The acetate switch

Abstract

To succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. One such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. This review explains why, when, and how cells excrete or dissimilate acetate. The central components of the "switch" (phosphotransacetylase [PTA], acetate kinase [ACK], and AMP-forming acetyl coenzyme A synthetase [AMP-ACS]) and the behavior of cells that lack these components are introduced. Acetyl phosphate (acetyl approximately P), the high-energy intermediate of acetate dissimilation, is discussed, and conditions that influence its intracellular concentration are described. Evidence is provided that acetyl approximately P influences cellular processes from organelle biogenesis to cell cycle regulation and from biofilm development to pathogenesis. The merits of each mechanism proposed to explain the interaction of acetyl approximately P with two-component signal transduction pathways are addressed. A short list of enzymes that generate acetyl approximately P by PTA-ACKA-independent mechanisms is introduced and discussed briefly. Attention is then directed to the mechanisms used by cells to "flip the switch," the induction and activation of the acetate-scavenging AMP-ACS. First, evidence is presented that nucleoid proteins orchestrate a progression of distinct nucleoprotein complexes to ensure proper transcription of its gene. Next, the way in which cells regulate AMP-ACS activity through reversible acetylation is described. Finally, the "acetate switch" as it exists in selected eubacteria, archaea, and eukaryotes, including humans, is described.

FIG. 1.

Schematics showing the “acetate switch” during aerobic growth in minimal medium supplemented with glucose as the sole carbon source (A) and in tryptone broth (B). The single-headed arrow points to the physiological acetate switch. OD, optical density. [glc] and [ace], extracellular glucose and acetate concentrations. [ser], [asp], [trp], [ala], [glu], and [thr], extracellular amino acid concentrations. The double-headed arrows denote the interval of amino acid consumption. [acCoA] and [ac∼P], intracellular acetyl-CoA and acetyl∼P concentrations.

FIG. 2.

Acetyl-CoA (acCoA) sits at the crossroads of central metabolism.

FIG. 3.

The pathways of central metabolism. For glycolysis, only some of the intermediates and enzymes of glycolysis are noted. PEP, phosphoenolpyruvate; Pyr, pyruvate; PFK, phosphofructokinase; TPIA, triosephosphate isomerase; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PDHC, pyruvate dehydrogenase complex. For acetate metabolism: POXB, pyruvate oxidase; PTA-ACKA, phosphotransacetylase-acetate kinase pathway; ACS, AMP-forming acetyl-CoA synthetase. The dotted arrows denote the proposed PDHC bypass formed by POXB and AMP-ACS. For the TCA cycle: CS, citrate synthase; ACN, aconitase; IDH, isocitrate dehydrogenase; 2-KG, 2-ketoglutarate; KGDH, 2-ketoglutarate dehydrogenase; SCSC, succinyl-CoA synthetase complex; SDH, succinate dehydrogenase; FUMA, fumarase; MDH, malate dehydrogenase; OAA, oxaloacetate. FRD, fumarate reductase, expressed under anaerobic conditions, bypasses SDH. For the glyoxylate bypass: ICL, isocitrate lyase; MAS, malate synthase; IDHK/P, isocitrate dehydrogenase kinase/phosphatase. Underlines and dashed arrows denote enzymes and steps unique to the glyoxylate bypass. For gluconeogenesis: PPSA, PEP synthase; PCKA, pyruvate carboxykinase; MAEB and SFCA, malic enzymes. Boxes and double-lined arrows denote enzymes and steps unique to gluconeogenesis.

FIG. 4.

Pathways for the excretion of partially oxidized metabolites. Excreted metabolites are underlined. LDH, lactate dehydrogenase; PFL, pyruvate-formate lyase; PTA, phosphotransacetylase; ACKA, acetate kinase; ADH, alcohol dehydrogenase; FDO, aerobic formate dehydrogenase; FHL, formate-hydrogen lyase.

FIG. 5.

Acetate activation pathways. PDHC, pyruvate dehydrogenase complex; POXB, pyruvate oxidase; PTA, phosphotransacetylase; ACKA, acetate kinase; ACS, AMP-forming acetyl-CoA synthetase; PPase, pyrophosphatase; TCA, tricarboxylic acid cycle; GB, glyoxylate bypass. The dotted arrows denote the proposed PDHC bypass formed by POXB and AMP-ACS.

