The Pseudovibrio genus: metabolically versatile facultative
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Table S 2. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted proteins involved in carbon metabolism, denitrification, oxidation of thiosulfate, and phosphonate utilization. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Absence of a gene name or an EC number indicates that no assignment was made due to missing of these parameters for the respective genes. Locus FO-BEG1 Locus JE062 PSE_0520 PJE062_2836 PSE_0524 PJE062_2549 PSE_1032 PSE_2344 PSE_2526 PSE_3200 PSE_3383 PSE_4148 PSE_4697 PSE_4698 PSE_4767 PSE_3532 PSE_0639 PSE_4866 PJE062_4521 PJE062_1398 PJE062_127 PJE062_1722 PJE062_1304 PJE062_4782 PJE062_2190 PJE062_2252 PJE062_2266 PJE062_1635 PJE062_2867 PJE062_2056 PSE_0520 PJE062_2836 PSE_0524 PJE062_2549 PSE_1300 PJE062_1936 PSE_1664 PJE062_417 PSE_1887 PSE_1922 PSE_3200 PSE_3907 PSE_3909 PSE_p0106 PSE_p0137 PSE_4145 PJE062_3941 PJE062_733 PJE062_1722 ─ ─ PJE062_762 PJE062_797 PJE062_4650 PSE_4146 PJE062_4945 PSE_4147 PSE_4148 PSE_4154 PSE_4697 PSE_4698 PSE_4767 PJE062_4760 PJE062_4782 PJE062_4973 PJE062_2190 PJE062_2252 PJE062_2266 Product Glycolysis / Gluconeogenesis 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase Glucokinase Fructose-bisphosphate aldolase Phosphomannomutase/phosphoglucomutase Enolase/2-phosphoglycerate dehydratase Triose-phosphate isomerase Glucose-6-phosphate isomerase Glyceraldehyde-3-phosphate dehydrogenase B Phosphoglycerate kinase Pyruvate kinase Fructose-1,6-bisphosphatase class II Phosphoenolpyruvate carboxykinase Pyruvate carboxylase Entner-Doudoroff pathway 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase SMP-30/Gluconolaconase/LRE-like region oxidoreductase, short chain dehydrogenase/reductase family protein SMP-30/Gluconolaconase/LRE-like region Gluconokinase (Gluconate kinase) Enolase/2-phosphoglycerate dehydratase KDPG and KHG aldolase 2-dehydro-3-deoxygluconokinase 2-dehydro-3-deoxygluconokinase 2-dehydro-3-deoxygluconokinase Glucose-6-phosphate 1-dehydrogenase Phosphogluconate dehydratase (6phosphogluconate dehydratase) KDPG and KHG aldolase Glucose-6-phosphate isomerase SMP-30/Gluconolaconase/LRE-like region Glyceraldehyde-3-phosphate dehydrogenase B Phosphoglycerate kinase Pyruvate kinase -1- Gene name EC number gpmA 5.4.2.1 gpmA 5.4.2.1 glk fbaA algC eno tpiA gpi gapB/epd pgk pyk glpX pckA pyc 2.7.1.2 4.1.2.13 5.4.2.2 4.2.1.11 5.3.1.1 5.3.1.9 1.2.1.12 2.7.2.3 2.7.1.40 3.1.3.37 4.1.1.49 6.4.1.1 gpmA 5.4.2.1 gpmA 5.4.2.1 3.1.1.17 gdh 1.1.1.47 gntK eno eda kdgK kdgK kdgK zwf 3.1.1.17 2.7.1.12 4.2.1.11 4.1.2.14 2.7.1.45 2.7.1.45 2.7.1.45 1.1.1.49 edd 4.2.1.12 eda gpi 4.1.2.14 5.3.1.9 3.1.1.17 1.2.1.12 2.7.2.3 2.7.1.40 gapB/epd pgk pyk Table S 2. Continued Locus FO-BEG1 Locus JE062 PSE_0476 PSE_0628 PSE_1044 PSE_1456 PSE_2114 PSE_2344 PSE_2648 PSE_2884 PSE_3532 PSE_4036 PSE_4437 PSE_4696 PJE062_2965 PJE062_3035 PJE062_4442 ─ PJE062_647 PJE062_1398 PJE062_4217 PJE062_1466 PJE062_1635 PJE062_4566 PJE062_4652 PJE062_2124 PSE_1664 PJE062_417 PSE_1300 PSE_1887 PSE_4154 PSE_1922 PSE_4148 PSE_4145 PJE062_1936 PJE062_3941 PJE062_4973 PJE062_733 PJE062_4782 PJE062_4650 Product Pentose phosphate pathway 6-phosphogluconate dehydrogenase Translaldolase Phosphopentomutase Fructose-bisphosphate aldolase Fructose-bisphosphate aldolase Fructose-bisphosphate aldolase Ribose-5-phosphate isomerase A Ribokinase Fructose-1,6-bisphosphatase class II Ribulose-phosphate 3-epimerase Ribose-phosphate pyrophosphokinase Transketolase oxidoreductase, short chain dehydrogenase/reductase family protein SMP-30/Gluconolaconase/LRE-like region SMP-30/Gluconolaconase/LRE-like region SMP-30/Gluconolaconase/LRE-like region Gluconokinase (Gluconate kinase) Glucose-6-phosphate isomerase Glucose-6-phosphate 1-dehydrogenase PSE_0214 PSE_0452 PJE062_3108 PJE062_3422 PSE_0603 PJE062_2553 PSE_0604 PJE062_2930 PSE_0605 PSE_0606 PSE_0614 PSE_0615 PSE_0616 PJE062_2640 PJE062_2569 PJE062_3013 PJE062_2857 ─ Citric acid cycle Aconitate hydratase Aconitate hydratase 2 Succinate dehydrogenase cytochrome b556 subunit (Cytochrome b-556) Succinate dehydrogenase hydrophobic membrane anchor subunit Succinate dehydrogenase flavoprotein subunit Succinate dehydrogenase iron-sulfur subunit Malate dehydrogenase Succinyl-CoA synthetase subunit beta succinyl-CoA synthetase subunit alpha PSE_0617 PJE062_2799 alpha-ketoglutarate decarboxylase PSE_0618 PSE_2580 PSE_4461 PJE062_2606 PJE062_4244 PJE062_4634 PSE_3294 PJE062_1258 PSE_3295 PJE062_1014 PSE_3296 PJE062_1075 PSE_3391 PSE_4065 PSE_4461 PSE_4866 PSE_4928 PJE062_1324 PJE062_4617 PJE062_4634 PJE062_2056 PJE062_2277 