New mechanisms for bacterial degradation of sulfoquinovose

Abstract

Sulfoquinovose (SQ, 6-deoxy-6-sulfo-D-glucose) is a sulfo-sugar with a ubiquitous distribution in the environment due to its production by plants and other photosynthetic organisms. Bacteria play an important role in degradation of SQ and recycling of its constituent sulfur and carbon. Since its discovery in 1963, SQ was noted to have a structural resemblance to glucose-6-phosphate and proposed to be degraded through a pathway analogous to glycolysis, termed sulfoglycolysis. Studies in recent years have uncovered an unexpectedly diverse array of sulfoglycolytic pathways in different bacteria, including one analogous to the Embden-Meyerhof-Parnas pathway (sulfo-EMP), one analogous to the Entner-Doudoroff pathway (sulfo-ED), and two involving sulfo-sugar cleavage by a transaldolase (sulfo-TAL) and transketolase (sulfo-TK), respectively, analogous to reactions in the pentose phosphate (PP) pathway. In addition, a non-sulfoglycolytic SQ degradation pathway was also reported, involving oxygenolytic C-S cleavage catalyzed by a homolog of alkanesulfonate monooxygenase (sulfo-ASMO). Here, we review the discovery of these new mechanisms of SQ degradation and lessons learnt in the study of new catabolic enzymes and pathways in bacteria.

Keywords: C-S cleavage; adolase; glycyl radical enzyme; mutarotase; sulfoglycolysis; sulfoquinovose.

Figure 1. Sulfo-EMP and Sulfo-ED pathways

(A) Sulfo-EMP pathway with representative gene clusters. (B) Sulfo-ED pathway with representative gene clusters. Both pathways contain YihR, a mutarotase labeled in red.

Figure 2. Sulfo-TAL, Sulfo-TK and Sulfo-EMP2 pathways

(A) Sulfo-TAL pathway with representative gene clusters. (B) Sulfo-TK pathway with representative gene clusters. (C) Sulfo-EMP2 pathway with representative gene clusters. These three pathways share SqvB, a putative mutarotase labeled in red and an isomerase SqvD labeled in blue.

Figure 3. Sulfo-ASMO pathway with a representative gene cluster

In the first step of sulfo-ASMO pathway, oxygenolytic C-S cleavage of SQ catalyzed by the flavin-dependent SQ monooxygenase SquD produces sulfite and 6-dehydroglucose. Many of the sulfo-ASMO gene clusters also encode a SsuE homolog that catalyzes the NAD(P)H-dependent regeneration of the reduced flavin cofactor for SquD. For those that lack SsuE, other flavin reductases may be involved (e.g. in N. aromaticivorans). In the second step, 6-dehydroglucose is reduced to glucose by the NAD(P)H-dependent glucose-6-dehydrogenase SquF, allowing the complete utilization of SQ carbons.

Figure 4. Structural models and proposed catalytic schemes for two key enzymes in the sulfo-EMP2 pathway

(A) Structural model of SqvD (left) and the zoom-in view of the active site (right), showing conserved Mn²⁺-binding residues. (B) Proposed catalytic scheme for SqvD involving an ene-diol intermediate. (C) Structural model of SqiA (left) and the zoom-in view of the active site (right), showing conserved Zn²⁺-binding residues. The mobile Zn²⁺ cofactor occupies two mutually exclusive sites. (D) Proposed catalytic scheme for SqiA. Both models were constructed using AlphaFold2 [29] in ColabFold [30]. The putative Mn²⁺ site of SqvD and two putative Zn²⁺ sites of SqiA were estimated by alignment with the crystal structures of E. coli FucI (PDB: 1FUI) [28] and Helicobacter pylori class II fructose-1,6-biphosphate adolase (5UCK) [33], respectively.

Figure 5. Extended sulfoglycolysis pathways

(A) Extended sulfoglycolysis pathway showing the fate of SL with a representative gene cluster. (B) Extended sulfoglycolysis pathway showing the fate of DHPS with representative gene clusters.