This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: pectin degradation, 4,5-dihydroxy-2,6-dioxohexanoate degradation
|Superclasses:||Degradation/Utilization/Assimilation → Secondary Metabolites Degradation → Sugar Derivatives Degradation|
Expected Taxonomic Range:
5-dehydro-4-deoxy-D-glucuronate is a metabolite resulting from the bacterial degradation of pectin, a complex polymer found in plant cell walls. 5-dehydro-4-deoxy-D-glucuronate is produced by the action of cytoplasmic exopolygalacturonate lyase W and oligogalacturonate lyase and is catabolized in the pathway shown here, as described below in About This Pathway.
The initial steps of pectin degradation to oligogalacturonides in pectinolytic bacteria involve the action of extracellularly secreted pectin methylesterases, pectin acetylesterases, pectate hydrolases (polygalacturonases) and pectate lyases. Pectate degrading hydrolases and lyases are found in the cytoplasm, periplasm and extracellular space. Extracellularly secreted hydrolases can also produce free D-galacturonate which is an important carbon source for microorganisms that catabolize plant material. Pectinolytic enzymes may be present in several different isoforms and may vary among species and strains. In [Kester99] and reviewed in [HugouvieuxCotte96].
Pectin is a heteropolymer present in plant cell walls. It s involved in crosslinking cellulose and hemicellulose fibers, which provides rigidity to the cell wall. The uronic acid D-galacturonate is the main monomeric constituent of pectin. In pectin the D-galacturonate monomers are in the α-pyranose form connected through a 1,4 linkage to form long chains. Homogalacturonan (polygalacturonate) (see a homogalacturonan), a polymer of α-1,4-linked-d-galacturonic acid, is the simplest form of pectin. Other structural classes are rhamnogalacturonan-I, rhamnogalacturonan-II, apiogalacturonan and xylogalacturonan. In natural pectin the carboxyl groups of D-galacturonate may be methyl esterified and some plants also contain acetylated D-galacturonate residues. The degree of esterification varies among plants. Non-esterified carboxyl groups may be linked through divalent cations such as Mg2+ or Ca2+, causing pectin to form a gel.
Pectin is used in the animal feed industry and in the food industry as a gelling agent. Phytopathogenic and saprophytic bacteria and fungi can produce variety of extracellular and intracellular enzymes that degrade pectin and its derivatives. Pectinolytic enzymes such as esterases, hydrolases and lyases, are used in the food, fiber and animal feed industries. There is commercial interest in pectinolytic enzymes to convert the pectin-rich by-products from citrus peel and sugar beet processing to higher value material. In [MartensUzunova09] [Abbott08] and reviewed in [Richard09, Reginault08, HugouvieuxCotte96]. Pectin structure is reviewed in [Caffall09].
About This Pathway
The degradation of pectin by bacteria has been extensively studied in Dickeya dadantii 3937 (previously known as Erwinia chrysanthemi strain 3937), a plant pathogen that causes soft rot disease. Multiple isozymes excreted from the cell (virulence factors) de-esterify and cleave homogalacturonan (polygalacturonate) into pectate oligogalacturonides which then enter the cell (see a pectate). They are degraded by periplasmic enzymes to shorter oligogalacturonides which are then transported through the inner membrane and metabolized. The oligogalacturonide-degrading enzymes involved each have preferences for oligogalacturonides of various lengths. Oligogalacturonide transport proteins involved include the porin KdgM [Blot02] and the inner membrane transporters TogMNAB complex and TogT. The inner membrane permease KdgT, and the ExuT transporter allow uptake of pathway metabolites. Low levels of 5-dehydro-4-deoxy-D-glucuronate, 3-deoxy-D-glycero-2,5-hexodiulosonateI and 2-dehydro-3-deoxy-D-gluconate can act as inducers (in [Blot02] and reviewed in [HugouvieuxCotte96]).
The entire series of reactions (not shown) spans three compartments, the extracellular space, the periplasm and the cytoplasm (see [Blot02]). Initial pectin degradation reactions include its extracellular demethylation to pectate by secreted pectin methylesterase A (PemA) as well as deacetylation by pectin acetylesterase Y (PaeY), and production of oligogalacturonides by at least eight isoforms of pectate lyase (PelA, PelB, PelC, PelD, PelE, PelI, PelZ and PelL) (see pectate lyase A, pectate lyase C and pectate lyase E). After passage into the periplasm via the porin KdgM, any remaining methylated oligogalacturonides can be demethylated by pectin methylesterase B (PemB). Demethylated oligogalacturonides can be further processed by exo- hydrolytic cleavage (PehX) (see exopolygalacturonan hydrolase X), or exo- lyase cleavage (PelX) before transport into the cytoplasm. A periplasmic binding protein may aid in retention and accumulation of oligogalacturonides (in [Abbott08]). In Pectobacterium carotovorum (previously known as Erwinia carotovora) a secreted endo-polygalacturonase PehA [Saarilahti90, Pickersgill98] and a pectin lyase (Pnl) [Nishida90] have been identified.
In the cytoplasm the action of exopolygalacturonate lyase W (PelW) releases unsaturated digalacturonate (4-(4-deoxy-α-D-galact-4-enuronosyl)-D-galacturonate). The subsequent action of oligogalacturonate lyase (Ogl) on unsaturated digalacturonate produces two molecules of 5-dehydro-4-deoxy-D-glucuronate, whereas its action on saturated digalacturonate produces equimolar amounts of 5-dehydro-4-deoxy-D-glucuronate and D-galacturonate. D-galacturonate is catabolized as shown in pathway D-galacturonate degradation I. In [Kester99, Shevchik99] and reviewed in [HugouvieuxCotte96].
In Erwinia chrysanthemi this is the main pathway for pectin degradation. Due to the relatively low activity of polygalacturonases in this organism, little D-galacturonate is produced. The reactions shown here begin with the isomerization of 5-dehydro-4-deoxy-D-glucuronate (also referred to as DKI) to 3-deoxy-D-glycero-2,5-hexodiulosonate (DKII). The kduI gene encoding the putatuve isomerase in Erwinia chrysanthemi has been identified [Condemine91], but the enzyme has not been characterized. Early work characterized this enzyme in a pseudomonad [Preiss63]. 3-deoxy-D-glycero-2,5-hexodiulosonate is reduced to the common metabolite 2-dehydro-3-deoxy-D-gluconate. This compound is also an intermediate in D-galacturonate degradation I. 2-dehydro-3-deoxy-D-gluconate is phosphorylated and then cleaved by an aldolase encoded by gene kdgA which produces the central metabolites D-glyceraldehyde 3-phosphate and pyruvate.
In Escherichia coli the aldolase encoded by gene eda is involved in the Entner-Doudoroff pathway I. However, in Erwinia chrysanthemi this enzyme does not appear to be involved in D-gluconate catabolism and no product of the edd gene that encodes the phosphogluconate dehydratase could be detected in various species of Erwinia. These observations question the existence of the Entner-Doudoroff pathway in these organisms ([HugouvieuxCotte94] and reviewed in [HugouvieuxCotte96]).
Most of the enzymes in this pathway are controlled by kdgR a transcriptional regulator that is induced by 2-dehydro-3-deoxy-D-gluconate [Reverchon91, Nasser91]. A comparative genomics analysis of the kdgR regulon in eight enterobacteria including Dickeya dadantii 3937 and Pectobacterium carotovorum and two members of the genus Vibrio, yielded a metabolic map of pectin and pectin-derivative degradation in these organisms [Rodionov04].
Relationship Links: KEGG:PART-OF:map00040
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