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Entner–Doudoroff Pathway for Sulfoquinovose Degradation in Pseudomonas Putida SQ1

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Entner–Doudoroff Pathway for Sulfoquinovose Degradation in Pseudomonas Putida SQ1 Entner–Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1 Ann-Katrin Feluxa, Dieter Spitellera, Janosch Klebensbergerb, and David Schlehecka,1 aDepartment of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany; and bInstitute of Technical Biochemistry, University of Stuttgart, D-70569 Stuttgart, Germany Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved June 25, 2015 (received for review April 10, 2015) Sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose) is the polar head group “normal” glycolysis. Sulfoglycolysis (EcoCyc pathway PWY-7446) of the plant sulfolipid SQ-diacylglycerol, and SQ comprises a major involves three newly discovered intermediates, 6-deoxy-6- proportion of the organosulfur in nature, where it is degraded by sulfofructose (SF), 6-deoxy-6-sulfofructose-1-phosphate (SFP), and bacteria. A first degradation pathway for SQ has been demonstrated 3-sulfolactaldehyde (SLA), and it is catalyzed by four newly discov- recently, a “sulfoglycolytic” pathway, in addition to the classical gly- ered enzymes, SQ isomerase, SF kinase, SFP aldolase, and SLA colytic (Embden–Meyerhof) pathway in Escherichia coli K-12; half reductase (12). The reactions yield dihydroxyacetone phosphate of the carbon of SQ is abstracted as dihydroxyacetonephosphate (DHAP), which supports energy conservation and growth of E. coli, (DHAP) and used for growth, whereas a C3-organosulfonate, 2,3- and the C3-organosulfonate SLA as an analog of glyceraldehyde- dihydroxypropane sulfonate (DHPS), is excreted. The environmental 3-phosphate (GAP). The SLA is reduced to 2,3-dihydroxypropane isolate Pseudomonas putida SQ1isalsoabletouseSQforgrowth, sulfonate (DHPS) by the SLA reductase, and the DHPS is ex- and excretes a different C3-organosulfonate, 3-sulfolactate (SL). In creted (12). Hence, E. coli K-12 can use only half of the carbon in this study, we revealed the catabolic pathway for SQ in P. putida SQ and is not able to catalyze a desulfonation reaction, whereas SQ1 through differential proteomics and transcriptional analyses, by other bacteria can degrade DHPS [or the 3-sulfolactate (SL) in vitro reconstitution of the complete pathway by five heterolo- formed from SQ, as discussed below] completely, including desulfo- gously produced enzymes, and by identification of all four organo- nation and release of sulfate, via defined pathways (MetaCyc pathway sulfonate intermediates. The pathway follows a reaction sequence PWY-6616) (13–15). Thus, the sulfur cycle for SQ can be closed analogous to the Entner–Doudoroff pathway for glucose-6-phos- + within bacterial communities (11, 12 and cf. 5, 7). phate: It involves an NAD -dependent SQ dehydrogenase, 6-deoxy- Several Pseudomonas strains that can use SQ for growth have 6-sulfogluconolactone (SGL) lactonase, 6-deoxy-6-sulfogluconate (SG) been isolated from soil (8, 9), and the excretion of another dehydratase, and 2-keto-3,6-dideoxy-6-sulfogluconate (KDSG) aldol- C3-organosulfonate, SL, insteadofDHPSorsulfate,hasbeen ase. The aldolase reaction yields pyruvate, which supports growth of reported (9, 10). We also isolated an SQ-utilizing member of the P. putida, and 3-sulfolactaldehyde (SLA), which is oxidized to SL by + genus Pseudomonas, Pseudomonas putida strain SQ1, from a an NAD(P) -dependent SLA dehydrogenase. All five enzymes are freshwater sediment (Lake Constance, Germany). This strain also encoded in a single gene cluster that includes, for example, genes excretes stoichiometric amountsofSLduringgrowthwithSQ,but for transport and regulation. Homologous gene clusters were found not DHPS or sulfate (11). In addition, we found high activity of in genomes of other P. putida strains, in other gamma-Proteobacte- ria, and in beta- and alpha-Proteobacteria, for example, in genomes of Enterobacteria, Vibrio,andHalomonas species, and in typical soil Significance bacteria, such as Burkholderia, Herbaspirillum,andRhizobium. Phototrophic organisms worldwide produce estimated 10 gig- bacterial biodegradation | organosulfonate | sulfolipid | atons of sulfoquinovose (SQ) per year; hence, complete deg- 6-deoxy-6-sulfoglucose | sulfur cycle radation of SQ by bacteria is an important part of the biogeochemical sulfur cycle. Here, we show that Pseudomonas putida SQ1 catabolizes SQ to 3-sulfolactate (SL) in analogy to the ulfoquinovose (SQ; 6-deoxy-6-sulfoglucose) is the polar head Entner–Doudoroff pathway for glucose-6-phosphate, involving group of the plant sulfolipids sulfoquinovosyl diacylglycerols S five newly discovered reactions, enzymes, and genes, and three (SQDGs), which were discovered more than 60 y ago (1). The newly discovered organosulfur intermediates. The SL can be sulfolipids are located in the photosynthetic (thylakoid) mem- mineralized by other bacteria, thus closing the sulfur cycle within branes of all higher plants, mosses, ferns, and algae, as well as in a bacterial community. The genes for the SQ Entner–Doudoroff most photosynthetic bacteria. They are also present in some non- pathway can be found in genomes of a wide range of Proteo- photosynthetic bacteria, and SQ is in the surface layer of some – bacteria, which shows that SQ utilization is a widespread and archaea (2 4). SQ is continuously degraded in all environments important, but still underrecognized, trait of bacteria in all en- where SQ is produced, or it would enrich in these environments. vironments where SQ is produced and degraded. The complete degradation of SQ to, ultimately, CO2, concomitant with a recycling of the bound sulfur in the form of inorganic sulfate, Author contributions: A.