title: Comprehensive genomic analysis of sulfur-relay pathway genes.
abstract: Many cofactors and nucleotides containing sulfur atoms are known to have important functions in a variety of organisms. Recently, the biosynthetic pathways of these sulfur containing compounds have been revealed, where many enzymes relay sulfur atoms. Increasing evidence also suggests that the prokaryotic sulfur-relay enzymes might be the evolutionary origin of ubiquitination and the related systems that control a wide range of physiological processes in eukaryotic cells. However, these sulfur-relay enzymes have been studied in only a small number of organisms. Here we carried out comparative genomic analysis and examined the presence and absence of sulfurtransferases utilized in the biosynthetic pathways of molybdenum cofactor (Moco), 2-thiouridine (S(2)U), and 4-thiouridine (S(4)U), and IscS, a cysteine desulfurase. We found that all eukaryotes and many other organisms lack the intermediate enzymes in S(2)U biosynthesis. It is also found that most genes lack rhodanese homology domain (RHD), a catalytic domain of sulfurtransferase. Some organisms have a conserved sequence composed of about 100 residues in the C terminus of TusA, different from RHD. Host-associated organisms have a tendency to lose Moco biosynthetic enzymes, and some organisms have MoaD-MoaE fusion protein. Our findings suggest that sulfur-relay pathways have been so diversified that some putative sulfurtransferases possibly function in other unknown pathways.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan. kot@kuicr.kyoto-u.ac.jp.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kotera
authors.forename: Takeshiko
authors.initials: T
authors.lastname: Bayashi
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hattori
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Tokimatsu
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Hisaaki
authors.initials: H
authors.lastname: Mihara
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
mesh_terms: D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics; D005656:Fungal Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics; D006801:Humans; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D012984:Software; D013455:Sulfur / Q000378:metabolism*; D013466:Sulfurtransferases / Q000378:metabolism*; D025801:Ubiquitin / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005656:Fungal Proteins; D025801:Ubiquitin; D013455:Sulfur; D013466:Sulfurtransferases