Editing Entner–Doudoroff pathway

{{Short description|Series of interconnected biochemical reactions}}
[[Image:Entner–Doudoroff pathway.svg|thumb|200px|Diagram of the Entner–Doudoroff pathway (KDPG: 2-keto-3-deoxy-6-phosphogluconate)]]The '''Entner–Doudoroff pathway''' (ED Pathway) is a [[metabolic pathway]] that is most notable in [[Gram-negative bacteria]], certain [[Gram-positive bacteria]] and [[archaea]].<ref name="Conway" /> [[Glucose]] is the substrate in the ED pathway and through a series of [[enzyme]] assisted [[chemical reaction]]s it is catabolized into [[Pyruvic acid|pyruvate]]. Entner and [[Michael Doudoroff|Doudoroff]] (1952) and MacGee and Doudoroff (1954) first reported the ED pathway in the bacterium ''[[Pelomonas saccharophila|Pseudomonas saccharophila]]''.<ref>{{Cite journal|last1=Kersters|first1=K.|last2=De Ley|first2=J.|date=December 1968|title=The occurrence of the Entner-Doudoroff pathway in bacteria|journal=Antonie van Leeuwenhoek|volume=34|issue=1|pages=393–408|doi=10.1007/BF02046462|pmid=5304016|s2cid=6151383|issn=0003-6072}}</ref> While originally thought to be just an alternative to [[glycolysis|glycolysis (EMP)]] and the [[pentose phosphate pathway|pentose phosphate pathway (PPP)]], some studies now suggest that the original role of the EMP may have originally been about [[anabolism]] and repurposed over time to [[catabolism]], meaning the ED pathway may be the older pathway.<ref>{{Cite journal|last1=Romano|first1=A. H.|last2=Conway|first2=T.|date=1996-07-01|title=Evolution of carbohydrate metabolic pathways|journal=Research in Microbiology|volume=147|issue=6|pages=448–455|doi=10.1016/0923-2508(96)83998-2|issn=0923-2508|pmid=9084754|doi-access=free}}</ref> Recent studies have also shown the prevalence of the ED pathway may be more widespread than first predicted with evidence supporting the presence of the pathway in [[cyanobacteria]], [[fern]]s, [[algae]], [[moss]]es, and [[plant]]s.<ref name="Chen 2016">Chen, Xi, et al. "The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants." ''Proceedings of the National Academy of Sciences'' (2016): 201521916.</ref> Specifically, there is direct evidence that [[Barley|''Hordeum vulgare'']] uses the Entner–Doudoroff pathway.<ref name="Chen 2016" />

Distinct features of the Entner–Doudoroff pathway are that it:

* Uses the unique enzymes 6-phosphogluconate dehydratase and 2-keto-deoxy-6-phosphogluconate (KDPG) aldolase and other common metabolic enzymes to other metabolic pathways to catabolize glucose to pyruvate.<ref name="Conway" />
* In the process of breaking down glucose, a net yield of 1 ATP is formed per every one glucose molecule processed, as well as 1 [[NADH]] and 1 [[NADPH]]. In comparison, glycolysis has a net yield of 2 ATP molecules and 2 NADH molecules per every one glucose molecule metabolized. This difference in energy production may be offset by the difference in protein amount needed per pathway.<ref name=":0">{{Cite journal|last1=Flamholz|first1=A.|last2=Noor|first2=E.|last3=Bar-Even|first3=A.|last4=Liebermeister|first4=W.|last5=Milo|first5=R.|date=2013-04-29|title=Glycolytic strategy as a tradeoff between energy yield and protein cost|journal=Proceedings of the National Academy of Sciences|volume=110|issue=24|pages=10039–10044|doi=10.1073/pnas.1215283110|pmid=23630264|pmc=3683749|bibcode=2013PNAS..11010039F|issn=0027-8424|doi-access=free}}</ref> 

== Archaeal variations ==
Archaea have variants of the Entner-Doudoroff Pathway. These variants are called the semiphosphorylative ED (spED) and the nonphosphorylative ED (npED):<ref name="Brasen14" />