-K.F. and D. Schleheck designed research; A.-K.F., D. Spiteller, J.K., is dominated by microbes (e.g., by soil bacteria) (2, 5–9). However, and D. Schleheck performed research; D. Spiteller and J.K. contributed new reagents/ a more detailed exploration of SQ-degrading microbes, of their analytic tools; A.-K.F., D. Spiteller, J.K., and D. Schleheck analyzed data; and A.-K.F. and SQ-degradation pathways, and of the enzymes and genes involved D. Schleheck wrote the paper. has only recently been initiated (10–12).ThecommonviewonSQ The authors declare no conflict of interest. degradation is based on the consideration that SQ is a structural This article is a PNAS Direct Submission. analog of glucose-6-phosphate (GP) (10) and, hence, that SQ Data deposition: The annotation of the Pseudomonas putida SQ1 genome sequence degradation may proceed in analogy to the Embden–Meyerhof reported in this paper has been deposited in the US Department of Energy Joint Genome – Institute’s Integrated Microbial Genomes (IMG) analysis system (img.jgi.doe.gov) under (glycolysis) pathway, or by analogy to the Entner Doudoroff IMG Project ID Gp0039102 (genome name, Pseudomonas putida SQ1; locus tag prefix, pathway or the pentose–phosphate (phosphoketolase) pathway. PpSQ1). We recently discovered that Enterobacterium Escherichia coli 1To whom correspondence should be addressed. Email: [email protected]. K-12 is able to use SQ for growth (12). E. coli K-12 catalyzes a This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. glycolytic breakdown of SQ, that is, “sulfoglycolysis” in addition to 1073/pnas.1507049112/-/DCSupplemental. E4298–E4305 | PNAS | Published online July 20, 2015 www.pnas.org/cgi/doi/10.1073/pnas.1507049112 Downloaded by guest on September 30, 2021 + PNAS PLUS an NAD -dependent SQ dehydrogenase in cell-free extracts of For this study, we had SQ available as a substrate through P. putida SQ1 cells (12). Thus, we had experimental access to a chemical synthesis (11) and the analytical chemistry established second catabolic pathway for SQ, in addition to sulfoglycolysis in for detection of SQ, its sulfosugar and C3-intermediates, and thus E. coli K-12, apparently via an initial oxidation of SQ this time. its enzyme activities (12), and we established a draft-genome se- Most pseudomonads use glucose exclusively via the Entner– quence of strain SQ1 for proteomics (21), which set the stage for an Doudoroff pathway enzymes and do not encode fructose-6-phos- exploration of its SQ degradation pathway. Here, we demonstrate phate kinase for glycolytic breakdown of glucose (e.g., the well- that P. putida SQ1 uses SQ via what we term the “Sulfo–Entner– studied isolate of P. putida, strain KT2440) (16–20). Its major Doudoroff” pathway, in addition to the classical Entner–Doudoroff cytosolic pathway for glucose (Fig. 1A) is relevant as an analogy to pathway for glucose, via five newly discovered enzymes and genes, a possible SQ degradation pathway: Glucose is taken up into the and via three newly identified organosulfur intermediates. cell and phosphorylated to GP, the analog of SQ (compare Fig. 1 + Results A and B). Then, GP is oxidized by an NAD(P) -dependent GP + Inducible NAD -Dependent SQ Dehydrogenase Activity and Conversion dehydrogenase to 6-phosphogluconolactone (PGL), and the PGL + is hydrolyzed to 6-phosphogluconate (PG), the PG is dehydrated of SQ to SL in Cell-Free Extracts of SQ-Grown Cells. The NAD - dependent SQ dehydrogenase activity was inducibly and highly to 2-keto-3-deoxy-6-phosphogluconate (KDPG), and the KDPG is produced during growth with SQ. The specific activity determined cleaved into pyruvate and GAP (Fig. 1A). The five enzymes [i.e., in cell-free extracts (soluble protein fraction) of SQ-grown cells glucose kinase (Glk), GP dehydrogenase (Zwf), PGL lactonase (633 ± 18 mU/mg of protein) was more than 90-fold higher than (Pgl), PG dehydratase (Edd), and KDPG aldolase (Eda)] are the specific activity determined in extracts of glucose- or succinate- encoded in a single gene cluster (not shown; refer to ref. 20), grown cells (each <7 mU/mg of protein), as determined in a pho- which is highly conserved in P. putida species, and also in P. putida tometrical assay by formation of the coproduct NADH (recorded + strain SQ1 (21). Even though it is conceivable that the classical at 365 nm). For comparison, GP caused similar high NAD - Entner–Doudoroff pathway enzymes for GP might also catalyze dependent dehydrogenase activity in extracts of glucose-grown cells the analogous reactions for the substrate SQ (Fig.
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