Oxygenolytic sulfoquinovose degradation by an iron-dependent alkanesulfonate dioxygenase

Anaerobic Faecalicatena spp. degrade sulfoquinovose via a bifurcated 6-deoxy-6-sulfofructose transketolase/transaldolase pathway to both C2- and C3-sulfonate intermediates

Plant-produced sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is one of the most abundant sulfur-containing compounds in nature and its bacterial degradation plays an important role in the biogeochemical sulfur and carbon cycles and in all habitats where SQ is produced and degraded, particularly in gut microbiomes. Here, we report the enrichment and characterization of a strictly anaerobic SQ-degrading bacterial consortium that produces the C2-sulfonate isethionate (ISE) as the major product but also the C3-sulfonate 2,3-dihydroxypropanesulfonate (DHPS), with concomitant production of acetate and hydrogen (H2). In the second step, the ISE was degraded completely to hydrogen sulfide (H2S) when an additional electron donor (external H2) was supplied to the consortium. Through growth experiments, analytical chemistry, genomics, proteomics, and transcriptomics, we found evidence for a combination of the 6-deoxy-6-sulfofructose (SF) transketolase (sulfo-TK) and SF transaldolase (sulfo-TAL) pathways in a SQ-degrading Faecalicatena-phylotype (family Lachnospiraceae) of the consortium, and for the ISE-desulfonating glycyl-radical enzyme pathway, as described for Bilophila wadsworthia, in an Anaerospora-phylotype (Sporomusaceae). Furthermore, using total proteomics, a new gene cluster for a bifurcated SQ pathway was also detected in Faecalicatena sp. DSM22707, which grew with SQ in pure culture, producing mainly ISE, but also 3-sulfolacate (SL) 3-sulfolacaldehyde (SLA), acetate, butyrate, succinate, and formate, but not H2. We then reproduced the growth of the consortium with SQ in a defined co-culture model consisting of Faecalicatena sp. DSM22707 and Bilophila wadsworthia 3.1.6. Our findings provide the first description of an additional sulfoglycolytic, bifurcated SQ pathway. Furthermore, we expand on the knowledge of sulfidogenic SQ degradation by strictly anaerobic co-cultures, comprising SQ-fermenting bacteria and cross-feeding of the sulfonate intermediate to H2S-producing organisms, a process in gut microbiomes that is relevant for human health and disease.

Study of sulfoglycolysis in Enterococcus gilvus reveals a widespread bifurcated pathway for dihydroxypropanesulfonate degradation

Sulfoquinovose (SQ), the polar head group of sulfolipids essential for photosynthesis, is naturally abundant. Anaerobic Firmicutes degrade SQ through a transaldolase-dependent (sulfo-TAL) pathway, producing dihydroxypropanesulfonate (DHPS). Some bacteria extend this pathway by the sequential action of HpfG and HpfD converting DHPS to 3-hydroxypropanesulfonate (3-HPS) via 3-sulfopropionaldehyde (3-SPA). Here, we report a variant sulfo-TAL pathway in Enterococcus gilvus, involving additional enzymes, a NAD+-dependent 3-SPA dehydrogenase HpfX, and a 3-sulfopropionyl-CoA synthetase HpfYZ, which oxidize 3-SPA to 3-sulfopropionate (3-SP) coupled with ATP formation. E. gilvus grown on SQ or DHPS produced a mixture of 3-HPS and 3-SP, indicating the bifurcated pathway. Similar genes are found in various Firmicutes, including gut bacteria. Importantly, 3-SP, but not 3-HPS, can serve as a respiratory terminal electron acceptor for Bilophila wadsworthia, a common intestinal pathobiont, resulting in the production of toxic H2S. This research expands our understanding of sulfonate metabolism and reveals cross-feeding in the anaerobic microbiome.

Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes

The sulfolipid sulfoquinovosyl diacylglycerol (SQDG), produced by plants, algae, and cyanobacteria, constitutes a major sulfur reserve in the biosphere. Microbial breakdown of SQDG is critical for the biological utilization of its sulfur. This commences through release of the parent sugar, sulfoquinovose (SQ), catalyzed by sulfoquinovosidases (SQases). These vanguard enzymes are encoded in gene clusters that code for diverse SQ catabolic pathways. To identify, visualize and isolate glycoside hydrolase CAZY-family 31 (GH31) SQases in complex biological environments, we introduce SQ cyclophellitol-aziridine activity-based probes (ABPs). These ABPs label the active site nucleophile of this enzyme family, consistent with specific recognition of the SQ cyclophellitol-aziridine in the active site, as evidenced in the 3D structure of Bacillus megaterium SQase. A fluorescent Cy5-probe enables visualization of SQases in crude cell lysates from bacteria harbouring different SQ breakdown pathways, whilst a biotin-probe enables SQase capture and identification by proteomics. The Cy5-probe facilitates monitoring of active SQase levels during different stages of bacterial growth which show great contrast to more traditional mRNA analysis obtained by RT-qPCR. Given the importance of SQases in global sulfur cycling and in human microbiota, these SQase ABPs provide a new tool with which to study SQase occurrence, activity and stability.

Widespread Family of NAD+-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism

The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+ as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+ provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.