Dihydrolipoamide acetyltransferase Fumarate hydratase class I Fumarate hydratase class II (Fumarase C) Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (E2) Pyruvate dehydrogenase E1 component subunit beta Pyruvate dehydrogenase E1 component subunit alpha Citrate synthase Isocitrate dehydrogenase Fumarate hydratase class II (Fumarase C) Pyruvate carboxylase Citrate synthase -2- Gene EC gnd tal deoB fbaA fbaA fbaA rpiA rbsK glpX rpe prs tkt 1.1.1.44 2.2.1.2 5.4.2.7 4.1.2.13 4.1.2.13 4.1.2.13 5.3.1.6 2.7.1.15 3.1.3.11 5.1.3.1 2.7.6.1 2.2.1.1 gdh 1.1.1.47 gntK gpi zwf 3.1.1.17 3.1.1.17 3.1.1.17 2.7.1.12 5.3.1.9 1.1.1.49 acnA acnB 4.2.1.3 4.2.1.3 sdhC 1.3.99.1 sdhD 1.3.99.1 sdhA sdhB mdh sucC sucD sucA (odhA) sucB fumA fumC 1.3.99.1 1.3.99.1 1.1.1.37 6.2.1.5 6.2.1.5 pdhC 2.3.1.12 pdhB 1.2.4.1 pdhA 1.2.4.1 cisY icd (idhA) fumC pyc cisY 2.3.3.1 1.1.1.42 4.2.1.2 6.4.1.1 2.3.3.1 1.2.4.2 2.3.1.61 4.2.1.2 4.2.1.2 Table S 2. Continued Locus FO-BEG1 Locus JE062 PSE_1913 PJE062_845 PSE_2272 PJE062_483 PSE_2278 Product Gene EC pcaC 4.1.1.44 1.14.13. 2 3.1.1.24 1.13.11. 3 1.13.11. 3 2.8.3.12 2.8.3.2.3.1.16 5.5.1.2 1.14.12. 1.14.12. 1.14.13. 82 PJE062_940 Aromatic compound degradation Carboxymuconolactone decarboxylase P-hydroxybenzoate hydroxylase (4hydroxybenzoate 3-monooxygenase) 3-oxoadipate enol-lactonase pcaD PSE_2279 PJE062_920 Protocatechuate 3,4-dioxygenase beta chain pcaH PSE_2280 PJE062_637 Protocatechuate 3,4-dioxygenase alpha chain pcaG PSE_2281 PSE_2282 PSE_2283 PSE_2284 PJE062_798 PJE062_821 PJE062_938 PJE062_754 3-oxoadipate:succinyl-CoA transferase, subunit A 3-oxoadipate:succinyl-CoA transferase, subunit B Beta-ketoadipyl-CoA thiolase 3-carboxy-cis,cis-muconate cycloisomerase pcaI pcaJ pcaF pcaB PSE_2827 PJE062_1336 Benzoate 1,2-dioxygenase subunit beta benB PSE_2828 PJE062_1217 Benzoate 1,2-dioxygenase subunit alpha benA PSE_2829 PJE062_1491 Vanillate O-demethylase oxidoreductase vanB PSE_1023 PSE_1024 PSE_1025 PSE_1027 PJE062_4489 PJE062_4477 PJE062_4485 PJE062_4412 Carbon monoxide oxidation Carbon monoxide dehydrogenase subunit G Carbon monoxide dehydrogenase small chain Carbon monoxide dehydrogenase large chain Carbon monoxide dehydrogenase medium chain coxG coxS coxL coxM 1.2.99.2 1.2.99.2 1.2.99.2 1.2.99.2 PSE_0477 PSE_1924 PSE_3254 PSE_3255 PSE_1331 PJE062_2774 PJE062_844 PJE062_1131 PJE062_1378 PJE062_1899 ldh dld tdcE pflA adhE 1.1.1.27 1.1.1.28 2.3.1.54 1.97.1.4 1.1.1.1 PSE_1086 PJE062_4486 pta 2.3.1.8 PSE_1087 PSE_0614 PSE_2580 PSE_4461 PJE062_4379 PJE062_3013 PJE062_4244 PJE062_4634 ackA mdh fumA fumC 2.7.2.1 1.1.1.37 4.2.1.2 4.2.1.2 PSE_2225 PJE062_741 PSE_4599 PSE_4597 PSE_2418 PSE_2419 PSE_3421 PJE062_2498 PJE062_2449 PJE062_156 PJE062_248 PJE062_1661 mutB mutA mceE 5.4.99.2 5.4.99.2 5.1.99.1 PSE_1247 PJE062_4342 scoA 2.8.3.5 PSE_1248 PJE062_4358 scoB 2.8.3.5 Mixed acid fermentation L-lactate dehydrogenase D-lactate dehydrogenase Formate acetyltransferase Pyruvate formate-lyase activating enzyme Aldehyde-alcohol dehydrogenase Phosphate acetyltransferase (Phosphotransacetylase) Acetate kinase Malate dehydrogenase Fumarate hydratase class I Fumarate hydratase class II (Fumarase C) Fumarate reductase/succinate dehydrogenase flavoprotein Propionyl-CoA carboxylase, beta subunit Propionyl-CoA carboxylase alpha chain Methylmalonyl-CoA mutase large subunit Methylmalonyl-CoA mutase small subunit Methylmalonyl-CoA epimerase succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B -3- pobA Table S 2. Continued Locus FO-BEG1 Locus JE062 PSE_0757 PSE_0758 PSE_0759 PSE_0760 PSE_0895 PSE_0897 PSE_0898 PSE_2203 PSE_2204 PSE_2205 PSE_2207 PSE_4550 PSE_4551 PSE_4552 PSE_4553 PSE_3127 PSE_3128 PSE_3129 PSE_3130 PSE_3131 PSE_3132 PSE_2100 PJE062_2921 PJE062_3029 PJE062_2637 PJE062_2605 PJE062_2542 PJE062_2612 PJE062_2813 PJE062_731 PJE062_627 PJE062_508 PJE062_853 PJE062_2454 PJE062_2491 PJE062_2475 PJE062_2486 PJE062_1200 PJE062_1080 PJE062_1307 PJE062_965 PJE062_1456 PJE062_1117 PJE062_842 PSE_2101 PJE062_629 PSE_2102 PSE_2103 PSE_2104 PSE_2105 PSE_4539 PJE062_585 PJE062_729 PJE062_910 PJE062_562 PJE062_2443 PSE_4540 PJE062_2471 PSE_4541 PSE_4542 PSE_4543 PSE_4544 PJE062_2490 PJE062_2479 PJE062_2442 PJE062_2506 PSE_1359 PJE062_5277 PSE_1360 PSE_1361 PSE_1362 PSE_1363 PSE_1364 PSE_1365 PSE_1366 PSE_1367 PSE_1368 PJE062_5324 PJE062_5237 PJE062_5256 PJE062_5219 PJE062_5333 PJE062_5182 PJE062_5189 PJE062_5241 PJE062_5328 Product Denitrification Respiratory nitrate reductase, alpha subunit Respiratory nitrate reductase beta subunit Respiratory nitrate reductase, delta subunit Respiratory nitrate reductase, gamma subunit Nitrite reductase protein (NO-forming) Denitrification system