Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

Dorett I. Odoni; Juan A. Tamayo-Ramos; Jasper Sloothaak; Ruben van Heck; Vitor A.P. Martins dos Santos; Leo H. de Graaff; Maria Suarez-Diez; Peter J. Schaap

doi:10.7717/peerj.3133

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

Dorett I. Odoni, Juan A. Tamayo-Ramos, Jasper Sloothaak, Ruben van Heck, Vitor A.P. Martins dos Santos, Leo H. de Graaff, Maria Suarez-Diez, Peter J. Schaap^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

4 Citations (Scopus)

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.

Original language	English
Article number	e3133
Journal	PeerJ
Volume	5
DOIs	https://doi.org/10.7717/peerj.3133
Publication status	Published - 30 Mar 2017

Keywords

Amino acid metabolism
Fumarate
Nitrogen metabolism
Proteomics
Rhizopus delemar
Transcriptomics

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10.7717/peerj.3133Licence: CC BY

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Rhizopus delemar grown under high and low oxygen conditions
Odoni, D. I. (Creator), Tamayo Ramos, J. A. (Creator), Sloothaak, J. (Creator), van Heck, R. G. A. (Creator), Martins dos Santos, V. (Creator), de Graaff, L. H. (Creator), Suarez Diez, M. (Creator) & Schaap, P. (Creator), Wageningen University, 16 Feb 2017
https://www.ebi.ac.uk/ena/data/view/PRJEB14210
Dataset
Rhizopus delemar LC-MS/MS high low oxygen
Odoni, D. I. (Creator) & Martins dos Santos, V. (Creator), Wageningen University, 15 Feb 2017
https://www.ebi.ac.uk/pride/archive/projects/PXD004600
Dataset

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@article{2b241fa51a8948fa92b50d815e33d911,

title = "Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation",

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.",

keywords = "Amino acid metabolism, Fumarate, Nitrogen metabolism, Proteomics, Rhizopus delemar, Transcriptomics",

author = "Odoni, {Dorett I.} and Tamayo-Ramos, {Juan A.} and Jasper Sloothaak and {van Heck}, Ruben and {Martins dos Santos}, {Vitor A.P.} and {de Graaff}, {Leo H.} and Maria Suarez-Diez and Schaap, {Peter J.}",

year = "2017",

month = mar,

day = "30",

doi = "10.7717/peerj.3133",

language = "English",

volume = "5",

journal = "PeerJ",

issn = "2167-8359",

publisher = "PeerJ",

}

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation. / Odoni, Dorett I.; Tamayo-Ramos, Juan A.; Sloothaak, Jasper; van Heck, Ruben; Martins dos Santos, Vitor A.P.; de Graaff, Leo H.; Suarez-Diez, Maria ; Schaap, Peter J.

In: PeerJ, Vol. 5, e3133, 30.03.2017.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

AU - Odoni, Dorett I.

AU - Tamayo-Ramos, Juan A.

AU - Sloothaak, Jasper

AU - van Heck, Ruben

AU - Martins dos Santos, Vitor A.P.

AU - de Graaff, Leo H.

AU - Suarez-Diez, Maria

AU - Schaap, Peter J.

PY - 2017/3/30

Y1 - 2017/3/30

N2 - 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.

AB - 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.

KW - Amino acid metabolism

KW - Fumarate

KW - Nitrogen metabolism

KW - Proteomics

KW - Rhizopus delemar

KW - Transcriptomics

U2 - 10.7717/peerj.3133

DO - 10.7717/peerj.3133

M3 - Article

AN - SCOPUS:85016445653

VL - 5

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e3133

ER -

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

Abstract

Keywords

Access to Document

Rhizopus delemar grown under high and low oxygen conditions

Rhizopus delemar LC-MS/MS high low oxygen

Cite this