Catalytic Mechanism of Sep-tRNA:Cys-tRNA Synthase

Liu, Yuchen; Santos, Patricia C. Dos; Zhu, Xiang; Orlando, Ron; Dean, Dennis R.; Söll, Dieter; Yuan, Jing

doi:10.1074/jbc.m111.313700

Cited by 16 publications

(3 citation statements)

References 32 publications

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“…It has also been shown that free Cys is not synthesized independently of tRNA Cys in Methanococcus maripaludis (5), consistent with later findings showing that, in contrast to aerobic cells, neither Hcy nor iron-sulfur clusters are synthesized with sulfur originating from Cys in that organism (6). Studies of SepCysS expressed in Escherichia coli suggested that the enzyme does not efficiently use sulfide as a sulfur source in vitro (7) but instead consumes sulfane from persulfide to form Cys-tRNA Cys (7,8) (Fig. 1).…”

supporting

confidence: 78%

Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein

Rauch

Perona

2016

J Bacteriol

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Conserved genes essential to sulfur assimilation and trafficking in aerobic organisms are missing in many methanogens, most of which inhabit highly sulfidic, anaerobic environmental niches. This suggests that methanogens possess distinct pathways for the synthesis of key metabolites and intermediates, including cysteine, homocysteine, and protein persulfide groups. Prior work identified a novel tRNA-dependent two-step pathway for cysteine biosynthesis and a new metabolic transformation by which sulfur is inserted into aspartate semialdehyde to produce homocysteine. Homocysteine biosynthesis requires two of the three proteins previously identified in our laboratory by a comprehensive bioinformatics approach. Here, we show that the third protein identified in silico, the ApbE-like protein COG2122, facilitates sulfide assimilation in Methanosarcina acetivorans. Knockout strains lacking the gene encoding COG2122 are severely impaired for growth when sulfide is provided as the sole sulfur source. However, rapid growth is recovered upon supplementation with cysteine, homocysteine, or cystathionine, suggesting that COG2122 is required for efficient biosynthesis of both cysteine and homocysteine. Deletion of the gene encoding COG2122 does not influence the extent of sulfur modifications in tRNA or the prevalence of iron-sulfur clusters, indicating that the function of COG2122 could be limited to sulfide assimilation for cysteine and homocysteine biosynthesis alone. IMPORTANCEWe have found that the conserved M. acetivorans ma1715 gene, which encodes an ApbE-like protein, is required for optimal growth with sulfide as the sole sulfur source and supports both cysteine and homocysteine biosynthesis in vivo. Together with related functional-genomics studies in methanogens, these findings make a key contribution to elucidating the novel pathways of sulfide assimilation and sulfur trafficking in anaerobic microorganisms that existed before the advent of oxygenic photosynthesis. The data suggest that the MA1715 protein is particularly important to sustaining robust physiological function when ambient sulfide concentrations are low. Phylogenetic analysis shows that MA1715 and other recently discovered methanogen sulfur-trafficking proteins share an evolutionary history with enzymes in the methanogenesis pathway. The newly characterized genes thus likely formed an essential part of the core metabolic machinery of the ancestral euryarchaeote. Genes that function in sulfate assimilation and sulfur trafficking in aerobic organisms are often not identifiable in the genomes of methanogens and other anaerobes, suggesting that these ancient organisms may retain metabolic vestiges characteristic of life on the early earth (1). In aerobes, sulfur is imported into the cell as sulfate, which is reduced to sulfide in an ATP-dependent pathway (2). In turn, sulfide is incorporated directly into activated serine and homoserine derivatives to yield cysteine (Cys) and homocysteine (Hcy), respectively (Fig. 1, left) (3). Cys and Hcy can al...

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supporting

confidence: 78%

Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein

Rauch

Perona

2016

J Bacteriol

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“…Although the exact mechanism of the SepCysS-catalyzed reaction has not yet been fully elucidated, the Sep-to-Cys conversion most likely proceeds through a PLP-dependent generation of a dehydroalanyl-tRNA Cys intermediate, which is subsequently attacked by a persulfide group to form Cys-tRNA Cys ( 60 , 61 ). Both “ Ca .…”

Section: Resultsmentioning

confidence: 99%

“…Both “ Ca . Parcubacteria” and Chloroflexi SepCysS possess residues involved in PLP binding ( 59 ), while only Chloroflexi SepCysS harbors conserved Cys residues implicated in persulfide ( 60 , 61 ) and Fe−S cluster formation ( 6 ). “ Ca .…”

Section: Resultsmentioning

confidence: 99%

RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

Mukai

Crnković

Umehara

et al. 2017

mBio

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The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“Candidatus Parcubacteria” and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.

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