses of CAR T-cell therapies: insights and potential. Expert Rev Proteomics 2021; 18:767-780. [PMID: 34628995 PMCID: PMC8626704 DOI: 10.1080/14789450.2021.1992276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Cancer immunotherapy is a rapidly growing field with exponential advancement in engineered immune cell-based therapies. For instance, an engineered chimeric antigen receptor (CAR) can be introduced in T-cells or other immune cells and adoptively transferred to target and kill cancer cells in hematologic malignancies or solid tumors. The first CAR-T-cell (CAR-T) therapy has been developed against CD19, a B-cell marker expressed on lymphoma and lymphoblastic leukemia. To allow for personalized treatment, proteomics approaches could provide insights into biomarkers for CAR-T therapy efficacy and toxicity. AREAS COVERED We researched the most recent technology methods of biomarker evaluation used in the laboratory and clinical setting. Publications of CAR-T biomarkers were then systematically reviewed to provide a narrative of the most validated biomarkers of CAR-T efficacy and toxicity. Examples of biomarkers include CAR-T functionality and phenotype as well as interleukin-6 and other cytokines. EXPERT COMMENTARY Biomarkers of CAR-T efficacy and toxicity have been identified, but still need to be validated and standardized across institutions. Moreover, few are used in the clinical setting due to limitations in real-time technology. Expansion of biomarker research could provide better understanding of patient response and risk of life-threatening side effects with potential for improved precision medicine.
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Affiliation(s)
- Brittany Paige DePriest
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Noah Vieira
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Alan Bidgoli
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Sophie Paczesny
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
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Vrzoňová R, Tóth R, Siváková B, Moťovská A, Gaplovská-Kyselá K, Baráth P, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J, Neboháčová M. OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway. FEMS Yeast Res 2021; 21:6293844. [PMID: 34089318 DOI: 10.1093/femsyr/foab034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.
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Affiliation(s)
- Romana Vrzoňová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Anna Moťovská
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Katarína Gaplovská-Kyselá
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), Jordi Girona 29, 08034 Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jozef Nosek
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Martina Neboháčová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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Abstract
Unlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression, relying instead on posttranscriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base (β-d-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP) tagging and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3), which is also part of another complex containing proteins with domains suggestive of a role in chromatin modification/remodeling. Additionally, JBP3 associates (albeit transiently and/or indirectly) with the trypanosomatid equivalent of the PAF1 complex involved in the regulation of transcription in other eukaryotes. The downregulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional readthrough at the 3′ end of most PTUs. We propose that JBP3 recruits one or more of these complexes to the J-containing regions at the end of PTUs, where they halt the progression of the RNA polymerase. This decoupling of transcription termination from the splicing of individual genes enables the parasites’ unique reliance on polycistronic transcription and posttranscriptional regulation of gene expression. IMPORTANCELeishmania parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of Leishmania and related trypanosomatids. Here, we describe a new J-binding protein (JBP3) associated with three different protein complexes that are reminiscent of those involved in the control of transcription in other eukaryotes. However, the parasite complexes have been reprogrammed to regulate transcription and gene expression in trypanosomatids differently than in the mammalian hosts, providing new opportunities to develop novel chemotherapeutic treatments against these important pathogens.
