Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation
- Published
- Accepted
- Subject Areas
- Biochemistry, Bioinformatics, Biotechnology, Microbiology
- Keywords
- Rhizopus delemar, fumarate, proteomics, transcriptomics, amino acid metabolism, nitrogen metabolism
- Copyright
- © 2017 Odoni et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation. PeerJ Preprints 5:e2742v1 https://doi.org/10.7287/peerj.preprints.2742v1
Abstract
The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood. We set out to increase the knowledge about fumarate accumulation in R. delemar. To this end, we combined a transcriptomics and proteomics approach to identify key metabolic pathways involved in fumarate production in R. delemar, and propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
R. delemar ATCC20344 RNA seq assembly fasta file
Fasta file of all de novo assembled transcripts obtained from the R. delemar ATCC 20344 transcriptomics experiment.
R. delemar ATCC20344 RNA seq assembly allORFs above cutoff 21 fasta file
In silico translation of de novo assembled transcripts from the R. delemar ATCC 20344 transcriptomics experiment. Minimun protein length >= 21 amino acids.
R. delemar ATCC20344 snapshot proteome
Relative protein abundance and average nucleotide coverage of enzymes identified in the proteomics data. Note that only enzymes that could be predicted by PRIAM are listed.
Metabolic pathway enrichment analysis
Metabolic pathway coverage and hypergeometric test results of proteins found in the R. delemar ATCC 20344 and R. delemar RA 99-880 in silico and snapshot proteomes.