Biodesulfurization Induces Reprogramming of Sulfur Metabolism in Rhodococcus qingshengii IGTS8: Proteomics and Untargeted Metabolomics

Abstract

For many decades, research on biodesulfurization of fossil fuels has persevered amid a complete lack of knowledge of sulfur metabolism and its regulation in fuel-biodesulfurizing bacteria, which has impeded the development of a commercially viable bioprocess. In addition, lack of understanding of biodesulfurization-associated metabolic and physiological adaptations prohibited the development of efficient biodesulfurizers.

The interplay between sulfur metabolism and desulfurization profile in Rhodococcus: Unraveling the role of the transsulfuration pathway

“…Our results indicate that biomass concentration and desulfurization capability are largely affected by the choice of sulfur source. This observation is in line with the findings of Hirschler et al and Tanaka et al (4, 29), as they report that the CysK-dependent alternative route for cysteine biosynthesis seems to be preferred under sulfate starvation conditions (BDS), however it is likely operating as a secondary pathway when sulfate is supplemented as the sole sulfur source. According to the same study, protein levels of CβS and METB were slightly higher, but not significantly different between the DBT and inorganic sulfate cultures.…”

“…The latter is then oxidized to sulfide, H2O2, and formaldehyde by a methyl mercaptan oxidase (MMO) present in Rhodococcus strain IGTS8 (10). A direct sulfhydrylation pathway can follow to convert sulfide to L-homocysteine, in condensation with either Osuccinyl-L-homoserine (OSHS) or O-acetyl-L-homoserine (OAHS), through the catalytic action of MetZ (OSHS) or MetY (OAHS), thus serving as a precursor for sulfur-containing amino acid biosynthesis (4,11). A second pathway for methionine catabolism, validated for Gram-positive bacteria, involves the sequential formation of S-Adenosyl-L-methionine (SAM), S-Adenosyl-L-homocysteine (SAH), and then L-homocysteine (4,(12)(13)(14)(15)(16).…”

“…A direct sulfhydrylation pathway can follow to convert sulfide to L-homocysteine, in condensation with either Osuccinyl-L-homoserine (OSHS) or O-acetyl-L-homoserine (OAHS), through the catalytic action of MetZ (OSHS) or MetY (OAHS), thus serving as a precursor for sulfur-containing amino acid biosynthesis (4,11). A second pathway for methionine catabolism, validated for Gram-positive bacteria, involves the sequential formation of S-Adenosyl-L-methionine (SAM), S-Adenosyl-L-homocysteine (SAH), and then L-homocysteine (4,(12)(13)(14)(15)(16). In the first step of the forward transsulfuration pathway, a γ-replacement reaction of L-cysteine and an activated L-homoserine ester (OSHS or OAHS) generates L-cystathionine and succinate or acetate, respectively, with the catalytic action of a Cystathionine γ-synthase (CγS; Figure 1B, Reactions M1 and M2) (17,18).…”

“…However, information on the repression mechanism is still limited, and until recently, the sulfur assimilation pathways of Rhodococci had only been investigated in silico (7, 8). An exception is a very recent report that conducted comparative genomics and untargeted metabolomics analyses in Rhodococcus qingshengii IGTS8 and proposed a working model for assimilatory sulfur metabolism reprogramming in the presence of DBT (4).…”

“…This reverse transsulfuration metabolic route for L-Cysteine biosynthesis from L-Methionine has been also reported in mammals, yeasts, archaea and several other bacteria (13, 23–27). An alternative pathway for L-cysteine biosynthesis reported for Corynebacterium glutamicum and Rhodococcus strain IGTS8 requires the O-acetyl-L-serine (OAS) sulfhydrylase, CYSK, for the condensation of sulfide and OAS (4, 28). In the opposite direction, a reaction mediated by L- cysteine desulfhydrase (CD) leads to L-cysteine degradation into sulfide, pyruvate, and ammonia (28).…”