Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
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| Title: | Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome |
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| Authors: | Petruschke, Hannes, Schori, Christian, Canzler, Sebastian, Riesbeck, Sarah, Poehlein, Anja, Daniel, Rolf, Frei, Daniel, Segessemann, Tina, Zimmerman, Johannes, Marinos, Georgios, Kaleta, Christoph, Jehmlich, Nico, Ahrens, Christian H., von Bergen, Martin, Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research – UFZ GmbH, Leipzig, Germany, Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland, Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany, Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany, Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany |
| Contributors: | Petruschke, Hannes, Schori, Christian, Canzler, Sebastian, Riesbeck, Sarah, Poehlein, Anja, Daniel, Rolf, Frei, Daniel, Segessemann, Tina, Zimmerman, Johannes, Marinos, Georgios, Kaleta, Christoph, Jehmlich, Nico, Ahrens, Christian H., von Bergen, Martin, Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research – UFZ GmbH, Leipzig, Germany, Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland, Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany, Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany, Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany |
| Source: | Microbiome Microbiome, Vol 9, Iss 1, Pp 1-19 (2021) |
| Publisher Information: | Springer Science and Business Media LLC, 2021. |
| Publication Year: | 2021 |
| Subject Terms: | Metabolic modelling, 0301 basic medicine, 2. Zero hunger, Bacteria, iPtgxDB, Research, QR100-130, Tandem Mass Spectrometry [MeSH], Human gut microbiome, Bacteria/metabolism [MeSH], Intestines/microbiology [MeSH], Humans [MeSH], Cell Communication [MeSH], Bacteria/genetics [MeSH], Small proteins (sProteins), Bacterial Proteins/analysis [MeSH], Metagenome/genetics [MeSH], Gastrointestinal Microbiome/genetics [MeSH], Intestines/chemistry [MeSH], Metatranscriptomics, Proteogenomics, Bacterial Proteins/chemistry [MeSH], Bacterial Proteins/genetics [MeSH], Bacteria/classification [MeSH], Metaproteomics, SIHUMIx, Bacteria/isolation, Cell Communication, Gastrointestinal Microbiome, Microbial ecology, Intestines, 03 medical and health sciences, Bacterial Proteins, Tandem Mass Spectrometry, Humans, Metagenome |
| Description: | BackgroundThe intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.ResultsWe created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.ConclusionsWe outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. |
| Document Type: | Article Other literature type |
| Language: | English |
| ISSN: | 2049-2618 |
| DOI: | 10.1186/s40168-020-00981-z |
| Access URL: | https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-020-00981-z https://pubmed.ncbi.nlm.nih.gov/33622394 https://doaj.org/article/81a31d395603419c8db097384e4bbb01 https://link.springer.com/article/10.1186/s40168-020-00981-z/tables/1 https://link.springer.com/content/pdf/10.1186/s40168-020-00981-z.pdf https://link.springer.com/article/10.1186/s40168-020-00981-z https://www.researchsquare.com/article/rs-318776/v1 https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00981-z https://pubmed.ncbi.nlm.nih.gov/33622394/ https://resolver.sub.uni-goettingen.de/purl?gro-2/123184 https://resolver.sub.uni-goettingen.de/purl?gs-1/17737 https://repository.publisso.de/resource/frl:6464413 |
| Rights: | CC BY |
| Accession Number: | edsair.doi.dedup.....ec20485a3badf070d659b511f6a93d79 |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstract: | BackgroundThe intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.ResultsWe created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.ConclusionsWe outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. |
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| ISSN: | 20492618 |
| DOI: | 10.1186/s40168-020-00981-z |