In last year's issue 4 of Biochemical Journal, Zhou et al. (Biochem J. 476, 733–746) kinetically and structurally characterized the reductase IsfD from Klebsiella oxytoca that catalyzes the reversible reduction in sulfoacetaldehyde to the corresponding alcohol isethionate. This is a key step in detoxification of the carbonyl intermediate formed in bacterial nitrogen assimilation from the α-aminoalkanesulfonic acid taurine. In 2019, the work on sulfoacetaldehyde reductase IsfD was the exciting start to a quite remarkable series of articles dealing with structural elucidation of proteins involved in taurine metabolism as well as the discovery of novel degradation pathways in bacteria.

Taurine is a widespread osmolyte in tissues of mammals, fish and other animals [1]. It is also found in red algae [2], marine diatoms and dinoflagellates [3,4], while it does not seem to be endogenous in higher plants and most microorganisms. In humans, taurine plays various important physiological roles, such as a broad-spectrum cytoprotective agent, a substrate for synthesis of bile acid conjugates and, possibly, also as neurotransmitter [1]. Furthermore, an endogenous derivative of taurine is its acetic acid amide N-acetyltaurine. Increased levels of this compound are a metabolic marker for alcoholic liver disease [5]. It is also one of the various low-molecular-mass compounds present in the adhesive droplets covering the fibers of spider webs [6]. In eukaryotes, the major taurine synthesis routes proceed from both α-amino acids cysteine and methionine via cysteine sulfinate and hypotaurine. The oxygenation of cysteine to the corresponding sulfinate is catalyzed by cysteine dioxygenase incorporating both atoms of dioxygen into the substrate. The mammalian enzyme is well studied and its structure as well as the determinants for substrate specificity have been elucidated [7]. Interestingly, distantly related enzymes can also be found in some prokaryotes, albeit not all of these thiol dioxygenases turned out to be specific for cysteine [7]. This, nevertheless, may be indicative of taurine synthesis in certain bacteria that, for example, employ the sulfonate as osmoprotectant when thriving in extreme acidic habitats [8]. However, taurine is not frequently found in bacterial metabolomes and, hence, the deoxygenation reaction may be mainly employed for the synthesis of other sulfonates in this group of organisms.

Bacterial taurine degradation, on the other hand, appears to be quite widespread, and various catabolic pathways have already been discovered. The taurine moiety from bile salts, for example, is mostly recycled in the body, but small amounts are degraded by microorganisms in the large intestine. Initially, bile salt hydrolases belonging to the N-terminal nucleophile hydrolase family catalyze the hydrolysis of the amide bond between bile acid and taurine [9]. Likewise, the amide N-acetyltaurine is hydrolyzed by metal-dependent amidohydrolase NaaS [10]. Then, depending on the environment and microbial physiology, taurine can serve as sulfur, nitrogen and carbon source (Figure 1). Under oxic conditions, removal of the sulfonate group is catalyzed by 2-oxoglutarate-dependent taurine dioxygenase TauD or alkanesulfonate dioxygenase SsuD, as found in Escherichia coli and many other bacteria [11]. For nitrogen assimilation, the resulting 2-aminoacetaldehyde can either be oxidized to glycine or reduced to ethanolamine. Release of ammonia from the latter is catalyzed by B12-dependent ethanolamine ammonia-lyase EutBC [12]. Alternatively, nitrogen assimilation from taurine is accomplished via deamination to sulfoacetaldehyde by pyridoxal phosphate-dependent aminotransferase reactions [13] or cytochrome c-using taurine dehydrogenase TauXY [14]. Like other aldehydes, the resulting sulfoacetaldehyde is potentially toxic and can be oxidized to sulfoacetate. In most taurine-degrading bacteria, however, it is reduced to the corresponding alcohol isethionate. In case this alcohol is excreted as the end product of taurine catabolism, the sulfur and carbon atoms are not assimilated. In contrast, other microorganisms are capable of degrading this sulfonate. In Bacillus krulwichiae, for example, isethionate can be used as sulfur source in a pathway involving oxidation to sulfoacetaldehyde and subsequent desulfonation to sulfite and acetyl-phosphate catalyzed by thiamine pyrophosphate-dependent sulfoacetaldehyde acetyltransferase Xsc [15]. For carbon assimilation, acetyl-phosphate may then be converted to acetyl-CoA by phosphotransacetylase Pta. In strict anaerobic bacteria, an alternative desulfonation route from isethionate to sulfite and acetaldehyde has recently been discovered [16,17]. This reaction is catalyzed by the glycyl radical enzyme IseG/IslA and its corresponding activator IseH/IslB. These catabolic pathways are not exclusively present in the gut microbial flora but seems to be widespread in many environments, for example, in oceanic phytoplankton [3] and highly acidic acid mine drainage sites [8]. This clearly demonstrates that taurine and its sulfonate metabolites sulfoacetaldehyde and isethionate play an important role in microbial sulfur, nitrogen and carbon assimilation.

Bacterial pathways for the degradation of taurine.

Figure 1.
Bacterial pathways for the degradation of taurine.

