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Chapter 11 : Carbohydrate Uptake and Metabolism

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Abstract:

The genes encoding the polysaccharide-hydrolyzing enzymes are often organized in an operon or regulon together with genes that encode the enzymes catalyzing the uptake of the extracellular hydrolytic products and the first intracellular steps in their catabolism. The genome encodes about 23 secondary and 11 ATP-binding cassette (ABC) carbohydrate transporters. The major facilitator superfamily (MFS) comprises eight proteins of unknown carbohydrate specificity exhibiting significant similarity to the GalP/XylE subfamily. The genes encoding the polysaccharide-hydrolyzing enzymes are often organized in an operon or regulon together with genes that encode the enzymes catalyzing the uptake of the extracellular hydrolytic products and the first intracellular steps in their catabolism. Glycolysis is one of the most conserved metabolic pathways in living organisms. To conserve cellular resources, expression of most of the hundreds of carbohydrate catabolism genes is induced only when the corresponding carbohydrate is present in the growth medium. Expression of antiterminator-controlled genes or operons usually occurs from a constitutive promoter; transcription stops at a terminator located in the leader region of these genes and operons, providing very short transcripts. The carbohydrate transport systems operative in gram-positive and gram-negative bacteria are very similar and most likely developed early in evolution.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11

Key Concept Ranking

Gene Expression and Regulation
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Major Facilitator Superfamily
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Amino Sugars
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Gram-Positive Bacteria
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Gram-Negative Bacteria
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Lactic Acid Bacteria
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Figures

Image of FIGURE 1
FIGURE 1

Schematic presentation of PTS-catalyzed sugar uptake and phosphorylation. Four different sugar-specific transport systems representing the four PTS classes (see Fig. 2 ) are shown. EI catalyzes the phosphoenolpyruvate (PEP)-dependent phosphorylation of HPr at His-15, and P~His-HPr phosphorylates one of the sugar-specific EIIAs (striped circles). The corresponding EIIB (white circles) transfers the phosphoryl group from P-EIIA to the sugar bound to the membrane-spanning EIIC (black ovals) or, in the case of the Lev-PTS, EIIC/EIID complex (black and checkerboard ovals). The phosphorylated sugar is subsequently released into the cytoplasm. EIIA and EIIB can exist as distinct proteins (Lic- and Lev-PTS) or can be fused to EIIC (Fru- and Glc-PTS).

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 2
FIGURE 2

Presentation of the various carbohydrate-specific Ells found in . The domain structure/subunit composition of each EII complex as well as the phosphorylation sites in EIIA (striped boxes) and EIIB (white boxes) are indicated. Phosphorylation sites have been experimentally determined only for LevD and LevE ( ) but are deduced from sequence alignments for the other EIIAs/EIIBs. The EII complexes belong to one of the four PTS classes, three of which contain only one membrane-spanning protein EIIC (black boxes). Only the Lev-PTS, which belongs to the mannose-class PTS, possesses two membrane-spanning proteins, LevF (EIIC, black box) and LevG (EIID, checkerboard box). Two monocistronic genes coding for the EIIA-like proteins YpqE and YyzE (truncated at the ? terminus) are also present in the genome. It is possible that YpqE is used by those glucose/sucrose-class PTSs that are missing an EIIA. When EIIA, EIIB, and EIIC are fused to a single protein, the domain order can vary. Within the fructose/mannitol class, the order is ABC for the fructose-specific PTS and BCA for the presumed mannose PTS, whereas it is CBA for PtsG and GamB (glucose subclass). Conflicting results have been reported about the domain organization of EII (MtlA). According to the published genome sequence, MtlA is composed of a single polypeptide chain (EIICBA) ( ). However, purification of a soluble distinct EIIA (MtlF) has been reported ( ), and sequencing mistakes in the region have been detected ( ). Since ( ) and other gram-positive bacteria also contain an EIIA, resequencing of the region will be necessary to obtain reliable information about the exact organization of the mannitol-specific EII complex and its phosphorylation sites.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 3
FIGURE 3

