Supplementary Figure S1. Genomic Context of the Ribosomal Protein Genes Identiﬁed in Viruses

Ribosomal proteins in viruses Fig S1 S30 Finkel-Biskis-Reilly murine sarcoma virus gag polyprotein multifunctional tRNA nudix lysozyme nucleotidyl transferase hydrolase Cronobacter phage vB_CsaM_GAP32

S21 Pelagibacter phage HTVC008M E. coli O157 typing phage 14 heat shock putative 2OG-Fe(II) cobalt chelatase subunit protein oxygenase S30AE Escherichia phage 2 JES-2013

E. coli bacteriophage rv5 L9 Mycobacterium phage 32HC Escherichia phage vB_EcoM_FFH2 virion protein major tail subunit Enterobacteria phage vB_EcoM-FV3

Ralstonia phage RSB3

RNA polymerase subunit N4 gp2-like protein Roseophage DSS3P2

Dinoroseobacter phage DEL12phi1

Sulﬁtobacter phage phiCB2047-B L7/L12

Salmonella phage FSL SP-058

Salmonella phage FSL SP-076

ATP-dependent putative NTP %identity (aa) molecular chaperone pyrophosphohydrolase DNA helicase Erwinia phage Ea9-2 60 70 75 80 85 90 92 94 96 98 100

Supplementary Figure S1. Genomic context of the ribosomal protein genes identiﬁed in viruses. Genes coding for ribosomal protein domains are shown in red. The exact positions of the domains are marked by a black line on top of the gene. tRNAs are colored in purple. All comparisons were done at the amino acid level. A color scale for the % identity is shown at the bottom right. Ribosomal proteins in viruses a Fig S2 Fubi (UBQ superfamily) Ribosomal_S30