component NirT Nitrite reductase Protein NirF Nitrite reductase heme biosynthesis D/L protein Protein NirG Nitrite reductase Protein NorD Protein NorQ Nitric oxide reductase subunit B Nitric oxide reductase subunit C Regulatory protein NosR Nitrous-oxide reductase nitrous oxide maturation protein NosD Copper transport ATP-binding protein NosF Membrane protein NosY NosL protein required for nitrous oxide reduction Cytochrome c-type protein NapC Nitrate reductase cytochrome c-type subunit (NapB) Nitrate reductase, large subunit, periplasmic Protein NapD Ferredoxin-type protein NapF Periplasmic nitrate reductase protein Cytochrome c-type protein NapC Nitrate reductase cytochrome c-type subunit (NapB) Ferredoxin-type protein NapH MauM/NapG ferredoxin-type protein Nitrate reductase, large subunit, periplasmic Protein NapD Oxidation of reduced sulfur compounds Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain Diheme cytochrome c SoxE Diheme cytochrome c SoxD Sulfur oxidation molybdopterin C protein, SoxC Sulfur oxidation B protein Diheme cytochrome c SoxA Sulfur oxidation Z protein Sulfur oxidation protein SoxY Monoheme cytochrome c SoxX Thioredoxin SoxW -4- Gene EC narG narH narJ narI nirN nirT nirS nriF 1.7.99.4 1.7.99.4 1.7.99.4 1.7.99.4 1.7.2.1 nirG nirS norD norQ norB norC nosR nosZ nosD nosF nosY nosL napC napB napD napF napE napC napB napH napG napD soxF soxE soxD soxC soxB soxA soxZ soxY soxX soxW 1.7.2.1 1.7.2.1 1.7.2.1 1.7.99.7 1.7.99.7 1.7.99.7 1.7.99.7 1.7.99.6 Table S 2. Continued Locus FO-BEG1 Locus JE062 PSE_4849 PSE_4850 PSE_4851 PSE_4852 PSE_4853 PSE_4854 PSE_4857 PSE_4858 PJE062_2269 PJE062_2196 PJE062_2313 PJE062_2247 PJE062_2188 PJE062_2041 PJE062_2279 PJE062_2090 PSE_3627 PJE062_1982 PSE_3628 PJE062_2033 PSE_3629 PJE062_2039 PSE_3630 PJE062_2265 Locus FO-BEG1 Locus JE062 PSE_2912 PJE062_997 PSE_2914 PJE062_1320 PSE_2915 PSE_2529 PSE_2913 PJE062_1654 PJE062_62 PJE062_1493 Product Gene Phosphonate utilization Phosphonate metabolism PhnG carbon-phosphorus lyase complex subunit Protein PhnI Protein PhnJ Phosphonates transport ATP-binding protein PhnK Phosphonates transport ATP-binding protein PhnL Protein PhnM ATP-binding protein PhnN Phosphonates transport system permease protein PhnE Phosphonates transport system permease protein PhnE ABC transporter, phosphonate, periplasmic substrate-binding protein PhnD Phosphonates import ATP-binding protein PhnC Product DMSP utilization DMSP cleavage L-carnitine dehydratase/bile acid-inducible protein F transporter, betaine/carnitine/choline transporter (BCCT) family Alcohol dehydrogenase methylmalonate-semialdehyde dehydrogenase transcriptional regulator, LysR family protein EC phnG phnH phnI phnJ phnK phnL phnM phnN phnE phnE phnD phnC Gene Evalue / identity [%] to Marinomonas sp. MWYl1 dddD 0.0 / 70% dddT 0.0 / 70% dddB dddC dddR 0.0 / 70% 0.0 / 56% 8.0E-107 / 53% Evalue / identity [%] to Rugeria pomeroyi DSS-3 PSE_2975 PSE_4733 PSE_1622 PSE_3286 PJE062_1074 PJE062_2234 PJE062_240 PJE062_1360 DMSP demethylation aminomethyl transferase family protein acyl-CoA synthetase L-aspartate oxidase Enoyl-CoA hydratase/isomerase -5- dmdA dmdB dmdC dmdD 5.0E-20 / 24% 3.0E-72 / 30% 2.0E-149 / 43% 5.0E-26 / 32% Table S 3. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted TRAP transporter subunits. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Locus FO-BEG1 Locus JE062 PSE_0923 PSE_0924 PSE_0925 PJE062_2908 PJE062_2533 PJE062_2627 TRAP Transporter TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_1209 PSE_1316 PSE_1317 PJE062_4388 PJE062_1939 PJE062_1874 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit dctP dctM dctQ PSE_1426 PSE_1427 PSE_1428 PJE062_5273 PJE062_5331 PJE062_5225 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_1834 PSE_1835 PSE_1836 ─ ─ ─ TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_1888 PSE_1889 PSE_1890 PJE062_3892 PJE062_3768 PJE062_3743 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_1919 PSE_1920 PSE_1921 PJE062_932 PJE062_501 PJE062_925 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_1925 PJE062_918 PSE_1926 PJE062_600 PSE_2239 PJE062_646 PSE_2240 PJE062_879 PSE_2274 PSE_2275 PSE_2276 PJE062_919 ─ PJE062_523 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit PSE_2337 PJE062_584 PSE_2338 PJE062_530 TRAP transporter solute receptor, TAXI family TRAP dicarboxylate transporter, fused membrane component DctQM PSE_2346 PSE_2347 PSE_2348 PJE062_1811 PJE062_1617 PJE062_1686 TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctP subunit dctQ dctM dctP PSE_2801 PSE_2802 PSE_2803 PJE062_303 PJE062_463 PJE062_103 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM Product TRAP dicarboxylate transporter, fused membrane component DctQM TRAP dicarboxylate transporter, DctP subunit TRAP transporter solute receptor, TAXI family TRAP dicarboxylate transporter, fused membrane component DctQM -6- Gene dctQM dctP dctQM dctM dctQ dctP dctQM Table S 3. Continued Locus FO-BEG1 PSE_2830 PSE_2831 PSE_2832 Locus JE062 PJE062_1070 PJE062_1159 PJE062_1444 PSE_2907 PJE062_1331 PSE_2908 PJE062_1118 PSE_2946 PSE_2947 PSE_2948 PJE062_1639 PJE062_1073 PJE062_1496 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_3111 PSE_3112 PSE_3113 ─ ─ ─ TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_3353 PJE062_1507 PSE_3354 PJE062_1151 PSE_3664 PSE_3665 PSE_3666 PJE062_1463 PJE062_1642 PJE062_1723 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_3721 PSE_3722 PSE_3723 PJE062_1201 PJE062_1120 PJE062_1561 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_3912 PSE_3913 PSE_3914 ─ ─ ─ TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_4136 PJE062_4972 TRAP dicarboxylate transporter- DctP subunit dctP PSE_4577 PJE062_2484 PSE_4578 PJE062_2464 PSE_4810 PSE_4811 PSE_4812 PJE062_2025 PJE062_2312 PJE062_2046 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_4845 PJE062_2117 TRAP dicarboxylate transporter, DctP subunit dctP PSE_4929 PSE_4930 PSE_4931 PSE_4932 PJE062_2193 PJE062_2118 PJE062_2335 PJE062_2112 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctP dctM dctQ dctP Product TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, fused membrane component DctQM TRAP transporter solute receptor, TAXI family protein TRAP dicarboxylate transporter, fused membrane component DctQM TRAP transporter solute receptor, TAXI family protein TRAP dicarboxylate transporter, fused membrane component DctQM TRAP transporter solute receptor, TAXI family protein -7- Gene dctP dctQ dctM dctQM dctQM dctQM Table S 3. Continued Locus FO-BEG1 PSE_p0100 PSE_p0101 PSE_p0102 Locus JE062 PJE062_587 PJE062_597 PJE062_692 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_p0107 PSE_p0108 PSE_p0109 PJE062_891 PJE062_791 PJE062_739 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_p0130 PSE_p0131 PSE_p0132 PJE062_726 PJE062_678 PJE062_526 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_p0325 PSE_p0326 PSE_p0327 PJE062_3836 PJE062_3646 PJE062_3830 TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctP subunit dctQ dctM dctP PSE_p0307 PJE062_3918 TRAP dicarboxylate transporter, DctP subunit dctP PSE_p0343 PSE_p0344 PSE_p0345 PJE062_3801 PJE062_3939 PJE062_3906 TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctP subunit dctQ dctM dctP PSE_p0362 PSE_p0363 PSE_p0364 PJE062_3865 PJE062_3671 PJE062_3954 TRAP dicarboxylate transporter, DctP subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctM subunit dctP dctQ dctM PSE_p0369 PSE_p0370 PSE_p0371 PJE062_3631 PJE062_3612 PJE062_3938 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP PSE_p0394 PSE_p0395 PSE_p0396 PJE062_3749 PJE062_3639 PJE062_3658 TRAP dicarboxylate transporter, DctM subunit TRAP dicarboxylate transporter, DctQ subunit TRAP dicarboxylate transporter, DctP subunit dctM dctQ dctP Product -8- Gene Table S 4. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted ABC transporter subunits. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Pfam model specifies the family, to which the identified protein belongs, according with the Pfam database (Bateman et al., 2004). Absence of a gene name indicates that no assignment was made due to missing of this parameter for the respective genes. Predicted substrate specificity was derived from the annotations of the genes belonging to the respective ABC transporter system. Locus FO-BEG1 Locus JE062 Pfam Model Product Gene Predicted substrate specificity proV proW proX Glycine betaine/ L-proline PSE_0112 PSE_0113 PSE_0114 PJE062_3499 PJE062_3280 PJE062_3213 ABC_tran BPD_transp_1 OpuAC ABC Transporter Glycine betaine/L-proline transport ATP-binding protein ProV Glycine betaine/L-proline transport system permease protein ProW Glycine betaine-binding protein PSE_0420 PSE_0421 PSE_0422 PJE062_3099 PJE062_3210 PJE062_3070 Peripla_BP_2 FecCD ABC_tran Hemin-binding periplasmic protein HmuT Hemin transport system permease protein HmuU Hemin import ATP-binding protein HmuV hmuT hmuU hmuV Hemin PSE_0430 PSE_0431 PSE_0432 PJE062_3307 PJE062_3373 PJE062_3413 OpuAC BPD_transp_1 ABC_tran Glycine betaine-binding protein Glycine betaine/L-proline transport system permease protein ProW Glycine betaine/L-proline transport ATP-binding protein ProV proX proW proV Glycine betaine/ L-proline PSE_0437 PSE_0438 PSE_0439 PSE_0440 PSE_0441 PJE062_3357 PJE062_3451 PJE062_3076 PJE062_3241 