* spED is found in [[Halophile|halophilic]] euryarchaea and ''[[Clostridium]]'' species.<ref name="Brasen14" />
* In spED, the difference is where [[phosphorylation]] occurs. In the standard ED, phosphorylation occurs at the first step from glucose to G-6-P. In spED, the glucose is first oxidized to [[gluconate]] via a glucose dehydrogenase. Next, gluconate dehydratase converts gluconate into 2-keto-3-deoxy-gluconate (KDG). The next step is where phosphorylation occurs as KDG kinase converts KDG into KDPG. KDPG is then cleaved into glyceraldehyde 3-phosphate (GAP) and pyruvate via KDPG aldolase and follows the same EMP pathway as the standard ED. This pathway produces the same amount of ATP as the standard ED.<ref name="Brasen14" />
* npED is found in [[Thermoacidophile|thermoacidophilic]] ''[[Sulfolobus]]'', [[Euryarchaeota]] ''[[Thermoplasma acidophilum|Tp. acidophilum]]'', and ''[[Picrophilus]]'' species.<ref name="Brasen14" />
* In npED, there is no phosphorylation at all. The pathway is the same as spED but instead of phosphorylation occurring at KDG, KDG is instead cleaved GA and pyruvate via KDG aldolase. From here, GA is oxidized via GA dehydrogenase into glycerate. The glycerate is phosphorylated by glycerate kinase into 2PG. 2PG then follows the same pathway as ED and is converted into pyruvate via ENO and PK. In this pathway though, there is no ATP produced.<ref name="Brasen14" />

Some archaea such as ''Crenacraeota Sul''. ''solfacaricus'' and ''Tpt. tenax'' have what is called branched ED. In branched ED, the organism have both spED and npED that are both operative and work in parallel.

==Organisms that use the Entner–Doudoroff pathway==
{{expand section|the further known species that use the ED or its variants, based on the reviews provided, and other modern secondary sources|small=no|date=August 2015}}
{{primary sources|section|date=August 2015}}
There are several bacteria that use the Entner–Doudoroff pathway for metabolism of glucose and are unable to catabolize via glycolysis (e.g., therefore lacking essential glycolytic enzymes such as [[phosphofructokinase-1|phosphofructokinase]] as seen in Pseudomonas).<ref name="Conway">Conway,T. (1992) "The Entner–Doudorodd pathway: history, physiology and molecular biology" ''Microbiology of Reviews'' '''103'''(19; May), pp. 1–28, DOI , see [http://www.ou.edu/microarray/oumcf/edrev.pdf]</ref>  Genera in which the pathway is prominent include Gram-negative,{{citation needed|date=August 2015}} as listed below, Gram-positive bacteria such as [[Enterococcus faecalis]],<ref>{{cite book |author=Willey |author2=Sherwood |author3=Woolverton |title=Prescott's Principles of Microbiology}}{{full citation needed|date=August 2015}}{{page needed|date=August 2015}}</ref>{{full citation needed|date=August 2015}}{{page needed|date=August 2015}}{{better source|date=August 2015}} as well as several in the [[Archaea]], the second distinct branch of the [[prokaryote]]s (and the "third domain of life", after the prokaryotic Eubacteria and the eukaryotes).<ref name="Brasen14">Bräsen C.; D. Esser; B. Rauch & B. Siebers (2014) "Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation," ''Microbiol. Mol. Biol. Rev.'' '''78'''(1; March), pp. 89–175, DOI 10.1128/MMBR.00041-13, see {{cite web |title=Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation |url=https://mmbr.asm.org/content/78/1/89.full.pdf+html |url-status=dead |archive-url=https://web.archive.org/web/20151122004330/http://mmbr.asm.org/content/78/1/89.full.pdf+html |archive-date=2015-11-22 |access-date=2015-08-04}} or [https://www.ncbi.nlm.nih.gov/pubmed/24600042], accessed 3 August 2015.</ref> Due to the low energy yield of the ED pathway, [[Anaerobic organism|anaerobic]] bacteria seem to mainly use glycolysis while [[Aerobic organism|aerobic]] and [[Facultative anaerobic organism|facultative anaerobes]] are more likely to have the ED pathway. This is thought to be due to the fact that aerobic and facultative anaerobes have other non-glycolytic pathways for creating ATP such as [[oxidative phosphorylation]]. Thus, the ED pathway is favored due to the lesser amounts of proteins required. While anaerobic bacteria must rely on the glycolysis pathway to create a greater percentage of their required ATP thus its 2 ATP production is more favored over the ED pathway's 1 ATP production.<ref name=":0" />

