Microbial degradation of sulfoquinovose and plant sulfolipids
Final Report Abstract
Microbial degradation of sulfoquinovose (SQ) and plant sulfolipids (SQDG) Sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose) is the polar headgroup of the sulfolipid sulfoquinovosyl diacylgycerol (SQDG) in the photosynthetic membranes of, essentially, all phototrophic organisms. Hence, the degradation of SQDG/SQ by aerobic bacteria - or by anaerobic bacteria - are important steps of the biogeochemical carbon and sulfur cycles. In our preliminary work, a first SQ degradation pathway was discovered in Escherichia coli K12, in analogy to the Embden-Meyerhof-Parnas pathway for glucose-6-phosphate, which is a structural analogue of SQ. E. coli utilizes the non-sulfonated C3-half of SQ as carbon and energy source, and it excretes the sulfonated C3-half in form of 2,3-dihydroxypropanesulfonate (DHPS), which can be mineralized by other (aerobic) bacteria to CO2 and sulfate. Importantly, SQ might also be a substrate for anaerobic human-gut microbes, through the greenvegetable diet (salad, spinach, etc.), and likely is an additional, yet unrecognized source of H2S, which is of biomedical relevance, since H2S in the gut has many recognized and potential contributions to human health and disease. Hence, the major aim of this DFG-Heisenberg fellowship and research grant was to define novel pathways, intermediates, enzymes and gene clusters involved in SQ utilization - in aerobic as well as anaerobic bacteria - through enrichment and isolation, genomics, reverse genetics, biochemistry and analytical chemistry. (i) We discovered a second type of SQ-degradation pathway in a Pseudomonas putida isolate, the SQ- Entner-Doudoroff pathway [https://BioCyc.org pathway map: PWY-7722]. It employs a new 2-keto- 3,6-dideoxy-6-sulfogluconate (KDSG) aldolase, and it excretes 3-sulfolactate (SL) as degradation product. Homologous gene clusters were found widespread in many freshwater, soil- and plantrhizosphere, and marine bacteria, as well as in gut symbionts, hence, in organisms from all habitats where SQ is produced and/or degraded; and in opportunistic plant and human pathogens. (ii) We discovered a third SQ-degradation pathway in an aerobic Bacillus isolate, which is present also in a wide range of anaerobic, SQ-fermenting human-gut Firmicutes, such as in members of the genera Bacillus, Enterococcus, Lactobacillus, Butyrivibrio, Pseudobutyrivibrio, Eubacterium and Clostridium, but also in individual genomes of members of the phyla Fusobacteria, Chloroflexi, Actinobacteria, Spirochaetes and Thermotogae. The pathway [BioCyc: sulfoquinovose degradation III] employs a new 6-deoxy-6-sulfofructose (SF) transaldolase that transfers the non-sulfonated C3-(glycerone)-moiety of SF onto GAP as acceptor molecule, yielding fructose-6-phosphate for growth. The product 3-sulfolactaldehyde is either oxidised to SL in the aerobic bacteria, or reduced to DHPS as an additional fermentation step in the SQ-fermenting bacteria. (iii) We demonstrated degradation of SQ to H2S using a consortium of E. coli K-12 and a Desulfovibrio isolate as laboratory model system. While E. coli catalyses a new mixed-acid fermentation with SQ as substrate [BioCyc: PWY-7446], the Desulfovibrio strain utilizes the DHPS produced by E. coli as electron acceptor for sulfite respiration (‘organosulfonate respiration’), employing 3-sulfolactate sulfitelyase [BioCyc: 3-sulfopropanediol degradation II]. (iv) We identified the missing desulfonation reaction in the human gut bacterium and opportunistic pathogen Bilophila wadsworthia for taurine degradation, and found a novel C-S bond cleaving glycylradical enzyme (GRE), isethionate sulfite-lyase. The pathway [BioCyc: PWY-8062] proceeds via taurine deamination to sulfoacetaldehyde, its reduction to isethionate, and its desulfonation, yielding sulfite for respiration and energy generation. In addition, we identified another novel C-S bond cleaving GRE, DHPS sulfite-lyase, in B. wadsworthia for respiration of the DHPS-sulfite [BioCyc: 3-sulfopropanediol degradation III]; the DHPS is produced by the SQ-fermenting gut bacteria (see below). As these type of GREs are widely distributed also in genomes of other gut bacteria, they may represent a novel target for control of intestinal H2S production. (iiv) We demonstrated that SQ is a select nutrient of prominent bacteria and a source of H2S in the human gut, when using anoxic microcosms of human feces as well as defined co-cultures. Predominantly Eubacterium rectale and Bilophila wadsworthia cooperatively catabolize SQ via DHPS as transient intermediate to H2S, involving the previously discovered SQ-transaldolase and DHPS-desulfonation pathways. Re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed consistently across various health states, suggesting their active contribution to gut functioning. The demonstration of green diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and may have implications for precision editing of the gut microbiota by dietary and prebiotic interventions.
Publications
- Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. PNAS (2015) 112: E4205-4305
Felux, A.-K., D. Spiteller, J. Klebensberger and D. Schleheck
(See online at https://doi.org/10.1073/pnas.1507049112) - Anaerobic degradation of the plant sugar sulfoquinovose concomitant with H2S production: Escherichia coli K-12 and Desulfovibrio sp. strain DF1 as co-culture model. Frontiers Microbiology (2018) 27: 2792
Burrichter, A., K. Denger, P. Franchini, T. Huhn, N. Müller, D. Spiteller and D. Schleheck
(See online at https://doi.org/10.3389/fmicb.2018.02792) - Wide-spread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nature Communications (2018) 9: 5071
Knorr, S., M. Sinn, R. Williams, D. Galetskiy, C. Wang, N. Müller, O. Mayans, D. Schleheck and J.S. Hartig
(See online at https://doi.org/10.1038/s41467-018-07563-6) - A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. PNAS (2019) 116: 3171-3176
Peck, S.C., K. Denger, A. Burrichter, S.M. Irwin, E.P. Balskus and D. Schleheck
(See online at https://doi.org/10.1073/pnas.1815661116) - Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway. iScience (2020) 23: 101510
Frommeyer, B., A.W. Fiedler, S.R. Oehler, B.T. Hanson, A. Loy, P. Franchini, D. Spiteller and D. Schleheck
(See online at https://doi.org/10.1016/j.isci.2020.101510) - Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME Journal
Hanson, B., K. Kits, J. Löffler, A. Burrichter, A.W. Fiedler, K. Denger, B. Frommeyer, C. Herbold, T. Rattei, N. Karcher, N. Segata, D. Schleheck and A. Loy.
(See online at https://doi.org/10.21203/rs.3.rs-49676/v1)
