Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1
Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00149/full |
| _version_ | 1817984990938398720 |
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| author | Deborah eLeon A. Jimmy Ytterberg Pinmanee eBoontheung Unmi eKim Joseph eLoo Rob eGunsalus Rachel R. Ogorzalek Loo |
| author_facet | Deborah eLeon A. Jimmy Ytterberg Pinmanee eBoontheung Unmi eKim Joseph eLoo Rob eGunsalus Rachel R. Ogorzalek Loo |
| author_sort | Deborah eLeon |
| collection | DOAJ |
| description | Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to mine information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more.This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified. |
| first_indexed | 2024-04-13T23:52:25Z |
| format | Article |
| id | doaj.art-2003f64e955f4b45a7806f2751acc2fc |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-13T23:52:25Z |
| publishDate | 2015-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-2003f64e955f4b45a7806f2751acc2fc2022-12-22T02:24:02ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-03-01610.3389/fmicb.2015.00149125133Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1Deborah eLeon0A. Jimmy Ytterberg1Pinmanee eBoontheung2Unmi eKim3Joseph eLoo4Rob eGunsalus5Rachel R. Ogorzalek Loo6University of California Los AngelesUniversity of California Los AngelesUniversity of California Los AngelesUniversity of California Los AngelesUniversity of California Los AngelesUniversity of California Los AngelesUniversity of California Los AngelesProteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to mine information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more.This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00149/fullConcanavalin AMembrane ProteinsS-layersMethanosarcina mazeiarchaeal surface proteinsprokaryotic glycosylation |
| spellingShingle | Deborah eLeon A. Jimmy Ytterberg Pinmanee eBoontheung Unmi eKim Joseph eLoo Rob eGunsalus Rachel R. Ogorzalek Loo Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 Frontiers in Microbiology Concanavalin A Membrane Proteins S-layers Methanosarcina mazei archaeal surface proteins prokaryotic glycosylation |
| title | Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 |
| title_full | Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 |
| title_fullStr | Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 |
| title_full_unstemmed | Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 |
| title_short | Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1 |
| title_sort | mining proteomic data to expose protein modifications in methanosarcina mazei strain g 246 1 |
| topic | Concanavalin A Membrane Proteins S-layers Methanosarcina mazei archaeal surface proteins prokaryotic glycosylation |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00149/full |
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