Examples of bacteria using the pathway are:
* ''[[Pseudomonas]]'',<ref name="pmid9657988"/> a genus of Gram-negative bacteria
* ''[[Azotobacter]]'',<ref>{{cite journal |author1=Michael P. Stephenson |author2=Frank A. Jackson |author3=Edwin A. Dawes |title=Further Observations on Carbohydrate Metabolism and its Regulation in ''Azotobacter beijerinckii'' |journal=Journal of General Microbiology |year=1978 |volume=109 |pages=89–96 |doi= 10.1099/00221287-109-1-89|url=http://mic.sgmjournals.org/cgi/content/abstract/109/1/89 |issue=1|doi-access=free }}</ref> a genus of Gram-negative bacteria
* ''[[Rhizobium]]'',<ref name="KuykendallRhizobium06">Kuykendall, L. David; John M. Young; Esperanza Martínez-Romero; Allen Kerr & Hiroyuka Sawada (2006) ''Genus I.'' Rhizobium ''Frank 1889, 389<sup>AL</sup>''  [Order VI. Rhizobiales ''ord. nov.'', Family I Rhizobiaceae Conn 1938, 321<sup>AL</sup> (L. David Kuykendall, Ed.)], pp. 324–339, in ''Bergey's Manual® of Systematic Bacteriology, ''Vol. 2'' The Proteobacteria, ''Part 3'' The Alpha-, Beta-, Delta-, and Epsilonproteobacteria,'' (Don J. Brenner, Noel R. Krieg, James T. Staley, Vol. Eds., George M. Garrity, Ed.-in-Chief), New York, NY, USA: Springer Science & Business, {{ISBN|0387241450}}, [https://books.google.com/books?isbn=0387241450], accessed 3 August 2015.</ref> a plant root-associated and plant differentiation-active genus of Gram-negative bacteria
* ''[[Agrobacterium]]'',<ref name="pmid128316">{{cite journal|vauthors=Arthur LO, Nakamura LK, Julian G, Bulla LA | title=Carbohydrate catabolism of selected strains in the genus Agrobacterium. | journal=Appl Microbiol | year= 1975 | volume= 30 | issue= 5 | pages= 731–7 | pmid=128316 | doi= 10.1128/AEM.30.5.731-737.1975| pmc=187263 }}</ref> a plant pathogen (oncogenic) genus of Gram-negative bacteria, also of biotechnologic use
* ''[[Escherichia coli]]'',<ref name="pmid9657988">{{cite journal|vauthors=Peekhaus N, Conway T | title=What's for dinner?: Entner–Doudoroff metabolism in Escherichia coli. | journal=J Bacteriol | year= 1998 | volume= 180 | issue= 14 | pages= 3495–502 | pmid=9657988 | doi= 10.1128/JB.180.14.3495-3502.1998| pmc=107313 }}</ref> a Gram-negative bacterium
* ''[[Enterococcus faecalis]]'',<ref name="pmid14137623">{{cite journal|author1=Goddard J. L. |author2=J.R. Sokatch| title=2-Ketogluconate fermentation by ''Streptococcus faecalis''. | journal=J. Bacteriol. | year= 1964 | volume= 87 | issue= 4| pages= 844–851 | pmid=14137623 | doi= 10.1128/JB.87.4.844-851.1964| pmc=277103 }}</ref> a Gram-positive bacterium
* ''[[Zymomonas mobilis]]'',{{citation needed|date=August 2015}} a Gram-negative [[Facultative anaerobic organism|facultative anaerobe]]
* ''[[Xanthomonas campestris]]'',<ref name="pmid19372163">{{cite journal|author1=Lu, G. T. |author2=J.R. Xie |author3=L. Chen |author4=J. R. Hu |author5=S. Q. An |author6=H. Z. Su | title=Glyceraldehyde-3-phosphate dehydrogenase of ''Xanthomonas campestris'' pv. campestris is required for extracellular polysaccharide production and full virulence. | journal=Microbiology | year= 2009 | volume= 155 | issue= 5 | pages= 1602–1612 | pmid=19372163 | doi=10.1099/mic.0.023762-0 |display-authors=etal| doi-access=free }}</ref> a Gram-negative bacterium which uses this pathway as main pathway for providing energy.