FBR-MuSV(NP_598374) 1 MQLFVRAQELHTLEVTGQGTVAQIKDHVTSLEGIAPDDQVVLLAGSPQEDEATLGQCGVEALTTLEVAGRMLGGKVHGFLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTLGKKKGPNANF 133/133 Mus musculus domesticus (BAB68608) 5 MQLFVRAQELHTLEVTGQETVAQIKDHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 137/137 Mus musculus (AAH81463) 1 MQLFVRAQELHTLEVTGQETVAQIKDHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 133/133 Rattus norvegicus (EDM12555) 24 MQLFVRAQELHTLEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGSPLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 156/156 Bos taurus (DAA29636) 1 MQLFVRAQELHTLEVTGQETVAQIKAHVASLEGIAPEDQVLLLAGSPLEDEATLGQCGVEALSTVEVAGRMLRGKVHGSLAHAGKVRGQTPKVAKQE---KKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 130/130 Sus scrofa (AHG94954) 1 MQLFVRAQELHTLEVTGQETVAQIKAHVASLEGIAPEDQVLLLAGTPLEDDAILGQCGVEALSTLEVAGRMLGGKVHGSPARAGKVRGQTPKVAKQEKRKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS 133/133 b Mycobacterium phage 32HC (AHJ86298) 1 MKVILTKPIRSR-QAGEVLDVDSGSAKNMV------EKRKVAQYFDPDKHKQTAERTAPRRGN 56/86 Mycobacterium smegmatis (ABK76149) 1 MKLILTAEVEHLGAAGDTVEVKDGYGRNYLLPRGLAIVASRGAERQAEEIRRARESKVIRDIEHANELKTALEG 74/151 Mycobacterium abscessus (EIV73821) 1 MKLILTTEVEHLGTAGDAVEVKDGYGRNYLLPRGLAIVATRGAERQANDIRRAREAKEIRGVEHANEIKQAIEG 74/151 Mycobacterium tuberculosis (AAK44284) 1 MKLILTADVDHLGSIGDTVEVKDGYGRNFLLPRGLAIVASRGAQKQADEIRRARETKSVRDLEHANEIKAAIEA 74/152 Lactobacillus jensenii 27-2-CHN (EEU20831) 1 MKVIFVQDVRGRGKRGEVKNVPDGYAQNYLIKRGLAKEANKGNLNTLKRVEANEKAAYEAEKADAIKIKKQLES 74/150 Lactobacillus sp wkB8 (AIS08334) 1 MKVIFTKDVKGRGKRGEVKNVPDGYAQNFLFKRGLAKAATKANMHTLERVAANEKAAYESEKAEAEKIKSELDK 74/151 Arthrobacter sp H20 (WP_026552610) 2 AKLILTHEVTGLGAAGDIVEVKNGYARNFLLPRGFALTWTKGGEKQVESIKAARVARVHSTLEEAQNQAAALSA 75/149 Ornithinimicrobium pekingense (WP_022920098) 1 MKLILTQPVSGLGSAGDVVDVKDGYARNFLLPRKVATPWTKGGQKQVDAITQGRAKRALKSAEDAAAAKDRLEG 74/148 Serinicoccus profundi (WP_010147232) 1 MKIILTQPVTGLGDAGDVVDVKDGYARNFLLPRKVATPWTKGGQKQVDSIKAARDKRAVRSAEDAAAAKARLES 74/150 Nocardiopsis dassonvilleigi DSM43111 (ADH70224) 1 MKLILTHEVNGLGAPGDVVEVKNGYGRNYLLPRGFAIRWTRGGQKQIDLIQRARSARDIRTLDEAQQVAGRVNA 74/148 Arcanobacterium haemolyticum DSM20595 (ADH93477) 1 MKIILTHEVENLGAAGEVVVVKDGYARNFLLPRGYATVWTKGAQRQIDQIAESRRKRATEDIEAAREIREALES 74/148 Desulfarculus baarsii DSM2075 (ADK85095) 1 MQVILIKEVLGLGDPGELVEVKRGYARNFLVPQGLAVLATKKNMAAVEAERKRIAVQQAKEAARIRQEAAGVSG 74/169 Selenomonas sputigena ATCC35185 (AEC00999) 1 MKVILQQDVKKVGSKGDIVEVSEGYGRNFLLPKKLAVEATAANLETAKQKANSAARKKQQATDEARLLAAQLEK 74/148 Desulfatibacillum alkenivorans AK-01 (ACL02621) 1 MKVILTENIDSLGLIGSEVAVADGYARNYLLPKKKAVLATEANRKVVELKRVKWEAKIAKEKALAEEMAKRIEG 74/148 Thermovirga lienii DSM 17291 (AER67051) 1 MKCILLSDVSKLGKKGELIEVSDGYARNYLIPRGLAEEATPAKLAEWKQKQKSMEIREKKLKEEALALQKKLNG 74/148 Shewanella baltica OS183 (EHQ16389) 1 MNVILLDKIANLGNLGDQVSVKAGYARNFLLPQGKAVVANESNVKVFEARRAELEAKLAAELAAANLRAEKITA 74/150 Enterobacteriaceae bacterium 1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNVEFFEARRAELEAKLADVLAAANARAEAINA 74/149 Rubidibacter lacunae KORDI 51-2 (ERN42890) 6 QQVVLRHDVKKLGSTDDVVDVAPGYARNYLIPQGLAAVATPGLLRQVEQRKEKERQAQLALLKDAQDRKTALAT 79/154 Cyanothece sp PCC 8802 (ACV02082) 5 VQIVLNKTINKLGQTGDLVEVAPGYARNYLIPQGMGVIATPGILRQVEQRKEKEMQRLLAEKQAAEARKVALST 78/152 Mycoplasma anseris (WP_033178508) 1 MKVILIKDFQ-KNKANEIIEVADGYAKNFLIKNGIAQPVNKQTLENLKRIKQNIANDVANQIFEAKLVKAEIEK 73/145 Mycoplasma cloacale (WP_029330539) 1 MKVILIKDFN-KHKANEIIEVADGYAKNYLIKNGIAQPINKQTMENLNRIKQNIADDLEQQIYQATLLKQEIEK 73/145 Mycoplasma spumans (WP_027122970) 1 MKVILIKNYE-KHKANEIIEVNDGFGKNFLIKKGIAQPVNEKTLANLQRVKNNIAENLAREIADANLIKEEIEK 73/145 *Geobacillus stearothermophilus (1DIV-A) 1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAEELANAKKLKEQLEK 74/149

*1DIV-A Cyanobacteria 2HBA (N-terminal) Firmicutes Gammaproteobacteria beta 3/10 alpha strand helix helix Actinobacteria Deltaproteobacteria Tenericutes

Supplementary Figure S2. Multiple sequence alignment of the phage-encoded ribosomal proteins S30 (a) and L9 (b) with homologous sequences encoded by cellular organisms. Taxonomic afﬁliations are represented by colored circles (see legend at the bottom right). Positions of the ribosomal protein domains (red arrows) within the full proteins (black lines) are shown at the right side of the alignment. Ribosomal proteins in viruses Fig S3