Thus far, two different deamination and three different desulfonation reaction steps have been discovered. Deamination can proceed via transamination (transfer of the amino group [–NH2] to 2-oxocarboxylic acids) or via direct release of ammonium. The reaction catalyzed by sulfoacetaldehyde reductase IsfD is highlighted in red. For comparison, the metabolic sequence from β-alanine to 3-hydroxypropionate is also shown. Asterisks indicate proteins with elucidated structures; BSH, bile salt hydrolase.

Figure 1.
Bacterial pathways for the degradation of taurine.

Thus far, two different deamination and three different desulfonation reaction steps have been discovered. Deamination can proceed via transamination (transfer of the amino group [–NH2] to 2-oxocarboxylic acids) or via direct release of ammonium. The reaction catalyzed by sulfoacetaldehyde reductase IsfD is highlighted in red. For comparison, the metabolic sequence from β-alanine to 3-hydroxypropionate is also shown. Asterisks indicate proteins with elucidated structures; BSH, bile salt hydrolase.

In the last year, one transport protein and several enzymes involved in these pathways have been structurally characterized revealing underlying reaction mechanisms and determinants of substrate specificity. For the first time, structures of the periplasmic taurine-binding protein TauA from E. coli [18], taurine:2-oxoglutarate aminotransferase Tpa from Bifidobacterium kashiwanohense [13], the glycyl radical enzyme isethionate sulfo-lyase IseG from Desulfovibrio vulgaris [17] as well as the unrelated sulfoacetaldehyde reductase IsfD [19] and TauF [20] from K. oxytoca and B. kashiwanohense, respectively, have been elucidated. Moreover, a new structure of the 2-oxoglutarate-dependent taurine dioxygenase TauD was published [21] and another sulfoacetaldehyde reductase, SarD, was discovered in the glycyl radical enzyme-dependent taurine degradation pathway of the human intestinal bacterium Bilophila wadsworthia [16]. With this in mind, 2019 can clearly be called a year yielding substantial progress in taurine, sulfoacetaldehyde and isethionate biochemistry.

As indicated in Figure 1, several isoenzymes have already been identified capable of catalyzing the reduction of sulfoacetaldehyde when produced during bacterial deamination of taurine. Recently, three sulfoacetaldehyde reductases, IsfD [19], SarD [16] and TauF [20], have been characterized. Moreover, as the reaction catalyzed is reversible, the dehydrogenases IseJ [22] and IseD [15] may contribute to sulfoacetaldehyde reduction as well, although their proposed physiological role is the oxidation of isethionate during assimilation of this sulfonate compound. Interestingly, among these dehydrogenases and reductases, only IsfD characterized by Zhou et al. [19] belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. Representatives of this large group of enzymes typically possess ∼250 aa and do not require metals for catalysis. IsfD is closely related to YdfG from E. coli (49% identical residues at 97% query cover) that has been characterized at first as serine dehydrogenase but functions also as malonic semialdehyde reductase in vivo [23]. Another example is a not yet kinetically characterized dehydrogenase/reductase (UniProt ID PA4907) from Pseudomonas aeruginosa that shows even closer relationship to IsfD than YdfG (61% identical residues at 98% query cover). Indeed, this type of 3-hydroxyacid dehydrogenases belonging to the SDR superfamily are widespread in bacteria. However, their physiological role is still widely unclear. In this connection, Zhou et al. [19] demonstrated that sulfoacetaldehyde reductase IsfD, like YdfG, also possesses high catalytic efficiencies for serine and 3-hydroxypropionate oxidation. Hence, among this group of metal-free 3-hydroxyacid dehydrogenases, substrate specificity may not be very distinct but only restricted to several short-chain carboxylic acids, the structurally related sulfonates and, possibly, other compounds possessing functional groups with similar negative charges. However, as both structures of YdfG (PDB ID: 3ASV) [24] and the uncharacterized enzyme PA4907 from P. aeruginosa (PDB ID: 2NWQ) do not show substrates in the active site, determinants of substrate specificity in this group of SDR enzymes were not revealed until the work of Zhou et al. [19]. Moreover, structure 2NWQ being one of the closest matches to the IsfD structure in the PDB (with a root mean square deviation across 218 α-carbon atom pairs of 0.64 Å) lacks part of the substrate-binding loop with unresolved residues S187 to A206. Consequently, the study on IsfD presents for the first time a complete structure (PDB ID: 6IXJ) [19] for this group of carbonyl-alcohol oxidoreductases with bound substrate/product and cofactor (isethionate and NADPH, respectively). In addition, the role of IsfD active site residues revealed by the structure has been proved by Zhou et al. [19] through testing enzyme variants with corresponding amino acid mutations.

