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EcoSal Plus

Domain 3:

Metabolism

Molecular Basis for Bacterial Growth on Citrate or Malonate

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  • Author: Peter Dimroth1
  • Editor: Valley Stewart2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Institute of Microbiology, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland; 2: University of California, Davis, Davis, CA
  • Received 06 February 2004 Accepted 21 April 2004 Published 06 July 2004
  • Address correspondence to Peter Dimroth dimroth@micro.biol.ethz.ch
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  • Abstract:

    Environmental citrate or malonate is degraded by a variety of aerobic or anaerobic bacteria. For selected examples, the genes encoding the specific enzymes of the degradation pathway are described together with the encoded proteins and their catalytic mechanisms. Aerobic bacteria degrade citrate readily by the basic enzyme equipment of the cell if a specific transporter for citrate is available. Anaerobic degradation of citrate in requires the so-called substrate activation module to convert citrate into its thioester with the phosphoribosyl dephospho-CoA prosthetic group of citrate lyase. The citryl thioester is subsequently cleaved into oxaloacetate and the acetyl thioester, from which a new citryl thioester is formed as the turnover continues. The degradation of malonate likewise includes a substrate activation module with a phosphoribosyl dephospho-CoA prosthetic group. The machinery gets ready for turnover after forming the acetyl thioester with the prosthetic group. The acetyl residue is then exchanged by a malonyl residue, which is easily decarboxylated with the regeneration of the acetyl thioester. This equipment suffices for aerobic growth on malonate, since ATP is produced via the oxidation of acetate. Anaerobic growth on citrate or malonate, however, depends on additional enzymes of a so-called energy conservation module. This allows the conversion of decarboxylation energy into an electrochemical gradient of Na ions. In citrate-fermenting , the Na gradient is formed by the oxaloacetate decarboxylase and mainly used to drive the active transport of citrate into the cell. To use this energy source for this purpose is possible, since ATP is generated by substrate phosphorylation in the well-known sequence from pyruvate to acetate. In the malonate-fermenting bacterium , however, no reactions for substrate level phosphorylation are available and the Na gradient formed in the malonate decarboxylation reaction must therefore be used as the driving force for ATP synthesis.

  • Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6

Key Concept Ranking

Integral Membrane Proteins
0.4342381
Lactic Acid Bacteria
0.40849537
Carboxylic Acids
0.37079585
Oxaloacetate Decarboxylase
0.35290468
Cyclic AMP
0.3355856
0.4342381

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/content/journal/ecosalplus/10.1128/ecosalplus.3.4.6
2004-07-06
2017-11-22

Abstract:

Environmental citrate or malonate is degraded by a variety of aerobic or anaerobic bacteria. For selected examples, the genes encoding the specific enzymes of the degradation pathway are described together with the encoded proteins and their catalytic mechanisms. Aerobic bacteria degrade citrate readily by the basic enzyme equipment of the cell if a specific transporter for citrate is available. Anaerobic degradation of citrate in requires the so-called substrate activation module to convert citrate into its thioester with the phosphoribosyl dephospho-CoA prosthetic group of citrate lyase. The citryl thioester is subsequently cleaved into oxaloacetate and the acetyl thioester, from which a new citryl thioester is formed as the turnover continues. The degradation of malonate likewise includes a substrate activation module with a phosphoribosyl dephospho-CoA prosthetic group. The machinery gets ready for turnover after forming the acetyl thioester with the prosthetic group. The acetyl residue is then exchanged by a malonyl residue, which is easily decarboxylated with the regeneration of the acetyl thioester. This equipment suffices for aerobic growth on malonate, since ATP is produced via the oxidation of acetate. Anaerobic growth on citrate or malonate, however, depends on additional enzymes of a so-called energy conservation module. This allows the conversion of decarboxylation energy into an electrochemical gradient of Na ions. In citrate-fermenting , the Na gradient is formed by the oxaloacetate decarboxylase and mainly used to drive the active transport of citrate into the cell. To use this energy source for this purpose is possible, since ATP is generated by substrate phosphorylation in the well-known sequence from pyruvate to acetate. In the malonate-fermenting bacterium , however, no reactions for substrate level phosphorylation are available and the Na gradient formed in the malonate decarboxylation reaction must therefore be used as the driving force for ATP synthesis.

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Figures

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Figure 1

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 2

The function of the encoded proteins is indicated. The genes having counterparts in are shown in dark gray; those without are indicated in light gray.

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 3

The overall translocation process is electroneutral and a transmembrane chemical gradient of the cotransported ions (ΔpNa/ΔpH) serves as driving force ().

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 4

ACP, acyl carrier protein; HS-R, prosthetic group; α-subunit, acetyl-ACP:citrate ACP transferase; β-subunit, citryl-ACP lyase. (B) Chemical reactions allowing specific acetylation, deacetylation, and carboxymethylation of the prosthetic group of citrate lyase.

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 5

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 6

The model depicts the location and interaction between subunits as well as individual reactions carried out by these subunits during the catalytic cycle. B-H, biotin prosthetic group; B-CO , carboxybiotin.

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 7

The model shows the location of important residues of helix IV and helix VIII and of region IIIa of the β subunit. Also shown is the participation of these residues in the vectorial and chemical events of the Na pump. (A) The empty binding site region with enzyme-bound carboxybiotin (B-COO), exposing the Na binding sites towards the cytoplasm. (B) The first Na binding site at the D203-N373 pair has been occupied and the second Na enters the Y229-S382-including site with simultaneous release of the proton from the hydroxyl side chain of Y229. This displacement may lead to the rearrangement of hydrogen bonding in the network involving Y220 and carboxybiotin to deliver the proton to the latter compound. This catalyzes the immediate decarboxylation of the acid-labile carboxybiotin, including a conformational change (B → C) which exposes the Na binding sites towards the periplasm (C). The Na ions are subsequently released into this reservoir, while a proton enters the periplasmic channel and restores the hydroxyl group of Y229. (D) The Na binding sites are empty and exposed toward the periplasm and the biotin prosthetic group is not modified (B-H). Upon carboxylation of the biotin, the protein switches back into the conformation where the Na binding sites are exposed toward the cytoplasm (D → A) ().

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Image of Figure 8
Figure 8

MdcA, acetyl-S-ACP:malonate ACP transferase; MdcC, acyl carrier protein (ACP); MdcD,E, malonyl-S-ACP decarboxylase; MdcF, malonate transporter; MdcH, malonyl-CoA:ACP-SH transferase; MdcB, ATP:dephospho-CoA 5′-triphosphoribosyltransferase; MdcG, 2′-(5″-triphosphoribosyl)-3′-dephospho-CoA:apoACP 2′-(5″-phophoribosyl)-3′-dephospho-CoA transferase; MdcR, regulator protein.

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 9

The deprotonated hydroxyl group of serine 25 from the ACP makes an in-line nucleophilic attack on the α phosphate of the prosthetic group precursor under reversion of the conformation on the α phosphate. The transition state is stabilized by two magnesium ions, which are coordinated by the three invariant aspartates. A, adenine; R, 4′-diphosphopantetheine moiety of the prosthetic group.

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Figure 10

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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Image of Figure 11
Figure 11

The enzyme is composed of a substrate activation module, which is related to citrate lyase and the non-energy-conserving malonate decarboxylase from . It also includes an energy conservation module with relationship to the Na-translocating decarboxylases, e.g., oxaloacetate decarboxylase from .

Citation: Dimroth P. 2004. Molecular Basis for Bacterial Growth on Citrate or Malonate, EcoSal Plus 2004; doi:10.1128/ecosalplus.3.4.6
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