a b

50S 50S 50S L33 23S RNA 23S RNA 23S RNA 5S RNA 5S RNA L31 L19 L9 L7/L12 L9 S20 L11 L2

S21 16S RNA S6 16S RNA 16S RNA S15 S9 30S 30S 30S

Supplementary Figure S3. Localization of virus-encoded proteins in the context of the 70S ribosome. a) Ribosomal proteins encoded by cultivated viruses shown on the structure of the Thermus thermophilus ribosome (PDB id: 4V42). b) Ribosomal proteins encoded by non-cultivated viruses shown on the structure of the E. coli ribosome (PDB id: 4V4Q). The 30S subunit is colored white and the 50S is in dark grey. Ribosomal RNAs are shown as ribbons (16S: blue, 23S: cyan, 5S: green). Ribosomal proteins found in viruses are colored and indicated with an arrow. Ribosomal proteins in viruses Fig S4 putative EF-G interaction site a putative EF-Tu interaction site * ** * L11 interface * * * ** * ** ** * ** * Ralstonia phage RSB3 DNA (BAN92321) 2 KIKATIQLTG---NNKVAQIKAIREATALGLKDAKDLVDHI-----HNRLSRSAP------LILTPHQYG------VLVALW 63/98 Roseophage DSS3P2 (ACL81275) 14 ---MSVDVSS---SQKINCIKLLRQITGEGLKETKDFFEQE----WMPFVLEGQRFGKPTMTPP-AQSLELVDIMDRLQALENIVS-- 90/107 Dinoroseobacter phage DFL12phi1 (AHX01035) 14 ---MNPEYVN---SKKINCIKHIRSLSGEGLKEAKDFFEQE-----WLPFVNGD------RKPP-ETIRELIEDTPD----FQA---- 77/106 Sulfitobacter phage phiCB2047-B (AGH07436) 80 -RMFDLDHVN---DHKISFIKNVRNMTGCGLREAKTVLDTF-----TQNHVKI------123/123 Salmonella phage FSL SP-058 (AGF88198) 278 PYPITITKVS--KENPVACIKAIRTATGLGLYEAKQAYDFVRDNEEPYSLQIIIS-----KG----ELTHLFTEAG------IEY--- 345/418 Salmonella phage FSL SP-076 (AGF88397) 278 PYPITVTKVS--KENPVACIKAIRTATGLGLYEAKQAYDFVRDNEEPYNLQIIIS-----KG----ELTHLFAEAG------IEY--- 345/418 Erwinia phage Ea9-2 (AHI60108) 145 -WQVILTGNNSNSLQKVAAIKLLRTVGGFDLSKAKTVLEQR----VPAVILAGYD-----EQTA-FTICQWLEEFG------YKANTN 215/724 Selenomonas sputigena ATCC35185 (AEB99742) 56 EFTVVLAAAG---DKKINVIKAVREATGLGLKEAKELVDGA-----PAPIKENIA-----KAEA-EELKKKLEEAG------ATVELK 123/123 Desulfarculus baarsii DSM2075 (ADK86299) 59 EFDVILETAG---DKKIQVIKVVRAITGLGLKEAKDLVDGA-----PKPVKEAVP-----KDEA-ESIKAQLEEAG------AVVQVK 126/126 Rhizobium leguminosarum WSM1325 (ACS55713) 58 EFDVILVEAG---ANKINVIKEVRAITGLGLKEAKDLVEAA-----PKAVKEGVN-----KAEA-ADIKKKLEDAG------AKADVK 125/125 Lactococcus raffinolactis 4877 (CCK20525) 54 EFDVELTSAG---DKKVATIKAVREATGLGLKEAKDLVDSA-----PVVIKEGLP-----KAEA-EAIVEAIGAAG------GSAGLK 121/121 Ca. Glomeribacter gigasporarum BEG34 (CCD29195) 57 EFTVVLLEAG---GNKVAVIKAVREITSLGLKEAKDLVDGA-----PKPIKENAP-----KAEA-EEIKKKLEAAG------AKAELK 124/124 Alicycliphilus denitrificans BC (ADU98234) 59 EFNVVLAEAG---ANKVAVIKAVREITGLGLKEAKDLVDGA-----PKNVKEGIA-----KADA-EAAVKKLVDAG------AKAELK 126/126 Actinobacillus succinogenes 130Z (ABR73423) 55 EFNVVLTEAG---ANKVAVIKAVRGATGLGLKEAKDLVESA-----PANLKEGIS-----KGEA-EELKKALEEAG------AKVEIK 122/122 Bacteroides salanitronis DSM18170 (ADY37055) 58 SFDVVLKSAG---AAKLQVVKAVKEACGLGLKEAKDLVDGA-----PSTVKEGLA-----KDEA-ESLKKTLEEAG------AEVELK 125/125 Zobellia galactanivorans (CAZ94716) 58 EFDVVLKAAG---ASKLAVVKLVKELTGLGLKDAKDIVDSA-----PKAVKEGVS-----KDEA-EGIKKSLEEAG------AEVELK 125/125 Yersinia pestis 91001 (AAS63281) 28 EFDVVLASFG---ENKVAVIKAVRGATGLGLKEAKDLVESA-----PAVLKEGVN-----KDEA-ETLKKSLEEAG------ASVEIK 95/95 Glaciecola nitratireducens FR1064 (AEP31141) 56 EFDVILTSFG---ANKVAVIKAVRSATGLGLKEAKDVVESA-----PKAIKEGVS-----KGEA-EELQKALTEAG------AEVEVK 123/123 Thiomicrospira crunogena XCL-2 (ABB40883) 56 EFDVVLTGAG---DNKVAAIKAVRGATGLGLKEAKSAVESA-----PFTLKEGVS-----KEEA-ETLANELKEAG------IEVEVK 123/123 Micromonospora sp L5 (ADU06179) 61 EFDVILDADG---GKKIQVIKVVRELTGLGLKEAKDLVEAA-----PKAVLEKAN-----KETA-EKAKAKLEGEG------AKVTLK 128/128 Streptomyces sp. SirexAA-E (AEN11798) 60 EFDVILTGAG---EKKIQVIKVVRELTSLGLKEAKDLVDGA-----PKPVLEKVA-----KEAA-EKAAESLKGAG------ASVEVK 127/127 Nocardiopsis dassonvillei DSM43111 (ADH70496) 62 EFDVILEGAG---DKKIQVIKEVRGLTSLGLKEAKDLVDNA-----PKPLLEGVN-----KETA-EKAKAALEGAG------ASVTLK 129/129 Arcobacter nitrofigilis DSM7299 (ADG94266) 56 EFNVVILDAG---DKKINVIKAIRALTGLGLKEAKAMSEEA-----GAIVKEGIG-----KEDA-EAAKAELEAAG------AKVELK 123/123 Streptococcus agalactiae COH1 (CDN66629) 54 SFDVELTAAG---DKKVGVIKVVREITGEGLKEAKAIVDNA-----PSVIKEGAS-----EAEA-NEIKEKLEAAG------ASVTLK 121/121 *Escherichia coli (1CTF-A) 1 EFDVILKAAG---ANKVAVIKAVRGATGLGLKEAKDLVESA-----PAALKEGVS-----KDDA-EALKKALEEAG------AEVEVK 68/68 *1CTF-A

