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Chapter 12 : The Krebs Citric Acid Cycle

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Abstract:

The Krebs citric acid cycle, a central pathway of intermediary metabolism, generates ATP, reducing power, and biosynthetic intermediates. This chapter provides a list of enzymes of the Krebs cycle and the genes that encode them. In , isocitrate dehydrogenase (IDH) reduces NADP, but in other organisms IDH is an NAD-reducing enzyme. Among the enzymes from gram-positive bacteria, IDH is unusual; it resembles the IDH in that it lacks the extra loop of amino acids found in IDH. The loss of aconitase activity causes a severe block in SpoOA~P-dependent gene expression and near-total blockage of sporulation at stage 0. In large measure, this defect can be attributed to accumulation of citrate, both inside the cells and in the medium. Citrate is a chelatot of divalent cations; in this case, Mn and Fe are the relevant cations. The gene encodes the sole malate dehydrogenase (MDH) of this organism, as judged by total loss of MDH enzyme activity and at least partial aspartate auxotrophy in a null mutant. The gene is upstream of and divergently transcribed from in all spp. examined. The enzymes for the dicarboxylic acid part of the cycle probably appeared very early in evolution, since they are found in species from all branches of life. The genes for isopropylmalate isomerase () and isopropylmalate dehydrogenase () are close homologs of the and genes, respectively, and the reactions catalyzed by the respective enzymes are chemically analogous.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12

Key Concept Ranking

Transcription Start Site
0.59148425
Acetyl Coenzyme A
0.5106383
Gene Expression and Regulation
0.5019132
Fatty Acid Biosynthesis
0.4468175
Fatty Acid Degradation
0.4468175
0.59148425
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Figures

Image of FIGURE 1
FIGURE 1

The Krebs citric acid cycle and related pathways. The pathway from acetyl coenzyme A (acetyl-CoA) to oxaloacetate is shown as it occurs in subtilis. The glyoxylate shunt, indicated by dashed lines, is absent from but is found in some other low-G+C gram-positive bacteria. Genes that encode the relevant enzymes are shown in italicized, lowercase lettering. Oxaloacetate to prime the cycle is generated by pyruvate carboxylase (encoded by conversion of oxaloacetate to phosphoenolpyruvate (PEP) for gluconeogenesis is mediated by PEP carboxykinase (encoded by During fermentative growth, pyruvate is converted to lactate, ethanol, acetoin, and acetate. Acetate production is catalyzed by phosphotransacetylase and acetate kinase, encoded by and respectively. The acetate kinase reaction is coupled to ATP synthesis. Acetate utilization is mediated by acetyl-CoA synthetase, the product of the gene.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
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Image of FIGURE 2
FIGURE 2

Genes for Krebs cycle enzymes and related pathways. Gene organization is shown as it occurs in For some genes, this organization is conserved in related organisms (see Table 2 ), but in other cases the genes are located in entirely different genetic environments.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
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Image of FIGURE 3
FIGURE 3