PJE062_3337 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran ABC_tran Periplasmic dipeptide transport protein Dipeptide transport system permease protein DppB Dipeptide transport system permease protein DppC Dipeptide transport ATP-binding protein DppD Dipeptide transport ATP-binding protein DppF dppA dppB dppC dppD dppF Oligopeptide PSE_0443 PSE_0444 PSE_0445 PJE062_3229 PJE062_3285 PJE062_3140 Peripla_BP_1 ABC_tran BPD_transp_2 D-ribose-binding protein Ribose import ATP-binding protein RbsA Ribose transport system permease protein RbsC rbsB rbsA rbsC Sugar -9- Table S 4. Continued Locus FO-BEG1 PSE_0470 PSE_0471 PSE_0472 PSE_0473 Locus JE062 PJE062_2829 PJE062_2766 PJE062_3014 PJE062_2743 BPD_transp_1 BPD_transp_1 SBP_bac_1 ABC_tran sn-glycerol-3-phosphate transport system permease protein UgpE sn-glycerol-3-phosphate transport system permease protein UgpA sn-glycerol-3-phosphate-binding periplasmic protein UgpB sn-glycerol-3-phosphate import ATP-binding protein UgpC PSE_0528 PSE_0529 PSE_0530 PSE_0531 PSE_0532 PJE062_2554 PJE062_2658 PJE062_2902 PJE062_2946 PJE062_2818 SBP_bac_5 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran peptide ABC transporter, periplasmic peptide-binding protein peptide ABC transporter, periplasmic peptide-binding protein peptide ABC transporter, permease protein peptide ABC transporter permease protein peptide ABC transporter, ATP-binding protein PSE_0587 PSE_0588 PSE_0589 PJE062_2984 PJE062_2677 PJE062_2700 FecCD Peripla_BP_2 ABC_tran Hemin transport system permease protein HmuU Hemin-binding periplasmic protein HmuT Hemin import ATP-binding protein HmuV hmuU hmuT hmuV Hemin PSE_0680 PSE_0681 PSE_0682 PSE_0683 PJE062_2538 PJE062_2885 PJE062_2602 PJE062_2790 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran sn-glycerol-3-phosphate-binding periplasmic protein UgpB sn-glycerol-3-phosphate transport system permease protein UgpA sn-glycerol-3-phosphate transport system permease protein UgpE sn-glycerol-3-phosphate import ATP-binding protein UgpC ugpB ugpA ugpE ugpC Glycerol-3-phosphate PSE_0763 PSE_0765 PSE_0766 PSE_0767 PJE062_2800 PJE062_2960 PJE062_2751 PJE062_2698 Bmp ABC_tran BPD_transp_2 BPD_transp_2 ABC transporter, periplasmic binding protein Ribose import ATP-binding protein RbsA sugar ABC transporter, permease protein sugar ABC transporter, permease protein Pfam Model Product - 10 - Gene Predicted substrate specificity ugpE ugpA ugpB ugpC Glycerol-3-phosphate Oligopeptide rbsA Sugar Table S 4. Continued Locus FO-BEG1 Locus JE062 Pfam Model PSE_0856 PJE062_2634 ABC_tran PSE_0857 PJE062_2943 ABC_tran PSE_0858 PJE062_2995 BPD_transp_2 PSE_0859 PJE062_2944 BPD_transp_2 PSE_0860 PJE062_2831 ANF_receptor PSE_0900 PSE_0901 PSE_0902 PSE_0903 PJE062_2932 PJE062_2619 PJE062_2590 PJE062_2733 ABC_tran SBP_bac_1 BPD_transp_1 BPD_transp_1 Maltose/maltodextrin import ATP-binding protein MalK sugar uptake ABC transporter periplasmic solute-binding protein sugar uptake ABC transporter permease protein sugar uptake ABC transporter permease protein PSE_0914 PSE_0915 PSE_0916 PSE_0918 PJE062_2898 PJE062_2980 PJE062_2684 PJE062_2573 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran sugar ABC transporter, periplasmic sugar-binding protein sugar ABC transporter, permease protein sugar ABC transporter, permease protein Lactose transport ATP-binding protein LacK lacK PSE_0933 PSE_0934 PSE_0935 PJE062_2872 PJE062_2914 PJE062_2710 BPD_transp_1 ABC_tran SBP_bac_3 Taurine transport system permease protein TauC Taurine import ATP-binding protein TauB Taurine-binding periplasmic protein tauC tauB tauA Taurine PSE_1036 PJE062_4410 SBP_bac_1 PSE_1037 PSE_1038 PSE_1039 PJE062_4371 PJE062_4507 PJE062_4366 ABC_tran BPD_transp_2 BPD_transp_2 uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein Ribose import ATP-binding protein RbsA permease protein, ABC-type sugar transporter sugar ABC transporter, permease protein rbsA Sugar Product High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) branched-chain amino acid ABC transporter, periplasmic substratebinding protein - 11 - Gene Predicted substrate specificity livF livG livM Amino acid livH malK Sugar Sugar Table S 4. Continued Locus FO-BEG1 Locus JE062 Pfam Model PSE_1120 PJE062_4425 ABC_tran PSE_1121 PJE062_4370 ABC_tran PSE_1122 PJE062_4385 BPD_transp_2 PSE_1123 PJE062_4430 BPD_transp_2 PSE_1124 PJE062_4454 ANF_receptor PSE_1141 PSE_1142 PSE_1143 PSE_1144 PSE_1145 PJE062_2757 PJE062_2912 PJE062_2884 PJE062_3038 PJE062_2878 TonB_dep_Rec Peripla_BP_2 FecCD FecCD ABC_tran PSE_1213 PJE062_4405 BPD_transp_2 PSE_1214 PJE062_4382 BPD_transp_2 PSE_1215 PJE062_4456 ABC_tran PSE_1216 PJE062_4457 