beta 3/10 alpha b strand helix helix Ralstonia phage RSB3 DNA (BAN92321) Roseophage DSS3P2 (ACL81275) Dinoroseobacter phage DFL12phi1 (AHX01035) Sulfitobacter phage phiCB2047-B (AGH07436) Salmonella phage FSL SP-058 (AGF88198) Salmonella phage FSL SP-076 (AGF88397) Erwinia phage Ea9-2 (AHI60108) Selenomonas sputigena ATCC35185 (AEB99742) Desulfarculus baarsii DSM2075 (ADK86299) Rhizobium leguminosarum WSM1325 (ACS55713) Lactococcus raffinolactis 4877 (CCK20525) Ca. Glomeribacter gigasporarum BEG34 (CCD29195) Alicycliphilus denitrificans BC (ADU98234) Actinobacillus succinogenes 130Z (ABR73423) Alphaproteobacteria Bacteroides salanitronis DSM18170 (ADY37055) Zobellia galactanivorans (CAZ94716) Betaproteobacteria Yersinia pestis 91001 (AAS63281) Firmicutes Glaciecola nitratireducens FR1064 (AEP31141) Gammaproteobacteria Thiomicrospira crunogena XCL-2 (ABB40883) Micromonospora sp L5 (ADU06179) Actinobacteria Streptomyces sp. SirexAA-E (AEN11798) Deltaproteobacteria Nocardiopsis dassonvillei DSM43111 (ADH70496) Bacteroidetes Arcobacter nitrofigilis DSM7299 (ADG94266) Streptococcus agalactiae COH1 (CDN66629) Epsilonproteobacteria Escherichia coli (1CTF-A)

Supplementary Figure S4. a) Multiple sequence alignment of ribosomal protein L7/12 identiﬁed in seven distinct phage genomes with cellular homologs. Conserved residues involved in the interaction with L11 and elongation factors EF-G and EF-Tu are indicated by (*). b) Positions of the ribosomal protein domains (red arrows) within the full proteins (black line) are indicated. Taxonomic afﬁliations are represented by colored circles (see legend at the bottom right). Ribosomal proteins in viruses Fig S5