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Yang N, Xiong Y, Wang Y, Yi Y, Zhu J, Ma F, Li J, Liu H. ADAP Y571 Phosphorylation Is Required to Prime STAT3 for Activation in TLR4-Stimulated Macrophages. THE JOURNAL OF IMMUNOLOGY 2021; 206:814-826. [PMID: 33431658 DOI: 10.4049/jimmunol.2000569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022]
Abstract
Adhesion and degranulation-promoting adapter protein (ADAP), originally identified as an essential adaptor molecule in TCR signaling and T cell adhesion, has emerged as a critical regulator in innate immune cells such as macrophages; however, its role in macrophage polarization and inflammatory responses remains unknown. In this study, we show that ADAP plays an essential role in TLR4-mediated mouse macrophage polarization via modulation of STAT3 activity. Macrophages from ADAP-deficient mice exhibit enhanced M1 polarization, expression of proinflammatory cytokines and capacity in inducing Th1 responses, but decreased levels of anti-inflammatory cytokines in response to TLR4 activation by LPS. Furthermore, overexpression of ADAP enhances, whereas loss of ADAP reduces, the LPS-mediated phosphorylation and activity of STAT3, suggesting ADAP acts as a coactivator of STAT3 activity and function. Furthermore, the coactivator function of ADAP mostly depends on the tyrosine phosphorylation at Y571 in the motif YDSL induced by LPS. Mutation of Y571 to F severely impairs the stimulating effect of ADAP on STAT3 activity and the ability of ADAP to inhibit M1-like polarization in TLR4-activated mouse macrophages. Moreover, ADAP interacts with STAT3, and loss of ADAP renders mouse macrophages less sensitive to IL-6 stimulation for STAT3 phosphorylation. Collectively, our findings revealed an additional layer of regulation of TLR4-mediated mouse macrophage plasticity whereby ADAP phosphorylation on Y571 is required to prime STAT3 for activation in TLR4-stimulated mouse macrophages.
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Affiliation(s)
- Naiqi Yang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China.,Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu Province, China
| | - Yiwei Xiong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Yan Wang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu Province, China
| | - Yulan Yi
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu Province, China
| | - Jingfei Zhu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China; and.,Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Feng Ma
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China; and.,Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Jing Li
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu Province, China
| | - Hebin Liu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China; .,Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu Province, China
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47
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Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol Cell 2021; 81:830-844.e13. [PMID: 33453168 DOI: 10.1016/j.molcel.2020.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
The MYC oncoprotein globally affects the function of RNA polymerase II (RNAPII). The ability of MYC to promote transcription elongation depends on its ubiquitylation. Here, we show that MYC and PAF1c (polymerase II-associated factor 1 complex) interact directly and mutually enhance each other's association with active promoters. PAF1c is rapidly transferred from MYC onto RNAPII. This transfer is driven by the HUWE1 ubiquitin ligase and is required for MYC-dependent transcription elongation. MYC and HUWE1 promote histone H2B ubiquitylation, which alters chromatin structure both for transcription elongation and double-strand break repair. Consistently, MYC suppresses double-strand break accumulation in active genes in a strictly PAF1c-dependent manner. Depletion of PAF1c causes transcription-dependent accumulation of double-strand breaks, despite widespread repair-associated DNA synthesis. Our data show that the transfer of PAF1c from MYC onto RNAPII efficiently couples transcription elongation with double-strand break repair to maintain the genomic integrity of MYC-driven tumor cells.
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48
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Abstract
Complex I (NADH dehydrogenase) is the first enzyme in the respiratory chain. It catalyses the electron transfer from NADH to ubiquinone that is associated with proton pumping out of the matrix. In this study, we characterized NADH dehydrogenase activity in seven monoxenous trypanosomatid species: Blechomonas ayalai, Herpetomonas tarakana, Kentomonas sorsogonicus, Leptomonas seymouri, Novymonas esmeraldas, Sergeia podlipaevi and Wallacemonas raviniae. We also investigated the subunit composition of the complex I in dixenous Phytomonas serpens, in which its presence and activity have been previously documented. In addition to P. serpens, the complex I is functionally active in N. esmeraldas and S. podlipaevi. We also identified 24-32 subunits of the complex I in individual species by using mass spectrometry. Among them, for the first time, we recognized several proteins of the mitochondrial DNA origin.
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49
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Liu T, Abboud MI, Chowdhury R, Tumber A, Hardy AP, Lippl K, Lohans CT, Pires E, Wickens J, McDonough MA, West CM, Schofield CJ. Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondii. J Biol Chem 2020; 295:16545-16561. [PMID: 32934009 PMCID: PMC7864055 DOI: 10.1074/jbc.ra120.013998] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/14/2020] [Indexed: 12/30/2022] Open
Abstract
In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, Dictyostelium discoideum, and the protozoan parasite, Toxoplasma gondii, both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, Trichoplax adhaerens, and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.
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Affiliation(s)
- Tongri Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - James Wickens
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Christopher M West
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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50
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Oxidative stress responses of pathogen bacteria in poultry to plasma-activated lactic acid solutions. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107355] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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