PXD020005-2

PXD020005 is an original dataset announced via ProteomeXchange.

Title	Searching for the small unknowns - Discovery of novel sProteins in a simplified human intestinal microbiome
Description	The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, in modulating immunity and in regulating metabolic processes. We use the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species to study potential synergistic effects with a particular focus on detecting novel proteins with less than 100 amino acids (= sProteins), some of which may contribute to regulate the simplified human intestinal microbiota. Although several studies have shown that 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. In this study, we created a multi-species integrated proteogenomics search database (multi-species iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were first sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied prior to mass spectrometric analysis to specifically increase the chances for novel sProtein discovery. Searching the MS/MS data against the multi-species iPtgxDB enabled us to identify 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. Importantly, when comparing the expression of these novel sProteins in single strain cultivations to the multi-species community grown in a bioreactor, we found that six of them were only identified in the SIHUMIx community, indicating a possible important role of sProteins in the organization of microbial communities. Furthermore, in silico prediction suggested that two of these novel sProteins have a potential antimicrobial function. We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in microbial communities that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the multi-species community is expected to enable new insights into the structure, regulation and function of bacterial communities such as those of the human intestinal tract.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:28:38.886.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Erysipelatoclostridium ramosum DSM 1402; NCBI TaxID: 445974; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Anaerostipes caccae DSM 14662; NCBI TaxID: 411490; scientific name: Bifidobacterium longum NCC2705; NCBI TaxID: 206672; scientific name: Clostridium butyricum DSM 10702; NCBI TaxID: 1316931; scientific name: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); NCBI TaxID: 226186; scientific name: Blautia producta ATCC 27340 = DSM 2950; NCBI TaxID: 1121114; scientific name: Lactobacillus plantarum subsp. plantarum; NCBI TaxID: 337330;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-24 22:54:55	ID requested
1	2021-09-09 02:39:17	announced
⏵ 2	2024-10-22 05:28:40	announced	2024-10-22: Updated project metadata.

10.1186/s40168-020-00981-z;

Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M, Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. Microbiome, 9(1):55(2021) [pubmed]

submitter keyword: Small proteins (sProteins)

SIHUMIx

human gut microbiome

proteogenomics

metatranscriptomics

metaproteomics

Nico Jehmlich
contact affiliation	Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15 04318 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD020005

PRIDE project URI

• PRIDE
  1. PXD020005
     1. Label: PRIDE project
     2. Name: Searching for the small unknowns - Discovery of novel sProteins in a simplified human intestinal microbiome