Salmonella_FSL_SP-058 (AGF88397) 1 MSTPCERLGYEEGMQFTLVNDDVDGLNAGDTLWLHNDDGSSNPEFRDTEKVIDDTETFYIDLICIARYTGDTTLAYNRGLREGDILQMVMDDDGEEAYEGDIITFIKDDGDTYPQFEVQKDGNRA 126 Salmonella_phage_FSL_SP-076 (AGF88198) 1 MSTPCERLGYEEGMQFTLVNDDVDGLSAGDTLWLHSDDGSSNPEFRDTEKVNDDTETYYIDLPYVARYTPNKTLAYNRGLREGDILQMVMDDNGEEAYEDDIITFIKDDGDTCPQFEVQKDGNRA 126 Escherichia phage Pollock (AIX12441) 1 MASPCEMLGYEEGMRFVVVSPNE-EFSVGDTIWLHHDDKSHCPLFRDTEEDNEDANTDYCYLNNVAPYSESHTLAYNRGFRKGDILLVTEDDEDEDALAGDIVTFIHDDGDTCPKFKVHRTGTEE 125

Salmonella_FSL_SP-058 (AGF88397) 127 LYLSHVGGLEPKVGRKVRVIHNCTGGFPSGTEGTIVEICSDGDYCIAARGDTMYHHADSCLVFGYAENESSDSKDPEPVKEDYPTKPASEWKQGDRGIVRGQQENDPHNFQIGEEIIFERKRDSE 252 Salmonella_phage_FSL_SP-076 (AGF88198) 127 LYLSHVGGLEPKVGRKVRVIHNCTGGFSAGTEGIIDEICSDGDFHITANGKGMYHHADSCLVFGYAENESSDSKDSEPVKQDYPTKPASEWKQGDRGIVRGQQDNDPHNFQIGEEIIFERKRCSE 252 Escherichia phage Pollock (AIX12441) 126 LYLGCIDSLKPKVGRKVRIIYNCTAGHPSGSEGIIEKIDADGDLMINVDGTCCFHHPYSCVVFGYSEDELSDNTKSEP-KTEWTTKPASEWKKGDKGIVRGQQKSDQHNFNIGAEVTFISHAWEN 250 L7/12 domain

Salmonella_FSL_SP-058 (AGF88397) 253 GIFRGTKYTSTQNIQYDLIEVVSIEPYPITVTKVSKENPVACIKAIRTATGLGLYEAKQAYDFVRDNEEPYNLQIIISKGELTHLFAEAGIEYIFDGQTKLSGTKPTAIICDELADTSKKYKYFI 378 Salmonella_phage_FSL_SP-076 (AGF88198) 253 GIFKGTKYTSTQNIEYALIEPISFEPYPITITKVSKENPVACIKAIRTATGLGLYEAKQAYDFVRDNEEPYSLQIIISKGELTHLFTEAGIEYFFDRQTEVSGTNPTVIICDELADTSKKYKYFI 378 Escherichia phage Pollock (AIX12441) 251 GRFESPSFHRSQTVEYDLIEPIE------SNKPSETKPTVVAVDELTDVSGKYKYFI 302

Salmonella_FSL_SP-058 (AGF88397) 379 GDSIEVTLVGYFDGEPICAYKDRWGDTQLFVAKPSLLVEE 418 Salmonella_phage_FSL_SP-076 (AGF88198) 379 GDSIEVTLVGYFEGEPICAYKDRWGDTQLFVAKPSLLVEE 418 Escherichia phage Pollock (AIX12441) 303 GDSIEVTLVGYFEGEPICAYKDRWGDTQVFVAKPSLLVKE 342

Supplementary Figure S5. Multiple sequence alignment of the L7/12 domain containing protein found in Salmonella phages FSL-SP- 058 and FSL-SP-076 with the homologous protein encoded by Escherichia phage Pollock. The position of L7/12 domain is identiﬁed by a black like. Ribosomal proteins in viruses Fig S6

S30AE

Escherichia coli O157:H7 str. 2011EL-2287 prophage

Escherichia coli O157 typing phage 14

Escherichia phage 2JES-2013

Escherichia coli bacteriophage rv5

Escherichia phage vB_EcoM-FFH2

Enterobacteria phage vB_EcoM-FV3

%identity 80 85 90 92 94 96 98 100

Supplementary Figure S6. Genome comparison of related viral genomes carrying ribosomal protein S30AE. All comparisons were done at the nucleotide level. A color scale for the % identity is shown at the bottom right. The position of the ribosomal protein-encoding genes is indicated by a red arrow. Ribosomal proteins in viruses Fig S7