Carbohydrate metabolism via glycolysis and the- pentose-P pathway and their interconnections to other central metabolic pathways. Presented are the genes coding for glycolytic and pentose-P pathway enzymes and for enzymes catalyzing the transport of several selected carbohydrates and their conversion to a glycolytic or pentose-P pathway intermediate. Genes for carbohydrate utilization: , EIICBA; , EIICB?; , mannitol-1-P dehydrogenase; , putative EIIBCA; , mannose-6-P isomerase (paralogues and ); , EIIABC; , 1-phosphofructokinase; , fructokinase ( and ;?); (formerly ), presumed glucitol/H symporter; , glucitol dehydrogenase; , glycerol facilator; , glycerol kinase; , glycerol dehydrogenase; , glucose permease; , glucose kinase ( ); , gluconate permease; , gluconate kinase. Glycolytic genes: , phospho glucose isomerase; , 6-phosphofructokinase; , fructose-1, 6-bisphosphatase ( ); , fructose-1,6-bisphosphate aldolase (paralogue ); , triose-phosphate isomerase; and , glycolytic and gluconeogenic glyceraldehyde-3-phosphate dehydrogenases ( ); , 3-phosphoglycerate kinase; , phosphoglycerate mutase; , enolase; , pyruvate kinase. Pentose-P pathway genes: , putative glucose-6-P dehydrogenase; , gluconate-6-P dehydrogenase ( is a paralogue of ); , putative ribose-5-P isomerase; , ribose-P pyrophosphokinase; , putative ribulose-5-P epimerase; , transketolase. Genes encoding other metabolic enzymes: , putative phosphoglucomutase; , UTP-glucose-l-P uridylyltransferase (paralogues and ); , lactate dehydrogenase; , α-acetolactate synthase; , α-acetolactate decarboxylase; , pyruvate dehydrogenase complex; , phosphotransacetylase; , acetate kinase; , acetyl-CoA synthetase. Gene encoding an anaplerotic enzyme: , pyruvate carboxylase.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 4
FIGURE 4

non-PTS proteins phosphorylated and regulated by PTS proteins. Presented are GlpK and all PTS regulation domain-containing transcriptional regulators possessing an RNA binding domain (black box in antiterminators) or an N-terminal NifA/NtrC or DeoR-type DNA binding motif (small white box in transcriptional activators). The central domain of LevR typical for proteins interacting with σ is indicated with dotted box. The conserved phosphorylatable histidyl residues in GlpK, in the PRDs (striped boxes) and in the EIIA-like domains (checkerboard boxes) of transcriptional activators are indicated by bold bars together with the corresponding sequence positions. Phosphorylation sites have been determined by site-directed mutagenesis (SDM) or by in vitro phosphorylation experiments (ivP). Although SacY and GlcT are phosphorylated by ?~His-HPr, these antiterminators are active in the absence of functional HPr. All PRD-containing regulators are probably negatively controlled by P~EIIB-mediated phosphorylation. The corresponding EIIB is listed for each PRD-containing regulator. Question marks indicate the lack of experimental proof for the indicated specificity of the PTS, for the suggested phosphorylation sites, or for the negative regulation by the indicated PTS proteins.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 7
FIGURE 7

Comparison of the major mechanisms regulating carbohydrate uptake and metabolism in and gram-positive bacteria. The major carbohydrate control protein in is EIIA. The presumed stimulating effect of P~EIIA on adenylate cyclase activity in is shown in panel A. CAP complexed with cyclic AMP recognizes specific DNA sequences located in front of catabolite-repressed genes and operons and allows their expression. Inducer exclusion, i.e., the inhibition of GlpK and non-PTS permeases by binding EIIA, which prevails over P~ElIA when a rapidly metabolizable carbohydrate is utilized, is presented in panel B. In gram-positive bacteria, HPr is the central protein regulating carbohydrate uptake and metabolism. P~His-HPr, formed when rapidly metabolizable carbohydrates are absent, phosphorylates and activates GlpK (C). The activity of PTS regulation domain-containing transcriptional regulators is also stimulated by PEP-dependent, EI and HPr-catalyzed phosphorylation, but since it occurs in both gram-positive and gram-negative bacteria, it has not been included in this comparison. By contrast, only in gram-positive bacteria does P-Ser-HPr, formed in response to the presence of rapidly metabolizable carbohydrates, interact with CcpA to exert CCR/CCA and with non-PTS permeases to exert inducer exclusion (D).

