GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16<i>S</i> small subunit ribosomal-RNA (16<i>S</i> rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify is...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/21/15692 |
| _version_ | 1797631865162563584 |
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| author | Simon Klaes Shobhit Madan Darja Deobald Myriel Cooper Lorenz Adrian |
| author_facet | Simon Klaes Shobhit Madan Darja Deobald Myriel Cooper Lorenz Adrian |
| author_sort | Simon Klaes |
| collection | DOAJ |
| description | Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16<i>S</i> small subunit ribosomal-RNA (16<i>S</i> rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution. |
| first_indexed | 2024-03-11T11:28:44Z |
| format | Article |
| id | doaj.art-771e6733a67f4b7fbd4578bf2cebced6 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T11:28:44Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-771e6733a67f4b7fbd4578bf2cebced62023-11-10T15:04:55ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-10-0124211569210.3390/ijms242115692GroEL-Proteotyping of Bacterial Communities Using Tandem Mass SpectrometrySimon Klaes0Shobhit Madan1Darja Deobald2Myriel Cooper3Lorenz Adrian4Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, GermanyDepartment of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, GermanyDepartment of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, GermanyFaculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, GermanyDepartment of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, GermanyProfiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16<i>S</i> small subunit ribosomal-RNA (16<i>S</i> rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.https://www.mdpi.com/1422-0067/24/21/15692shotgun proteomicsproteotypingmicrobial communitiesGroELchaperontaxonomic profiling |
| spellingShingle | Simon Klaes Shobhit Madan Darja Deobald Myriel Cooper Lorenz Adrian GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry International Journal of Molecular Sciences shotgun proteomics proteotyping microbial communities GroEL chaperon taxonomic profiling |
| title | GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry |
| title_full | GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry |
| title_fullStr | GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry |
| title_full_unstemmed | GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry |
| title_short | GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry |
| title_sort | groel proteotyping of bacterial communities using tandem mass spectrometry |
| topic | shotgun proteomics proteotyping microbial communities GroEL chaperon taxonomic profiling |
| url | https://www.mdpi.com/1422-0067/24/21/15692 |
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