Interestingly, inspection of the tetrameric structure of IsfD indicated that the respective diagonal subunits cross-interact strongly via their C-terminal tails. The latter region with β-sheets 8 and 9 protrudes away from the main subunit body and reaches the active site of the opposite subunit. Thus, stabilization of the substrate-binding loop in the closed conformation is accomplished. In particular, C-terminal residue F248 is located close to side chains of active site amino acids I142 and Y148 of the diagonal subunit. This important interaction results in a proper positioning of Y148 for hydrogen bonding with the sulfonate group of isethionate (Figure 2). The protruding C-terminal tail has already been noticed in the structures of YdfG and PA4907 [24], and a mutant enzyme lacking the seven C-terminal residues completely abolishes serine dehydrogenase activity of YdfG. However, due to the lack of a bound substrate in structure 3ASV, the crucial role of this feature for substrate binding could not be interpreted satisfactorily in the preceding YdfG study [24]. Nevertheless, as shown in Figure 2, active site amino acids are well conserved in all three SDR 3-hydroxyacid dehydrogenases. Compared with IsfD, only two minor deviations are found in dehydrogenase/reductase PA4907, as I142 and I186 of IsfD are replaced by V and L, respectively, in the uncharacterized enzyme (Figure 2A). Now, considering the high similarity with the resolved IsfD active site architecture showing the specific interaction with the bound isethionate, it is reasonable to propose that enzyme PA4907 is likewise capable of catalyzing sulfoacetaldehyde reduction. On the other hand, the supposed serine dehydrogenase YdfG shows already three changes, IsfD I142, I186 and F249 are replaced by T135, L179 and L243 in YdfG. Particularly, the latter mutation from an aromatic to a smaller aliphatic side chain may change positioning of the active site Y141 in YdfG. Actually, this residue (corresponding to Y148 in IsfD) shows deviating orientation (Figure 2B) and its side chain might be better suited to interact with the carboxyl groups of serine, threonine and 3-hydroxypropionate than with the sulfonate of isethionate. Consequently, the homologous C-terminal residues IsfD F249 and YdfG L243 appear to fulfill different roles. In YdfG, additional hydrogen bonding may be accomplished by T135, indicating a deviating substrate specificity compared with IsfD and enzyme PA4907. In line with this, YdfG is capable of threonine dehydrogenation, while IsfD cannot use this amino acid as substrate [19]. Thus far, the protruding C-terminal tail feature is unique to structures 2NWQ, 3ASV and 6IXJ, and the corresponding enzymes may define a subgroup within the 3-hydroxyacid dehydrogenases in the SDR superfamily.

Active sites of three SDR 3-hydroxyacid dehydrogenases.

Figure 2.
Active sites of three SDR 3-hydroxyacid dehydrogenases.

Superposition of the IsfD structure with bound substrate isethionate and cofactor NADPH (PDB ID: 6IXJ) with (A) uncharacterized dehydrogenase/reductase PA4907 (PDB ID: 2NWQ) and (B) dehydrogenase YdfG (PDB ID: 3ASV). Residues of IsfD substrate-binding pocket and the F249 of the opposite subunit are colored in green and blue, respectively. Corresponding residues of superposed structures are colored in grey and black, respectively.

Figure 2.
Active sites of three SDR 3-hydroxyacid dehydrogenases.

Superposition of the IsfD structure with bound substrate isethionate and cofactor NADPH (PDB ID: 6IXJ) with (A) uncharacterized dehydrogenase/reductase PA4907 (PDB ID: 2NWQ) and (B) dehydrogenase YdfG (PDB ID: 3ASV). Residues of IsfD substrate-binding pocket and the F249 of the opposite subunit are colored in green and blue, respectively. Corresponding residues of superposed structures are colored in grey and black, respectively.

Although catalyzing serine and 3-hydroxypropionate oxidation as well, the role of IsfD in taurine metabolism and sulfoacetaldehyde reduction to isethionate is clearly corroborated by the operon-like association of the corresponding gene isfD together with genes encoding taurine uptake by transporter TauABC and deamination by transaminase Toa in K. oxytoca. Moreover, expression of isfD in Chromohalobacter salexigens is inducible by taurine [25]. Using bioinformatics tools, Zhou et al. [19] provided also evidence that many other bacteria employ IsfD as sulfoacetaldehyde reductase in taurine metabolism. However, with a changing gene neighborhood and regulation, IsfD and related SDR 3-hydroxyacid dehydrogenases may be involved in other pathways as well, for example, for the detoxification of malonic semialdehyde. In this connection, the metabolic sequence for the deamination of β-alanine via malonic semialdehyde and 3-hydroxypropionate catalyzed by pyridoxal phosphate-dependent transaminase PydD and reductase PydE, respectively, has recently been elucidated in the bacterium Lysinibacillus massiliensis [26]. Like SarD and TauF, PydE is a metal-depending dehydrogenase not related to the SDR superfamily. However, considering the high similarity of the β-alanine route to 3-hydroxypropionate with the taurine deamination to isethionate (Figure 1), pathways likely exists or may evolve employing an IsfD-related enzyme for the reduction in malonic semialdehyde or structurally related short-chain aldehydes. The work by Zhou et al. [19] paved the way for the discovery of these new physiological roles of IsfD-related SDR 3-hydroxyacid dehydrogenases in the future.

Competing Interests

The author declares that there are no competing interests associated with this manuscript.

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