Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator
- Science for Life Laboratory, KTH - Royal Institute of Technology, Sweden
- The Broad Institute and Boston Children's Hospital, United States
- Heidelberg University, Germany
Abstract
Bacteria must balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment. Of all cellular macromolecules, the bacterial proteome is by far the most important resource and its size is limited. Here, we investigated how the highly versatile 'knallgas' bacterium Cupriavidus necator reallocates protein resources when grown on different limiting substrates and with different growth rates. We determined protein quantity by mass spectrometry and estimated enzyme utilization by resource balance analysis modeling. We found that C. necator invests a large fraction of its proteome in functions that are hardly utilized. Of the enzymes that are utilized, many are present in excess abundance. One prominent example is the strong expression of CBB cycle genes such as Rubisco during growth on fructose. Modeling and mutant competition experiments suggest that CO2-reassimilation through Rubisco does not provide a fitness benefit for heterotrophic growth, but is rather an investment in readiness for autotrophy.
Data availability
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD024819. Protein quantification results can be browsed and interactively analyzed using the web application available at https://m-jahn.shinyapps.io/ShinyProt.Sequencing data for TnSeq and BarSeq experiments are available at the European Nucleotide Archive with accession number PRJEB43757. The data for competition experiments performed with the transposon mutant library can be browsed and interactively analyzed using the web application available at https://m-jahn.shinyapps.io/ShinyLib/.
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Gene fitness in the versatile chemolithoautotroph Cupriavidus necatorEuropean Nucleotide Archive, PRJEB43757.
Article and author information
Author details
Johannes Asplund-Samuelsson
Funding
Swedish Research Council Vetenskapsrådet (2016-06160)
- Nick Crang
- Kyle Kimler
- Johannes Asplund-Samuelsson
Swedish Research Council Formas (2019-01491)
- Michael Jahn
Swedish Research Council Formas (2015-939)
- Michael Jahn
Novo Nordisk Fonden (NNF20OC0061469)
- Markus Janasch
- Elton Paul Hudson
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Gisela Storz, National Institute of Child Health and Human Development, United States
Version history
- Preprint posted: March 22, 2021 (view preprint)
- Received: April 1, 2021
- Accepted: October 30, 2021
- Accepted Manuscript published: November 1, 2021 (version 1)
- Version of Record published: November 11, 2021 (version 2)
- Version of Record updated: November 16, 2021 (version 3)
Copyright
© 2021, Jahn et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator
eLife 10:e69019.
https://doi.org/10.7554/eLife.69019
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