ABC_tran PSE_1217 PJE062_4428 SBF PSE_1243 PSE_1244 PSE_1245 PSE_1246 PJE062_4352 PJE062_4362 PJE062_4348 PJE062_4343 SBP_bac_1 ABC_tran BPD_transp_1 BPD_transp_1 Product High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) ABC branched amino acid transporter family, periplasmic substratebinding protein Ferrichrome-iron receptor Ferrienterobactin-binding periplasmic protein Ferric enterobactin transport system permease protein FepD Ferric enterobactin transport system permease protein FepG Ferric enterobactin transport ATP-binding protein FepC High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) P3 protein (Solute carrier family 10 member 3) Putrescine-binding periplasmic protein Putrescine transport ATP-binding protein PotG Putrescine transport system permease protein PotH Putrescine transport system permease protein PotI - 12 - Gene Predicted substrate specificity livG livF Amino acid livH livM fhuA fepB fepD fepG fepC Enterobactin livM livH livF Amino acid livG potF potG potH potI Putrescine/ Spermidine Table S 4. Continued Locus FO-BEG1 PSE_1292 PSE_1294 PSE_1296 PSE_1297 Locus JE062 PJE062_1965 PJE062_1894 PJE062_1958 PJE062_1975 ABC_tran SBP_bac_1 BPD_transp_1 BPD_transp_1 PSE_1322 PSE_1323 PSE_1324 PSE_2536 PJE062_1888 PJE062_1960 ─ PJE062_14 PSE_1389 PSE_1390 PSE_1391 PSE_1392 Pfam Model Product Gene Lactose transport ATP-binding protein LacK ABC transporter, substrate-binding protein sugar ABC transporter, permease protein, sugar ABC transporter, permease protein lacK ABC_tran ABC-3 FUR SBP_bac_9 Zinc import ATP-binding protein ZnuC High-affinity zinc uptake system membrane protein ZnuB Zinc uptake regulation protein (Zinc uptake regulator) High-affinity zinc uptake system protein ZnuA znuC znuB zur znuA PJE062_5224 PJE062_5312 PJE062_5176 PJE062_5319 BPD_transp_1 BPD_transp_1 SBP_bac_1 ABC_tran sugar uptake ABC transporter permease protein sugar uptake ABC transporter permease protein extracellular solute-binding protein family 1 Maltose/maltodextrin import ATP-binding protein MalK PJE062_116 SBP_bac_9 PSE_1676 PJE062_387 ABC_tran PSE_1677 PJE062_164 ABC-3 PSE_1678 PJE062_301 ABC-3 PSE_1679 PSE_1681 PSE_1682 PSE_1683 PJE062_321 PJE062_41 PJE062_317 PJE062_261 SBP_bac_1 ABC_tran BPD_transp_1 BPD_transp_1 PSE_1675 Manganese-binding lipoprotein MntA / periplasmic zinc-binding protein TroA Manganese transport system ATP-binding protein MntB / zinc transport system ATP-binding protein TroB Manganese transport system membrane protein MntC / zinc transport system membrane protein TroC Manganese transport system membrane protein MntD / zinc transport system membrane protein TroD Spermidine/putrescine-binding periplasmic protein 2 Spermidine/putrescine import ATP-binding protein PotA Putrescine transport system permease protein PotH Spermidine/putrescine transport system permease protein PotC - 13 - Predicted substrate specificity Sugar Zinc Sugar malK mntA/troA mntB/troB Manganese mntC/troC mntD/troD potD potA potH potC Putrescine/ Spermidine Table S 4. Continued Locus FO-BEG1 PSE_1688 PSE_1689 PSE_1690 PSE_1691 PSE_1692 Locus JE062 PJE062_408 PJE062_354 PJE062_413 PJE062_39 PJE062_279 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran PhoU phosphate ABC transporter, periplasmic binding protein Phosphate transport system permease protein PstC Phosphate transport system permease protein PstA Phosphate import ATP-binding protein PstB 1 Phosphate transport system protein PhoU PSE_1815 PSE_1816 PSE_1817 PJE062_176 PJE062_31 PJE062_162 Peripla_BP_1 BPD_transp_2 ABC_tran periplasmic substrate-binding protein, ABC-type sugar transporter sugar ABC transporter, permease protein sugar ABC transporter, ATP-binding protein Sugar PSE_1875 PSE_1876 PSE_1877 PSE_1878 PJE062_2861 PJE062_2615 PJE062_3016 PJE062_2608 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran ABC sugar transporter extracellular solute-binding protein, family 1 ABC-type sugar transport system, permease component ABC-type sugar transport system, permease component ABC-type sugar transport system, ATPase component Sugar PSE_1900 PSE_1901 PSE_1902 PJE062_4447 PJE062_4491 PJE062_4514 SBP_bac_1 BPD_transp_1 ABC_tran Thiamine-binding periplasmic protein Thiamine transport system permease protein ThiP Thiamine import ATP-binding protein ThiQ thiB thiP thiQ PSE_1931 PSE_1932 PSE_1933 PJE062_859 PJE062_632 PJE062_685 NMT1 BPD_transp_1 ABC_tran ABC-type sulfonate transport system periplasmic component Aliphatic sulfonates transport permease protein SsuC Aliphatic sulfonates import ATP-binding protein SsuB ssuC ssuB Sulfonates PSE_1938 PSE_1939 PSE_1940 PJE062_519 PJE062_888 PJE062_677 SBP_bac_1 BPD_transp_1 ABC_tran