Enterobacteria phage vB_EcoM-FV3 (AEZ65272) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMAFIFDNSGKEVIAKAKGSDAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Escherichia coli bacteriophage rv5 (ABI79209) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMAFIFDNSGKEVIAKAKGSDAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Escherichia coli O157 typing phage 14 (AKE47110) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMALIFDNSGKEVIAKAKGSDAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Escherichia phage 2 JES-2013 (AGM12525) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMAFIFDTSGKEVIAKAKGSNAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Escherichia phage vB_EcoM_FFH2 (KJ190158) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMALIFDNSGKEVIARAKGSDAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Cronobacter phage vB_CsaM_GAP32 (AFC21633) 3 HHTIVYNDNIAVSEELEFHTFDSFD-KLEKFIGND---NVSFRTTYSKEGN-----SFKVHSHGVHN-GVQFDAHVVDDDMYKGVDLMVAKLESQLRKEKGKRTNI 98/111 E. coli O157-H7 str2011EL-2287 prophage (EYW21796) 1 MQIEITG-NVEITEGMVSFISHKMS-KLERLHPSA----NYARVSVKVEND-----HQEVMAFIFDNSGKEVIAKAKGSDAYEATDRMVDVAARQLAKCGGKKGKG 95/105 Yokenella regensburgei ATCC 43003 (EHM49682) 1 MQLNITGHNVEITEALREFLNSKFS-KLEQYFDRI----NQVYIVLKVEKV-----THVSDATLHVN-GGEIHASAEGQDMYAAIDGLIDKLARQLNKHKDKLKQH 95/95 Cronobacter malonaticus ENBT0334 (KIU62042) 1 MQLNITGHNVEITEALREFVNTKFA-KLEQYFERI----NQVYIVLKVEKV-----TQIADATLHVN-GGELHASSEGQDMYAAIDGLIDKLARQLTKHKDKLKQH 95/95 Escherichia albertii KF1 (AHE60603) 1 MQLNITGNNVEITEALREFVTSKFA-KLEQYFDRI----NQVYVVLKVEKV-----THTSDATLHVN-GGEIHASAEGQDMYAAIDGLIDKLARQLTKHKDKLKQH 95/95 Shigella boydii 965-58 (EIQ26280) 1 MQLNITGNNVEITEALREFVTAKFA-KLEQYFDQI----NQVYVVLKVEKV-----THTSDATLHVN-GGEIHASAEGQDMYAAIDGLIDKLARQLTKHKDKLKQH 95/95 Providencia rettgeri (KLN46962) 1 MEFQITGHNIEVTPALRETVEKKLK-KLEQLFDRI----NGIQVVLKVEKV-----QQIAEATVQVN-GAELHASAEENDMYAAIDLLVDKLSRQLTKHKEKLRQH 95/95 Thauera sp 63 (ENO77456) 1 MNLNITGRHVEVTPAIRDYVSTKLD-RVIRHFDNV----TSVAVILSVEKL-----KQKAEVTLHVR-GKDLFVESDDADMYAAIDSMADKLDRQVQKYKQKMADH 95/107 Methyloversatilis universalis FAM5 (EGK70253) 1 MNLTITGHHLEVTPAIREYIETKLD-RVIRHFDHV----TSVSVILSVEKL-----RQKAEVTLHVR-GKDIFVEAESEDMYATLDNLIDKLDRQVLKHKEKTGDH 95/106 Sulfuricella sp. T08 (GAO35907) 1 MNLNVTGHHVEVTPAIRDYVTDKLG-RVTRHFDHV----IDVNVILAVEKL-----VQKAEVNVHVS-GKDIFVKSEDADMYAAIDSLVDKLDRQIVKHKEMNGGP 95/108 Synechococcus sp. WH8109 (AHF64443) 