FIG. 6.

Regulation of nitrogen assimilation. Uridylyltransferase (UTase) and uridylyl-removing enzyme (UR) sense the relative amount of nitrogen. Under limiting conditions, UTase uridylylates PII to PII-UMP. In excess nitrogen, the UR deuridylylates PII-UMP to PII. PII favors adenylyltransferase (ATase) activity. ATase inactivates GS by adenylylating it to GS-AMP. PII (or its ortholog GlnK) also enhances the phosphatase activity of the histidine kinase/phosphatase NRII, which then dephosphorylates NRI∼P. This diminishes transcription from the nitrogen-regulated promoters such as ntr, nac, glnK, and glnALG. In contrast, PII-UMP enhances the deadenylylation of GS-AMP, hence activating the enzyme. PII-UMP exerts no direct effect on NRII; however, the lack of PII favors the kinase activity of NRII, which donates its phosphoryl group to NRI. Acetyl∼P also donates its phosphoryl group to NRI. Transcription from the glnALG promoter requires low amounts of NRI∼P (thin arrow), whereas transcription from the other promoters requires high amounts of NRI∼P (thick arrows).

FIG. 7.

(A) Acetyl∼P can donate its phosphoryl group to two-component RRs. HK-P, histidine kinase/phosphatase. (B) Model depicting how acetyl∼P can influence diverse cellular processes through the RR OmpR and its ability to repress transcription of flhDC. In contrast to acetyl∼P-dependent control of flagellar biosynthesis, its control of cell division does not require FlhC. ED, Entner-Doudoroff.

FIG. 8.

Acetyl∼P-responsive processes and the RRs known to regulate them.

FIG. 9.

Other acetyl∼P-forming enzymes. (A) ACP-POX, acetyl∼P-forming pyruvate oxidase; ThDP, thiamine diphosphate. (B) XSC, sulfoacetaldehyde acetyltransferase. (C) XPK, xylulose 5-phosphate phosphoketolase; GA-3-P, glyceraldehyde-3-phosphate. (D) GR, glycine reductase.

FIG. 10.

Transcription of acs by cells grown in glucose minimal medium relative to optical density, consumption of carbon sources, excretion of acetate, and intracellular concentrations of FIS and IHF. OD, optical density.

FIG. 11.

Regulation of acs transcription. (A) Organization of the nrf-acs locus. The bent arrows represent transcription initiation sites. (B) nrf-acs intergenic region, showing the location of binding sites for CRP, FIS, and IHF. The numbers are relative to the transcription initiation site of acsP2. Numbers in parentheses are relative to the transcription initiation site of acsP1. (C) Proposed interactions for synergistic class III CRP-dependent activation. Cross-hatched double oval, CRP dimer; light gray ovals, α-CTD. Although RNAP possesses only two α-CTDs, several are depicted to demonstrate vacillation amongst various possible sites. Other gray and cross-hatched shapes represent the rest of RNAP.

FIG. 12.

Simple CRP regulation operates through two related mechanisms, designated class I and class II. Both classes depend on specific interactions between CRP and RNAP. At class I promoters, a CRP dimer (cross-hatched double oval) binds to DNA at a site centered near position −61.5, −71.5, −82.5, or −92.5. CRP bound at any of these positions uses a defined surface (activating region 1 [AR1]) in the downstream subunit of CRP to contact a specific surface determinant (287) of the C-terminal domain of the α-subunit of RNAP (α-CTD; gray double oval). Two additional α-CTD determinants contribute to class I activation: the 261 determinant, proposed to interact with the σ subunit of RNAP (checkered shape), and the 265 determinant, which binds DNA, preferably A+T-rich sequences, e.g., the UP element. At class II promoters, a CRP dimer binds to DNA at a site centered near position −41.5. When bound at this position, CRP uses AR1 of the upstream subunit of CRP to contact determinant 287 of the α-CTD. CRP uses a second surface (AR2) of the downstream subunit to contact the 162-165 determinant of the N-terminal domain of α. The 265 determinant of the α-CTD also contributes by binding DNA. Class III promoters use more complex mechanisms that utilize two CRP dimers to achieve maximal transcription activation. In class III activation, the CRP dimers can bind either to tandem class I positions (as is the case at acs) or to one class II and one class I position. For reviews, see references , , and .