iron(III) ABC transporter, substrate-binding protein iron(III) transport system permease protein FbpB Fe(3+) ions import ATP-binding protein FbpC fbpB fbpC Iron Pfam Model Product - 14 - Gene Predicted substrate specificity pstS pstC pstA pstB phoU Phosphate Thiamine Table S 4. Continued Locus FO-BEG1 PSE_1957 PSE_1958 PSE_1959 PSE_1960 Locus JE062 PJE062_572 PJE062_541 PJE062_553 PJE062_599 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran Sugar-binding periplasmic protein ABC-type sugar transport systems, permease components ABC sugar transporter inner membrane binding protein Sugar ABC transporter, ATP-binding protein PSE_1987 PSE_1988 PSE_1989 PSE_1990 PSE_1991 PJE062_601 PJE062_645 PJE062_931 PJE062_886 PJE062_540 ABC_tran ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 Oligopeptide transport ATP-binding protein OppF Oligopeptide transport ATP-binding protein OppD Oligopeptide transport system permease protein OppC oligopeptide transport system permease protein OppB Periplasmic oligopeptide-binding protein oppF oppD oppC oppB oppA PSE_2045 PJE062_684 SBP_bac_5 PSE_2048 PSE_2049 PSE_2050 PSE_2051 PSE_2052 PJE062_902 PJE062_662 PJE062_554 PJE062_901 PJE062_642 ABC_tran ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein Oligopeptide transport ATP-binding protein OppF Oligopeptide transport ATP-binding protein OppD Glutathione transport system permease protein GsiD Glutathione transport system permease protein GsiC Glutathione-binding protein GsiB oppF oppD gsiD gsiC gsiB PSE_2195 PSE_2196 PJE062_510 PJE062_602 SBP_bac_3 BPD_transp_1 PSE_2532 PJE062_402 ABC_tran PSE_2229 PSE_2230 PSE_2231 PJE062_837 PJE062_711 PJE062_898 ABC_tran BPD_transp_2 Peripla_BP_1 ABC sugar transporter, ATPase subunit ABC sugar transporter, inner membrane subunit ABC sugar transporter, periplasmic ligand binding protein PSE_2242 PSE_2243 PSE_2244 PJE062_557 PJE062_594 PJE062_592 ABC_tran BPD_transp_1 SBP_bac_1 Fe(3+) ions import ATP-binding protein FbpC iron(III) transport system permease protein FbpB Iron(III) binding periplasmic protein Pfam Model Product Gene Sugar extracellular solute-binding protein family 3 Inner membrane amino-acid ABC transporter permease protein YecS Cysteine/glutathione ABC transporter membrane/ATP-binding component - 15 - Predicted substrate specificity Oligopeptide Oligopeptide Amino acid Sugar fbpC fbpB fpbA Iron Table S 4. Continued Locus FO-BEG1 PSE_2252 PSE_2253 PSE_2254 PSE_2255 Locus JE062 PJE062_905 PJE062_503 PJE062_809 PJE062_799 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran Oligopeptide-binding protein AppA Oligopeptide transport system permease protein OppB Oligopeptide transport system permease protein OppC Glutathione import ATP-binding protein GsiA PSE_2267 PSE_2268 PJE062_899 PJE062_509 SBP_bac_3 BPD_transp_1 PSE_2531 ─ ABC_tran Cystine-binding periplasmic protein polar amino acid ABC transporter, inner membrane subunit Cysteine/glutathione ABC transporter membrane/ATP-binding component PSE_2358 PSE_2359 PSE_2360 PSE_2361 PJE062_12 PJE062_245 PJE062_4 PJE062_378 ABC_tran FecCD FecCD Peripla_BP_2 Ferrichrome transport ATP-binding protein FhuC Ferrichrome transport system permease protein FhuG Ferrichrome transport system permease protein FhuB Iron(III) dicitrate-binding periplasmic protein fhuC fhuG fhuB fecB PSE_2389 PSE_2390 PSE_2391 PSE_2392 PSE_2393 PJE062_334 PJE062_243 PJE062_43 ─ PJE062_72 ABC_tran SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran ABC transporter, ATP-binding protein Periplasmic oligopeptide-binding protein Oligopeptide transport system permease protein OppB Oligopeptide transport system permease protein OppC Glutathione import ATP-binding protein GsiA oppA oppB oppC gsiA PSE_2493 PSE_2494 PSE_2495 PSE_2496 PJE062_418 PJE062_435 PJE062_318 PJE062_225 ABC_tran SBP_bac_5 BPD_transp_1 BPD_transp_1 Glutathione import ATP-binding protein GsiA Periplasmic oligopeptide-binding protein Oligopeptide transport system permease protein AppB Oligopeptide transport system permease protein AppC gsiA oppA appB appC Oligopeptide PSE_2513 PSE_2514 PSE_2515 PJE062_36 PJE062_24 PJE062_383 BPD_transp_1 ABC_tran SBP_bac_1 aliphatic sulfonates transport permease protein SsuC Aliphatic sulfonates import ATP-binding protein SsuB Putative aliphatic sulfonates-binding protein ssuC ssuB ssuA Sulfonates Pfam Model Product - 16 - Gene Predicted substrate specificity appA oppB oppC gsiA Oligopeptide Amino acid Ferrichrome Oligopeptide Table S 4. Continued Locus FO-BEG1 PSE_2520 PSE_2521 PSE_2522 PSE_2523 Locus JE062 PJE062_357 PJE062_204 PJE062_434 PJE062_42 ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 Glutathione import