1 MKLLIHGRNLEITPSLRDYTQTKLE-RATSHFGDA---VREADVHLSVARNP-RVPQQTAEVTVFAN-GTVIRAQERSENLYASIDLAAGKLARQLRRWKERHSDH 100/195 Rubidibacter lacunae KORDI 51-2 (ERN41765) 1 MKFSIQGKNVNVTSAVRDHIEKKMH-HAIEHFQGM---TSKVDVNLSVERNPRIEAKHITEVTVRAN-GKVIRACVDHGNLYASIDLAADKISRQLRKYKERNLAK 101/236 Haemophilus parasuis Nagasaki (EYE72215) 1 MTINISSKQMEVTPAIRTHIEERLA-KLNKWQTQL----INPHFIIHKLPN-----GYEVEASIGTP-VGDLFAKAHDEDLYKAINEVESKLETQLNKQKHKGEAR 95/108 Thermosediminibacter oceani DSM 16646 (ADL08343) 1 MKVTVSGKNFEVTPALREYAEKKIG-KLGRHFNHLNNDNLEAQVTLHVEKD-----RHIVEVTIPVN-DIILRGEEETQDMYSSIDLVVDKLNRQIEKYKTKLTKA 99/180 Syntrophomonas zehnderi OL-4 (CQB52001) 1 MKMDIRGRNIEITDALKDYTTKRLS-KLEKYIDDA----STAQVVLSVEGE-----RHKVEVTIPLN-GVILRGEVAGEDMYASIDLVVEKLEKQIEKHKTKLYRS 95/182 Clostridium spiroforme DSM1552 (EDS75250) 1 MKISVRGKNIEITEAIESKISDKLS-KLDKYFIVSD--NVEAKVLCRVYPY-----GQKLEVTIPTE-YVLLRAEVVDSDLYTAMDLVVDKLEGQIRKYKTRLSRK 97/175 Streptococcus suis S735 (AFQ99896) 2 IKFSIRGENLEVTEALRTYVEEKVA-KIEKYFNEE----QELNAKVNLKVY--RDKRAKVEVTIPVG-AVTLRAEDISQEMYGSIDLVVDKIERQIRRNKTKIERK 99/180 Listeria monocytogenes ScottA (EGJ26036) 2 LKYNIRGENIEVTEPIRDYVEKKID-KLERYFTET----PDANVHVNLKVY--SDKNAKVEVTIPLP-NLVLRAEETSGDLYASIDLIVDKLERQIRKHKTKVNRK 99/187 Staphylococcus aureus Newman (BAF66993) 2 IRFEIHGDNLTITDAIRNYIEEKIG-KLERYFNDV----PNAVAHVKVKTY--SNSATKIEVTIPLK-NVTLRAEERNDDLYAGIDLINNKLERQVRKYKTRINRK 99/190 Bacillus coagulans 2-6 (AEH52728) 2 MNYNIRGENIEVTPAIRDYVEKKVN-KLDRYFVET----PDTSVNVKLKVN--PDKTSKVEITIPMP-QLVLRAEETNEDMYAAIDLIADKLERQIRKHKTKVNRK 99/186 Thalassospira xiamenensis M-5 DSM17429 (AJD54042) 1 MQITVIGKQLDVGNALRQHVVETLDPAVEKYFDHA----IEATVTITKEAH-----LYITQISVHVGKGMLVQAKASANEVYPAFDSACDRVAKQLRRYKRRLRDH 97/198 Rhizobium sp. Pop5 (EJZ22250) 1 MSVRVSGKHMEIGESFRQKIEDQIGMAITKYFDGG----YSGQVTVVKASS-----RFSADCKLHLDSGVVLHAAGEATDPQLAFDAASERIEKRLRRYKRKLKDH 97/191 Mesorhizobium ciceri (ABO40476) 1 MNLRISGKHMDIGDAFRTRINDRVGEAIGKYFDRG----FAGHVTVIKSGS-----RYSADCMIRLDSGASLQATGDAQDPTLAFEAAADRLETRLRRYKRRLKSH 97/194 Clostridium beijerinckii (KLE16988) 1 MRVSTIAKNTTVTPALKEMIEKKLS-KVKRYFDPE----VEAKATLSVQRN-----KQKVEITIPFN-GIILRAEEATEDMYKSIDLVVAKLERQIRKQRTKLSRR 95/178 Vibrio cholerae (4HEI-A) 1 MQINIQGHHIDLTDSMQDYVHSKFD-KLERFFDHI----NHVQVILRVEKL-----RQIAEATLHVN-QAEIHAHADDENMYAAIDSLVDKLVRQLNKHKEKL--- 92/92 *Coxiella burnetti (3TQM-A) 1 MHIQMTGQGVDISPALRELTEKKLH-RIQPCRDEI----SNIHIIFHINKL-----KKIVDANVKLP-GSTINAQAESDDMYKTVDLLMHKLETQLSKYKAK---- 91/91