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 5
FIGURE 5

The P~His-HPr- and P~LevE (EIIB)-catalyzed phosphorylations of LevR and their antagonistic effects on LevR activity. P~LevE-mediated phosphorylation leading to inactivation of LevR occurs at His-869. As a consequence, replacement of His-869 with a nonphosphorylatable amino acid or inactivation of LevD (EIIA) or LevE leads to constitutive expression from the promoter ( ). P~LevE can transfer its phosphoryl group either to His-869 of LevR or to fructose bound to the membrane-spanning LevF/LevG complex. The transfer to fructose is assumed to occur at a faster rate, leading to dephosphorylation of LevR at His-869 when fructose is present. This dephosphorylation activates LevR and therefore allows induction of the operon by fructose. The P~His-HPr-mediated phosphorylation causing stimulation of LevR activity occurs at His-585. Replacement of His-585 with a nonphosphorylatable amino acid leads to reduced expression from the promoter ( ). His-585 is not located in PRD1 but in an EIIA-like domain (checkerboard box). Phosphorylation at His-585 is probably prevented when a rapidly metabolizable PTS sugar is taken up, since the phosphoryl group of P~His-HPr is primarily used for phosphorylation of the PTS sugar. The uptake of rapidly metabolizable PTS substrates leads therefore to dephosphorylation of LevR at His-585 and consequently to reduced LevR activity. This represents a secondary CCR mechanism operative for the operon and probably several other operons controlled by PRD-containing transcriptional regulators.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Image of FIGURE 6
FIGURE 6

The mechanism of OCR/CCA in . The uptake of a rapidly metabolizable carbon source, such as glucose, fructose, or mannose, leads to an increase in the FBP concentration in the cell, which stimulates the ATP-dependent HprK/P-catalyzed phosphorylation of HPr and Crh at Ser-46. Only the seryl-phosphorylated forms of HPr and Crh are capable of binding to CcpA, an interaction also stimulated by FBP. The P-Ser-HPr/CcpA and P-Ser-Crh/CcpA complexes can bind to the operator sites, , located in front or at the beginning of catabolite-repressed or -activated genes and operons and either inhibit or stimulate their expression. Similar mechanisms are probably operative in most other gram-positive bacteria, with the restriction that Crh has so far been detected only in bacilli.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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Tables

Generic image for table
TABLE 1

Carbohydrate transporters in

Question marks indicate that there is no experimental proof for the suggested regulator. Potential regulators encoded by genes located within or next to the operon are listed. CcpA has been established to function as regulator for only a few genes or operons. For the others, CcpA is suggested as regulator when a potential ere site can be detected in the corresponding gene or operon (see Table 2 ).

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11
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TABLE 2

genes for which sites have been identified or the expression of which has been shown to be sensitive to or () mutations

Numbers indicate the position of the ere sites relative to the first base of the translation start (based on the genome sequence available at http://genolist.pasteur.fr/SubtiList/). For , a homology search with a consensus sequence revealed 126 cre sites ( ), including the following sites not listed above: , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , . A slightly different search carried out by the authors revealed the following additional 51 potential sites (the numbers indicate the position of the ere sites relative to the first base of the translation start): , +361; , — 178; , -204; , -132; , -86; , +761; () +286; , + 155; , +52; , -67; , -211; , -223; , -92; , +565; , +1; , -212; (), -122; , -71; , -37; , -92; (mdR), -98; , -32; , -318; , -28; , -187; , -157; , -53; , +60; , -225; , + 169; , -126;, -40; , +377; , +76; , -26; , -67;, -79; , -106; , -51;, -37; , + 243; , +1; , -300; , -38; , -215; , -137; , -78; , -224; , -194; , -56; , -45.

+ indicates carbon catabolite activation (CCA); — indicates carbon catabolite repression (CCR).

Numbers in boldface type indicate that the ere site has been experimentally identified. Numbers in italics indicate the position for putative sites.

n.i. indicates that a site has not been identified for the corresponding gene, although its CCR or CCA is affected by or mutations.

encodes citrate synthase, isocitrate dehydrogenase, and malate dehydrogenase.

There is a discrepancy for position 9 of the located at the beginning of , which was reported to be a ? ( ) but is a C in the genome sequence ( ). This discrepancy could be due to strain differences.

Citation: Deutscher J, Galinier A, Martin-Verstraete I. 2002. Carbohydrate Uptake and Metabolism, p 129-150. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch11

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