Regulation of transcription of citZ and citB. (A) The citZ promoter is repressed directly by CcpA (small dark ovals; shown as a dimer) and CcpC (light ovals; shown as a pair of dimers). The binding site for CcpA appears to be centered at position +89 with respect to the transcription start site. CcpA bound at this site presumably acts as a roadblock to transcription; CcpC binds to a dyad symmetry element centered at position + 32 and to a second copy of one arm of the dyad element located at about position +1 ( ). Binding of CcpC is reduced in the presence of citrate ( ). In the fully derepressed state, neither CcpA nor CcpC binds to the DNA, and RNA polymerase (large dark oval) has unrestricted access to the promoter and downstream DNA. (B) The citB promoter is repressed directly by CcpC (light ovals; shown as dimers) and indirectly by CcpA. CcpC binds to two sites, a high-affinity, dyad symmetry site centered at position −66 and a weaker half-dyad site at position − 27 ( ). Mutations in either one of these sites cause derepression of the citB gene in cells grown in glucose-glutamate medium. Binding of CcpC to the promoter region induces a 60° bend in the DNA (at position −41), presumably owing to interaction between CcpC molecules bound at positions −66 and −27 ( ). According to a model currently being tested, this bent complex cannot serve as a binding site for RNA polymerase (large dark oval), and the citB gene is repressed. The model postulates that citrate induces the citB gene by binding to CcpC and interfering with protein-protein interaction, thereby unbending the DNA and making the promoter accessible for transcription. A mutant is also partially derepressed for citB transcription ( ), but the citB gene region does not contain any apparent binding site for CcpA. It appears that in the absence of CcpA there is enough expression of citZ that some citrate can accumulate and partially inactivate CcpC. In cells growing in nutrient broth medium, the citB gene is induced as cells make the transition from exponential phase to stationary phase ( ). This induction requires the inactivation of CcpC., AbrB (a global repressor of stationary-phase genes), and CodY, a GTP-sensing repressor of many stationary-phase genes ( ). Binding of AbrB covers the region from positions −35 to + 14 ( ); the CodY binding site has not yet been defined.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
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Image of FIGURE 4
FIGURE 4

A putative pathway for propionate metabolism in Gene and enzyme assignments have been made by analogy with known pathways in and . (see text and Table 3 ). The precursor of propionyl-CoA may be propionate or an intermediate in fatty acid degradation.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
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Tables

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TABLE 1

Enzymes and genes of the Krebs citric acid cycle and related pathways

Based on studies with PDHC (65). One E2 60-mer associates with 30–60 El tetramers and 30–60 E3 dimers.

PDHC and OGDC contain identical E3 components.

The overall structure of OGDC is likely to be analogous to that of PDHC., although the El subenzyme is encoded in a single gene for OGDC and in two genes for PDHC.

Based on studies with SCS ( ).

Identity at protein sequence level based on Blast 2 alignment of sequences obtained from SubtiList (http://genolist.pasteur.fr/SubtiList/) and Colibri (http://geno-list.pasteur.fr/Colibri/) databases. A minus sign indicates no significant similarity.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
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TABLE 2

Krebs cycle gene organization in low-G+C gram-positive bacteria

Gene assignments and organization depicted hete wete based in part on data available as of November 2000 at the following websites: SubtiList (http://genolist.pasteur. fr/SubtiList/), The Institute for Genome Research (http://www.tigr.org/tdb/mdb/mdbcomplete.html), The Sanger Centre (http://www.sanger.ac.uk/Projects/), the National Library of Medicine (http://www.ncbi.nlm.nih.gov/BLAST/), the Japan Marine Science and Technology Center (http://www.jamstec.go.jp/jamstece/bio/DEEPSTAR/exbase.html), and the University of Oklahoma (http://www.genome.ou.edu/bstearo-blast.html). Only the . and . sequences were completed and annotated at the time of analysis. A minus sign indicates the absence of a coding sequence of substantial similarity when the genome in question was probed with the relevant coding sequence.

Abbreviations of species names: Bacillus strain 168; Bha, halodurans strain C-125; Ban, Ames; Bst, strain 10; , ; , strain RP62A; Smu, strain UAB159; , type 4; Manfredo; , strain V583; Clostridium strain 630; ssp. C2; Clostridium acetobutylicum ATCC 824.

For definitions of abbreviations of enzymes, see Table 1 .

ND, not detected. The incomplete sequence of the genome (as of November 2000) did not contain a significant homolog of and lacked the N-terminal coding region of C.

The reported sequence of the B gene has an apparent frameshift mutation at residue 46.

The H gene is not linked to ZC

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12
Generic image for table
TABLE 3

Putative pathway for propionate metabolism

Identity at protein sequence level as defined by BestFit analysis.

acetyl-CoA synthetase and long-chain acyl-CoA synthetases are homologs of S. PrpE, but none is encoded by a gene linked to the locus.

Citation: Sonenshein A. 2002. The Krebs Citric Acid Cycle, p 151-162. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch12

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