*3TQM-A

Alphaproteobacteria beta 3/10 alpha Betaproteobacteria strand helix helix Cyanobacteria Firmicutes Gammaproteobacteria

Supplementary Figure S7. Multiple sequence alignment of ribosomal protein S30AE identiﬁed in six phage genomes with cellular homologs. Taxonomic afﬁliations are represented by colored circles (see legend at the bottom). Positions of the ribosomal protein domains (red arrows) within the full proteins (black line) are shown at the right side of the alignment. Ribosomal proteins in viruses Fig S8

Clostridium beijerinckii (KLE16988) 61 76 Syntrophomonas zehnderi OL-4 (CQB52001)

84 Cronobacter phage vB_CsaM_GAP32 (AFC21633)

83 Clostridium spiroforme DSM1552 (EDS75250) 93 Firmicutes (5) 99 Thermosediminibacter oceani DSM 16646 (ADL08343) Mangrovibacter sp MFB070 (KEA53786) 89 81 Cronobacter turicensis 564 (CCJ91031) Cronobacter malonaticus ENBT0334 (KIU62042) 76 90 Cronobacter sakazakii SP291 (AGE87909)

39 Cedecea neteri (AIR05824)

Cedecea davisae DSM 4568 (EPF13995) 92 Kosakonia radicincitans DSM 16656 (EJI92448) Gammaproteobacteria (14) 7 6 Franconibacter pulveris (WP_024558819) 83 Franconibacter helveticus (WP_024553048) Yokenella regensburgei ATCC 43003 (EHM49682) 78 Shigella boydii 965-58 (EIQ26280) 82 Escherichia coli (WP_044861032)

Escherichia coli (WP_028132088) 65 79 Escherichia albertii KF1 (AHE60603) Escherichia phage vB_EcoM_FFH2 (KJ190158) Escherichia coli O157 typing phage 14 (AKE47110) 94 100 Escherichia phage 2 JES-2013 (AGM12525) Enterobacteria phage vB_EcoM-FV3 (AEZ65272)

74 Escherichia coli bacteriophage rv5 (ABI79209) 92 Escherichia coli O157-H7 str 2011EL-2287 (EYW21796) prophage Gammaproteobacteria (3) 94 Betaproteobacteria (5) 97 98 Alphaproteobacteria (4) Alphaproteobacteria 89 Cyanobacteria (2) Betaproteobacteria Cyanobacteria Firmicutes 0.2 Gammaproteobacteria

Supplementary Figure S8. Maximum likelihood phylogenetic tree of ribosomal protein S30AE. Nodes corresponding to viral sequences are shown in bold. Both viruses and hosts are highlighted with the same color. Taxonomic afﬁliations are represented by colored circles (see legend at the bottom). Ribosomal proteins in viruses Fig S9

Supplementary Figure S9. Ribosomal proteins S21 identiﬁed in uncultivated viral genomes. Top: Phylogenetic tree of ribosomal protein S21. Viral clades are highlighted with blue branches. The position of the sequences presented in the bottom panel is shown with colored circles. Bottom: Genome comparison of viral contigs encoding ribosomal protein S21. Comparisons were done at the amino acid level, with the %identity displayed with a color scale. The predicted gene encoding ribosomal protein S21 is indicated in red. Ribosomal proteins in viruses Fig S10

Supplementary Figure S10. Ribosomal proteins L12 identiﬁed in uncultivated viral genomes. Top: Phylogenetic tree of ribosomal protein L12. Viral clades are highlighted with blue branches. All branches with support < 50% were collapsed, and branches with support ≥ 80% are noted with a black dot. The position of the sequences presented in the bottom panel is shown with colored circles. Bottom: Genome comparison of viral contigs encoding ribosomal protein L12. Comparisons were done at the amino acid level, with the %identity displayed with a color scale. The predicted gene encoding ribosomal protein L12 is indicated in red. Ribosomal proteins in viruses Fig S11

Supplementary Figure S11. Ribosomal proteins L31 identiﬁed in uncultivated viral genomes. Top: Phylogenetic tree of ribosomal protein L31. Viral clades are highlighted with blue branches. All branches with support < 50% were collapsed, and branches with support ≥ 80% are noted with a black dot. The position of the sequences presented in the bottom panel is shown with colored circles. Bottom: Genome maps of viral contigs encoding ribosomal protein L31. The predicted gene encoding ribosomal protein L31 is indicated in red. Ribosomal proteins in viruses Fig S12

Supplementary Figure S12. Figure SXX. Ribosomal proteins L33 identiﬁed in uncultivated viral genomes. Top: Phylogenetic tree of ribosomal protein L33. Viral clades are highlighted with blue branches. All branches with support < 50% were collapsed, and branches with support ≥ 80% are noted with a black dot. The position of the sequences presented in the bottom panel is shown with colored circles. Bottom: Genome comparison of viral contigs encoding ribosomal protein L33. Comparisons were done at the amino acid level, with the %identity displayed with a color scale. The predicted gene encoding ribosomal protein L33 is indicated in red. Ribosomal proteins in viruses Fig S13

Supplementary Figure S13. Genome map comparison of uncultivated viruses encoding distinct ribosomal proteins. Comparisons were done at the amino acid level, with the %identity displayed with a color scale. Predicted genes encoding ribosomal proteins are indicated in red.