To date there is evidence of Eukaryotes using the pathway, suggesting it may be more widespread than previously thought: 
*''[[Hordeum vulgare]]'', barley uses the Entner–Duodoroff pathway.<ref name="Chen 2016"/>
*''[[Phaeodactylum tricornutum]]'' diatom model species presents functional phosphogluconate dehydratase and dehoxyphosphogluconate aldolase genes in its genome <ref>Fabris M., et al., "[https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2012.04941.x The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner–Doudoroff glycolytic pathway]", ''The Plant Journal'' (2012) '''70''', 1004–1014</ref>

The Entner–Doudoroff pathway is present in many species of Archaea (caveat, see following), whose metabolisms "resemble... in [their] complexity those of Bacteria and lower Eukarya", and often include both this pathway and the [[glycolysis|Embden-Meyerhof-Parnas]] pathway of glycolysis, except most often as unique, modified variants.<ref name=Brasen14/>

== Catalyzing enzymes ==

=== Conversion of glucose to glucose-6-phosphate   ===
The first step in ED is phosphorylation of glucose by a family of enzymes called [[hexokinase]]s to form [[glucose 6-phosphate]] (G6P). This reaction consumes ATP, but it acts to keep the glucose concentration low, promoting continuous transport of glucose into the cell through the plasma membrane transporters. In addition, it blocks the glucose from leaking out – the cell lacks transporters for G6P, and free diffusion out of the cell is prevented due to the charged nature of G6P. Glucose may alternatively be formed from the [[phosphorolysis]] or [[hydrolysis]] of intracellular starch or glycogen.

In [[animal]]s, an [[isozyme]] of hexokinase called [[glucokinase]] is also used in the liver, which has a much lower affinity for glucose (K<sub>m</sub> in the vicinity of normal glycemia), and differs in regulatory properties. The different substrate affinity and alternate regulation of this enzyme are a reflection of the role of the liver in maintaining blood sugar levels.

''Cofactors:'' Mg<sup>2+</sup>

=== Conversion of glucose-6-phosphate to 6-phosphogluconolactone ===
The G6P is then converted to 6-[[6-Phosphogluconolactone|phosphogluconolactone]] in the presence of enzyme [[glucose-6-phosphate dehydrogenase]] ([[Oxidoreductase|an oxido-reductase]]) with the presence of  [[co-enzyme]] [[Nicotinamide adenine dinucleotide|nicotinamide adenine dinucleotide phosphate]] (NADP<sup>+</sup>). which will be reduced to nicotinamide adenine dinucleotide phosphate hydrogen along with a free hydrogen atom H<sup>+</sup>.

=== Conversion of 6-phosphogluconolactone to 6-phosphogluconic acid ===
The 6PGL is converted into 6-phosphogluconic acid in the presence of enzyme [[hydrolase]].

=== Conversion of 6-phosphogluconic acid to 2-keto-3-deoxy-6-phosphogluconate ===
The 6-phosphogluconic acid is converted to 2-keto-3-deoxy-6-phosphogluconate (KDPG) in the presence of enzyme 6-phosphogluconate dehydratase; in the process, a water molecule is released to the surroundings.

=== Conversion of 2-keto-3-deoxy-6-phosphogluconate to pyruvate and glyceraldehyde-3-phosphate ===
The KDPG is then converted into pyruvate and glyceraldehyde-3-phosphate in the presence of enzyme KDPG aldolase. For the pyruvate, the ED pathway ends here, and the pyruvate then goes into further metabolic pathways (TCA cycle, ETC cycle, etc).

