Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans

Katharina Kremer, Muriel C.F. van Teeseling, Lennart Schada von Borzyskowski, Iria Bernhardsgrütter, Rob J.M. van Spanning, Andrew J. Gates, Mitja N.P. Remus-Emsermann, Martin Thanbichler, Tobias J. Erb

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

During growth, microorganisms have to balance metabolic flux between energy and biosynthesis. One of the key intermediates in central carbon metabolism is acetyl coenzyme A (acetyl-CoA), which can be either oxidized in the citric acid cycle or assimilated into biomass through dedicated pathways. Two acetyl-CoA assimilation strategies in bacteria have been described so far, the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). Here, we show that Paracoccus denitrificans uses both strategies for acetyl-CoA assimilation during different growth stages, revealing an unexpected metabolic complexity in the organism's central carbon metabolism. The EMCP is constitutively expressed on various substrates and leads to high biomass yields on substrates requiring acetyl-CoA assimilation, such as acetate, while the GC is specifically induced on these substrates, enabling high growth rates. Even though each acetyl-CoA assimilation strategy alone confers a distinct growth advantage, P. denitrificans recruits both to adapt to changing environmental conditions, such as a switch from succinate to acetate. Time-resolved single-cell experiments show that during this switch, expression of the EMCP and GC is highly coordinated, indicating fine-tuned genetic programming. The dynamic metabolic rewiring of acetyl-CoA assimilation is an evolutionary innovation by P. denitrificans that allows this organism to respond in a highly flexible manner to changes in the nature and availability of the carbon source to meet the physiological needs of the cell, representing a new phenomenon in central carbon metabolism.IMPORTANCE Central carbon metabolism provides organisms with energy and cellular building blocks during growth and is considered the invariable "operating system" of the cell. Here, we describe a new phenomenon in bacterial central carbon metabolism. In contrast to many other bacteria that employ only one pathway for the conversion of the central metabolite acetyl-CoA, Paracoccus denitrificans possesses two different acetyl-CoA assimilation pathways. These two pathways are dynamically recruited during different stages of growth, which allows P. denitrificans to achieve both high biomass yield and high growth rates under changing environmental conditions. Overall, this dynamic rewiring of central carbon metabolism in P. denitrificans represents a new strategy compared to those of other organisms employing only one acetyl-CoA assimilation pathway.

Original languageEnglish
Pages (from-to)1-15
Number of pages15
JournalmBio
Volume10
Issue number4
DOIs
Publication statusPublished - 9 Jul 2019

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Paracoccus denitrificans
Acetyl Coenzyme A
Carbon
Growth
Biomass
Acetates
Bacteria
Citric Acid Cycle
Succinic Acid

Bibliographical note

Copyright © 2019 Kremer et al.

Keywords

  • acetate
  • carbon metabolism
  • ecophysiology
  • metabolic regulation
  • Paracoccus denitrificans

Cite this

Kremer, K., van Teeseling, M. C. F., Schada von Borzyskowski, L., Bernhardsgrütter, I., van Spanning, R. J. M., Gates, A. J., ... Erb, T. J. (2019). Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. mBio, 10(4), 1-15. https://doi.org/10.1128/mBio.00805-19
Kremer, Katharina ; van Teeseling, Muriel C.F. ; Schada von Borzyskowski, Lennart ; Bernhardsgrütter, Iria ; van Spanning, Rob J.M. ; Gates, Andrew J. ; Remus-Emsermann, Mitja N.P. ; Thanbichler, Martin ; Erb, Tobias J. / Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. In: mBio. 2019 ; Vol. 10, No. 4. pp. 1-15.
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abstract = "During growth, microorganisms have to balance metabolic flux between energy and biosynthesis. One of the key intermediates in central carbon metabolism is acetyl coenzyme A (acetyl-CoA), which can be either oxidized in the citric acid cycle or assimilated into biomass through dedicated pathways. Two acetyl-CoA assimilation strategies in bacteria have been described so far, the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). Here, we show that Paracoccus denitrificans uses both strategies for acetyl-CoA assimilation during different growth stages, revealing an unexpected metabolic complexity in the organism's central carbon metabolism. The EMCP is constitutively expressed on various substrates and leads to high biomass yields on substrates requiring acetyl-CoA assimilation, such as acetate, while the GC is specifically induced on these substrates, enabling high growth rates. Even though each acetyl-CoA assimilation strategy alone confers a distinct growth advantage, P. denitrificans recruits both to adapt to changing environmental conditions, such as a switch from succinate to acetate. Time-resolved single-cell experiments show that during this switch, expression of the EMCP and GC is highly coordinated, indicating fine-tuned genetic programming. The dynamic metabolic rewiring of acetyl-CoA assimilation is an evolutionary innovation by P. denitrificans that allows this organism to respond in a highly flexible manner to changes in the nature and availability of the carbon source to meet the physiological needs of the cell, representing a new phenomenon in central carbon metabolism.IMPORTANCE Central carbon metabolism provides organisms with energy and cellular building blocks during growth and is considered the invariable {"}operating system{"} of the cell. Here, we describe a new phenomenon in bacterial central carbon metabolism. In contrast to many other bacteria that employ only one pathway for the conversion of the central metabolite acetyl-CoA, Paracoccus denitrificans possesses two different acetyl-CoA assimilation pathways. These two pathways are dynamically recruited during different stages of growth, which allows P. denitrificans to achieve both high biomass yield and high growth rates under changing environmental conditions. Overall, this dynamic rewiring of central carbon metabolism in P. denitrificans represents a new strategy compared to those of other organisms employing only one acetyl-CoA assimilation pathway.",
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Kremer, K, van Teeseling, MCF, Schada von Borzyskowski, L, Bernhardsgrütter, I, van Spanning, RJM, Gates, AJ, Remus-Emsermann, MNP, Thanbichler, M & Erb, TJ 2019, 'Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans' mBio, vol. 10, no. 4, pp. 1-15. https://doi.org/10.1128/mBio.00805-19

Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. / Kremer, Katharina; van Teeseling, Muriel C.F.; Schada von Borzyskowski, Lennart; Bernhardsgrütter, Iria; van Spanning, Rob J.M.; Gates, Andrew J.; Remus-Emsermann, Mitja N.P.; Thanbichler, Martin; Erb, Tobias J.

In: mBio, Vol. 10, No. 4, 09.07.2019, p. 1-15.

Research output: Contribution to JournalArticleAcademicpeer-review

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T1 - Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans

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AU - van Teeseling, Muriel C.F.

AU - Schada von Borzyskowski, Lennart

AU - Bernhardsgrütter, Iria

AU - van Spanning, Rob J.M.

AU - Gates, Andrew J.

AU - Remus-Emsermann, Mitja N.P.

AU - Thanbichler, Martin

AU - Erb, Tobias J.

N1 - Copyright © 2019 Kremer et al.

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N2 - During growth, microorganisms have to balance metabolic flux between energy and biosynthesis. One of the key intermediates in central carbon metabolism is acetyl coenzyme A (acetyl-CoA), which can be either oxidized in the citric acid cycle or assimilated into biomass through dedicated pathways. Two acetyl-CoA assimilation strategies in bacteria have been described so far, the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). Here, we show that Paracoccus denitrificans uses both strategies for acetyl-CoA assimilation during different growth stages, revealing an unexpected metabolic complexity in the organism's central carbon metabolism. The EMCP is constitutively expressed on various substrates and leads to high biomass yields on substrates requiring acetyl-CoA assimilation, such as acetate, while the GC is specifically induced on these substrates, enabling high growth rates. Even though each acetyl-CoA assimilation strategy alone confers a distinct growth advantage, P. denitrificans recruits both to adapt to changing environmental conditions, such as a switch from succinate to acetate. Time-resolved single-cell experiments show that during this switch, expression of the EMCP and GC is highly coordinated, indicating fine-tuned genetic programming. The dynamic metabolic rewiring of acetyl-CoA assimilation is an evolutionary innovation by P. denitrificans that allows this organism to respond in a highly flexible manner to changes in the nature and availability of the carbon source to meet the physiological needs of the cell, representing a new phenomenon in central carbon metabolism.IMPORTANCE Central carbon metabolism provides organisms with energy and cellular building blocks during growth and is considered the invariable "operating system" of the cell. Here, we describe a new phenomenon in bacterial central carbon metabolism. In contrast to many other bacteria that employ only one pathway for the conversion of the central metabolite acetyl-CoA, Paracoccus denitrificans possesses two different acetyl-CoA assimilation pathways. These two pathways are dynamically recruited during different stages of growth, which allows P. denitrificans to achieve both high biomass yield and high growth rates under changing environmental conditions. Overall, this dynamic rewiring of central carbon metabolism in P. denitrificans represents a new strategy compared to those of other organisms employing only one acetyl-CoA assimilation pathway.

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KW - acetate

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Kremer K, van Teeseling MCF, Schada von Borzyskowski L, Bernhardsgrütter I, van Spanning RJM, Gates AJ et al. Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. mBio. 2019 Jul 9;10(4):1-15. https://doi.org/10.1128/mBio.00805-19