Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase

Abstract

The euryarchaeon Methanosarcina acetivorans has no homologues of the first three enzymes that produce the essential methanogenic coenzyme M (2-mercaptoethanesulfonate) in Methanocaldococcus jannaschii. A single M. acetivorans gene was heterologously expressed to produce a functional sulfopyruvate decarboxylase protein, the fourth canonical enzyme in this biosynthetic pathway. An adjacent gene, at locus MA3297, encodes one of the organism's two threonine synthase homologues. When both paralogues from this organism were expressed in an Escherichia coli threonine synthase mutant, the MA1610 gene complemented the thrC mutation, whereas the MA3297 gene did not. Both PLP (pyridoxal 5'-phosphate)-dependent proteins were heterologously expressed and purified, but only the MA1610 protein catalysed the canonical threonine synthase reaction. The MA3297 protein specifically catalysed a new beta-replacement reaction that converted L-phosphoserine and sulfite into L-cysteate and inorganic phosphate. This oxygen-independent mode of sulfonate biosynthesis exploits the facile nucleophilic addition of sulfite to an alpha,beta-unsaturated intermediate (PLP-bound dehydroalanine). An amino acid sequence comparison indicates that cysteate synthase evolved from an ancestral threonine synthase through gene duplication, and the remodelling of active site loop regions by amino acid insertion and substitutions. The cysteate product can be converted into sulfopyruvate by an aspartate aminotransferase enzyme, establishing a new convergent pathway for coenzyme M biosynthesis that appears to function in members of the orders Methanosarcinales and Methanomicrobiales. These differences in coenzyme M biosynthesis afford the opportunity to develop methanogen inhibitors that discriminate between the classes of methanogenic archaea.

Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment

“…However, our results suggest that cysteamine could have also formed readily from electric discharges. The recently discovered enzymatic conversion of cysteate into sulfopyruvate in the biosynthesis of coenzyme M (2-mercaptoethanesulfonic acid, HSCH 2 CH 2 SO 3 H) in Methanosarcina acetivorans (Graham et al 2009) supports the idea that products of cysteine degradation and other sulfur-bearing organic compounds of prebiotic origin may have been involved in early biological processes.…”

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

“…This is the case of genes required for the biosynthesis of the coenzyme M and coenzyme B involved in the last step of methanogenesis. Inferred CoM biosynthesis uses sulfopyruvate, which originates from 3-phosphoserine converted to cysteate by a cysteate synthase and then to sulfopyruvate (ComDE), as observed in Methanosarcinales, Methanomicrobiales [61] and Methanocellales (Additional file 1: Table S11). An alternative pathway takes place in other methanogens, where CoM originates from phosphoenolpyruvate and sulfite to produce sulfolactate, which is then oxidized [62–64].…”

Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

“…Members of this family are sometimes annotated as IMP dehydrogenase, but according to the Pfam curators, this annotation is spurious. The genomes of some methanogens contain two members of this family, one of which may be an ortholog of Dde_3007 and the other of which is often in proximity to genes that are involved in the synthesis of coenzyme M. For example, in Methanoculleus marisnigri JR1, Memar_0110 is a member of DUF39 and is adjacent to genes encoding cysteate synthase (47) and sulfopyruvate decarboxylase (a fused ComDE) (48). Subsequent steps in coenzyme M synthesis involve the transfer of a sulfide group from sulfotoacetaldehyde to form coenzyme M, but the genes involved are not known.…”