The other product (glyceraldehyde-3-phosphate) is further converted by entering into the [[glycolysis]] pathway, via which it, too, gets converted into pyruvate for further metabolism.

=== Conversion of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate ===
The G3P is converted to 1,3-bisphosphoglycerate in the presence of enzyme glyceraldehyde-3-phosphate dehydrogenase (an oxido-reductase).

The aldehyde groups of the triose sugars are [[oxidised]], and [[inorganic phosphate]] is added to them, forming [[1,3-bisphosphoglycerate]].

The hydrogen is used to reduce two molecules of [[NAD+|NAD<sup>+</sup>]], a hydrogen carrier, to give NADH '''+''' H<sup>+</sup> for each triose.

Hydrogen atom balance and charge balance are both maintained because the phosphate (P<sub>i</sub>) group actually exists in the form of a [[Phosphoric acid#Orthophosphoric acid chemistry|hydrogen phosphate]] anion (HPO<sub>4</sub><sup>2−</sup>), which dissociates to contribute the extra H<sup>+</sup> ion and gives a net charge of -3 on both sides.

=== Conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate ===
This step is the enzymatic transfer of a phosphate group from [[1,3-bisphosphoglycerate]] to ADP by [[phosphoglycerate kinase]], forming ATP and [[3-phosphoglycerate]].

=== Conversion of 3-phosphoglycerate to 2-phosphoglycerate ===
[[Phosphoglycerate mutase]] isomerises [[3-phosphoglycerate]] into [[2-phosphoglycerate]].

=== Conversion of 2-phosphoglycerate to phosphoenolpyruvate ===
[[Enolase]] next converts [[2-phosphoglycerate]] to [[phosphoenolpyruvate]]. This reaction is an elimination reaction involving an [[E1cB-elimination reaction|E1cB]] mechanism.

''Cofactors:'' 2 Mg<sup>2+</sup>: one "conformational" ion to coordinate with the carboxylate group of the substrate, and one "catalytic" ion that participates in the dehydration

=== Conversion of phosphoenol pyruvate to pyruvate ===
A final [[substrate-level phosphorylation]] now forms a molecule of [[pyruvate]] and a molecule of ATP by means of the enzyme [[pyruvate kinase]]. This serves as an additional regulatory step, similar to the phosphoglycerate kinase step.

''Cofactors:'' Mg<sup>2+</sup>

==References==
<references />

==Further reading==
* Bräsen C.; D. Esser; B. Rauch & B. Siebers (2014) "Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation," ''Microbiol. Mol. Biol. Rev.'' '''78'''(1; March), pp.&nbsp;89–175, DOI 10.1128/MMBR.00041-13, see [https://web.archive.org/web/20151122004330/http://mmbr.asm.org/content/78/1/89.full.pdf+html] or [https://www.ncbi.nlm.nih.gov/pubmed/24600042], accessed 3 August 2015.
* Ahmed, H.; B. Tjaden; R. Hensel & B. Siebers (2004) "Embden–Meyerhof–Parnas and Entner–Doudoroff pathways in Thermoproteus tenax: metabolic parallelism or specific adaptation?," ''Biochem. Soc. Trans.'' '''32'''(2; April 1), pp.&nbsp;303–304, DOI 10.1042/bst0320303, see [http://www.biochemsoctrans.org/content/ppbiost/32/2/303.full.pdf], accessed 3 August 2015.
* Conway T. (1992) "The Entner-Doudoroff pathway: history, physiology and molecular biology," ''FEMS Microbiol. Rev.,'' '''9'''(1; September), pp.&nbsp;1–27, see [https://www.ncbi.nlm.nih.gov/pubmed/1389313], accessed 3 August 2015.
* Snyder, L., Peters, J. E., Henkin, T. M., & Champness, W. (2013). Molecular genetics of bacteria. American Society of Microbiology.

{{DEFAULTSORT:Entner-Doudoroff pathway}}
[[Category:Biochemical reactions]]
[[Category:Carbohydrate metabolism]]
[[Category:Metabolic pathways]]