Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanopyrus kandleri Euryarchaeota; Methanopyri; Methanopyrales; Methanopyraceae Methanosarcina acetivorans Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosarcina barkeri_fusaro Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosarcina mazei Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosphaera stadtmanae Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanospirillum hungatei_JF_1 Euryarchaeota; Methanomicrobia; Methanomicrobiales; Methanospirillaceae Natronomonas pharaonis Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natronomonas Picrophilus torridus_DSM_9790 Euryarchaeota; Thermoplasmata; Thermoplasmatales; Picrophilaceae Pyrococcus abyssi Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Pyrococcus furiosus Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Pyrococcus horikoshii Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Thermococcus kodakaraensis_KOD1 Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Thermoplasma acidophilum Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae Thermoplasma volcanium Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae Nanoarchaea Nanoarchaeum equitans Nanoarchaeota Bacteria Acidobacteria Acidobacteria bacterium_Ellin345 Fibrobacteres/Acidobacteria group * Actinobacteria Bifidobacterium longum Actinobacteria; Actinobacteria (class); Actinobacteridae; Bifidobacteriales; Bifidobacteriaceae Corynebacterium diphtheriae Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium efficiens_YS_314 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium glutamicum_ATCC_13032_K Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium glutamicum_ATCC_13032_K Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium jeikeium_K411 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Frankia CcI3 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Frankineae; Frankiaceae Leifsonia xyli_xyli_CTCB0 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Microbacteriaceae Mycobacterium avium Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium bovis Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium leprae Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae urbonavicus_MIE_2007_tableS1.xls 1 01/02/2007 Mycobacterium MCS Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium tuberculosis_CDC1551 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium tuberculosis_H37Rv Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Nocardia farcinica_IFM10152 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Nocardiaceae Propionibacterium acnes_KPA171202 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Propionibacterineae; Propionibacteriaceae Rubrobacter xylanophilus_DSM_9941 Actinobacteria; Actinobacteria (class); Rubrobacteridae; Rubrobacterales; Rubrobacterineae; Rubrobacteraceae * Streptomyces avermitilis Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae Streptomyces coelicolor Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae Thermobifida fusca_YX Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptosporangineae; Nocardiopsaceae Tropheryma whipplei_TW08_27 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Cellulomonadaceae Tropheryma whipplei_Twist Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Cellulomonadaceae Aquificae Aquifex aeolicus Aquificae; Aquificae (class); Aquificales; Aquificaceae * Bacteroidetes Bacteroides fragilis_NCTC_9434 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Bacteroides fragilis_YCH46 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Bacteroides thetaiotaomicron_VPI_5482 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Chlorobium chlorochromatii_CaD3 Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Chlorobium tepidum_TLS Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Pelodictyon luteolum_DSM_273 Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Porphyromonas gingivalis_W83 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Porphyromonadaceae Salinibacter ruber_DSM_13855 Bacteroidetes/Chlorobi group; Bacteroidetes; Sphingobacteria; Sphingobacteriales; Crenotrichaceae PVC group Chlamydia muridarum Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydia trachomatis Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydia trachomatis_A_HAR_13 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila abortus_S26_3 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila caviae Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila felis_Fe_C_56 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_AR39 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_CWL029 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_J138 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_TW_183 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Protochlamydia amoebophila UWE25 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Parachlamydiaceae Rhodopirellula baltica SH1 Planctomycetes; Planctomycetacia; Planctomycetales; Planctomycetaceae; Rhodopirellula Chloroflexi Dehalococcoides CBDB1 Chloroflexi; Dehalococcoidetes Dehalococcoides ethenogenes_195 Chloroflexi; Dehalococcoidetes Cyanobacteria Anabaena variabilis_ATCC_29413 Cyanobacteria; Nostocales; Nostocaceae * Gloeobacter violaceus Cyanobacteria; Gloeobacteria; Gloeobacterales * Nostoc sp Cyanobacteria; Nostocales; Nostocaceae * Prochlorococcus marinus_CCMP1375 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MED4 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MIT_9312 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MIT9313 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_NATL2A Cyanobacteria; Prochlorales; Prochlorococcaceae * Synechococcus CC9605 Cyanobacteria; Chroococcales * Synechococcus CC9902 Cyanobacteria; Chroococcales * Synechococcus elongatus_PCC_6301