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Cited by 7Advanced Proteomics Techniques and ApplicationsClick Chemistry and ApplicationsMicrobial Community Ecology and Physiology

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Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesized proteins

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Hellwig, Patrick, Kautzner, Daniel, Heyer, Robert, Dittrich, Anna, Wibberg, Daniel, Busche, Tobias, Winkler, Anika, Reichl, Udo, Benndorf, Dirk·2024·ISME Communications
DOI 10.1093/ismeco/ycae153PMC PMC11683836

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Abstract

A comprehensive understanding of microbial community dynamics is fundamental to the advancement of environmental microbiology, human health, and biotechnology. Metaproteomics, defined as the analysis of all proteins present within a microbial community, provides insights into these complex systems. Microbial adaptation and activity depend to an important extent on newly synthesized proteins (nP), however, the distinction between nP and bulk proteins is challenging. The application of BONCAT with click chemistry has demonstrated efficacy in the enrichment of nP in pure cultures for proteomics. However, the transfer of this technique to microbial communities and metaproteomics has proven challenging and thus it has not not been used on microbial communities before. To address this, a new workflow with efficient and specific nP enrichment was developed using a laboratory-scale mixture of labelled Escherichia coli and unlabeled yeast. This workflow was then successfully applied to an anaerobic microbial community with initially low bioorthogonal non-canonical amino acid tagging efficiency. A substrate shift from glucose to ethanol selectively enriched nP with minimal background. The identification of bifunctional alcohol dehydrogenase and a syntrophic interaction between an ethanol-utilizing bacterium and two methanogens (hydrogenotrophic and acetoclastic) demonstrates the potential of metaproteomics targeting nP to trace microbial activity in complex microbial communities.

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Metadata

Authors
Hellwig, P., Kautzner, D., Heyer, R., Dittrich, A., Wibberg, D., Busche, T., Winkler, A., Reichl, U., & Benndorf, D.
Affiliations
  • Max Planck Institute for Dynamics of Complex Technical Systems (DE)
  • Bielefeld University (DE)
  • Otto-von-Guericke-Universität Magdeburg (DE)
  • Forschungszentrum Jülich (DE)
  • Anhalt University of Applied Sciences (DE)
Corresponding author
  • Hellwig, Patrick
  • Benndorf, Dirk
ORCID
Venue
ISME Communications
Publisher
Oxford University Press (OUP)
Published
2024-01
Volume
4
Issue
1
Pages
ycae153-ycae153
ISSN
2730-6151 (ISSN-L)
DOI
10.1093/ismeco/ycae153
PMC
PMC11683836
OpenAlex
W4405233147
Cited by
7
References
2
Citations by year
2026: 3 · 2025: 4
FWCI
0.87
Type
journal article
Language
en
Open access
Licence
Locations
  • ISME Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion)
Funders
  • Bielefeld-Gießen Center for Microbial Bioinformatics (031A533)
  • German Network for Bioinformatics Infrastructure
  • Deutsche Forschungsgemeinschaft (446327964)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
newly synthesized proteins, BONCAT, click chemistry, metaproteomics, microbial community dynamics, anaerobic microbial communities, ethanol utilization, syntrophic interactions, methanogenic archaea, Escherichia coli, yeast

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