ATP-binding protein GsiA Glutathione transport system permease protein GsiD Glutathione transport system permease protein GsiC Glutathione-binding protein GsiB PSE_2141 PSE_2564 PSE_2565 PSE_2566 PSE_2567 PSE_2568 PJE062_513 PJE062_4100 PJE062_4285 PJE062_4170 PJE062_4189 PJE062_4253 ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_3 SBP_bac_3 SBP_bac_3 ATP-binding component of ABC transporter Nopaline transport system permease protein NocM Nopaline transport system permease protein NocQ Nopaline-binding periplasmic protein Nopaline-binding periplasmic protein Nopaline-binding periplasmic protein PSE_2638 PSE_2639 PSE_2640 PSE_2641 PSE_2642 PSE_2643 PJE062_4138 PJE062_4284 PJE062_4303 PJE062_4336 PJE062_4101 PJE062_4114 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran ABC_tran SBP_bac_5 periplasmic dipeptide binding protein Dipeptide transport system permease protein DppB Dipeptide transport system permease protein DppC Dipeptide transport ATP-binding protein DppD Dipeptide transport ATP-binding protein DppF periplasmic dipeptide transport protein dppA dppB dppC dppD dppF dppA PSE_2783 PSE_2784 PSE_2785 PJE062_1514 PJE062_1111 PJE062_1709 Peripla_BP_2 FecCD ABC_tran periplasmic binding protein Hemin transport system permease protein HmuU Hemin import ATP-binding protein HmuV hmuU hmuV PSE_2808 PSE_2809 PSE_2810 PSE_2811 PJE062_1377 PJE062_1731 PJE062_1776 PJE062_1552 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran Periplasmic alpha-galactoside-binding protein Oligopeptide transport system permease protein AppB Oligopeptide transport system permease protein AppC Oligopeptide transport ATP-binding protein AppD appB appC appD Pfam Model Product - 17 - Gene Predicted substrate specificity gsiA gsiD gsiC gsiB Oligopeptide nocM nocQ Nopaline Oligopeptide Hemin Oligopeptide Table S 4. Continued Locus FO-BEG1 PSE_2816 PSE_2817 PSE_2818 PSE_2819 Locus JE062 PJE062_1140 PJE062_1562 PJE062_1154 PJE062_1225 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran sugar ABC transporter, periplasmic sugar-binding protein sugar ABC transporter, permease protein sugar ABC transporter, permease protein sugar ABC transporter, ATP-binding protein PSE_2868 PSE_2869 PSE_2870 PSE_2871 PSE_2872 PJE062_1053 PJE062_1539 PJE062_1757 PJE062_1524 PJE062_1035 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran ABC_tran Oligopeptide-binding protein appA Oligopeptide transport system permease protein AppB Oligopeptide transport system permease protein AppC Oligopeptide transport ATP-binding protein AppD Oligopeptide transport ATP-binding protein AppF appA appB appC appD appF Oligopeptide PSE_2879 PSE_2880 PSE_2881 PSE_2882 PJE062_1337 PJE062_1777 PJE062_1423 PJE062_1180 RbsD_FucU ABC_tran BPD_transp_2 Peripla_BP_1 High affinity ribose transport protein RbsD Ribose import ATP-binding protein RbsA Ribose transport system permease protein RbsC D-ribose-binding periplasmic protein rbsD rbsA rbsC rbsB Sugar PSE_2918 PSE_2919 PSE_2920 PSE_2921 PJE062_1472 PJE062_1003 PJE062_1476 PJE062_1533 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran extracellular solute-binding protein, family 1 Maltose transport system permease protein MalF Maltodextrin transport system permease protein MalD Maltose/maltodextrin import ATP-binding protein MalK malF malD malK PSE_2963 PSE_2964 PSE_2965 PSE_2966 PSE_2967 PJE062_1648 PJE062_1405 PJE062_1553 PJE062_1288 PJE062_1589 ANF_receptor BPD_transp_2 BPD_transp_2 ABC_tran ABC_tran ABC transporter, urea, substrate-binding, UrtA urea ABC transporter, permease protein UrtB urea ABC transporter, permease protein UrtC urea ABC transporter, ATP-binding protein UrtD urea ABC transporter, ATP-binding protein UrtE urtA urtB urtC urtD urtE PSE_2977 PSE_2978 PJE062_1645 PJE062_1063 BPD_transp_1 ABC_tran proW proV PSE_2979 PJE062_1143 OpuAC Glycine betaine/L-proline transport system permease protein ProW Glycine betaine/L-proline transport ATP-binding protein ProV Substrate-binding region of ABC-type glycine betaine transport system Pfam Model Product - 18 - Gene Predicted substrate specificity Sugar Sugar Urea Glycine betaine/ L-proline Table S 4. Continued Locus FO-BEG1 PSE_2987 Locus JE062 PJE062_1332 PSE_2988 ─ BPD_transp_1 PSE_2989 PJE062_1578 ABC_tran PSE_2990 PJE062_1498 BPD_transp_1 PSE_3097 PSE_3098 PSE_3099 PSE_3100 PJE062_1174 PJE062_1095 PJE062_1044 PJE062_1329 Peripla_BP_2 FecCD FecCD ABC_tran Ferric anguibactin-binding protein Ferric anguibactin transport system permease protein FatD Ferric anguibactin transport system permease protein FatC Ferrichrome transport ATP-binding protein FhuC fatB fatD fatC fhuC PSE_3153 PJE062_1631 ANF_receptor livB PSE_3154 PJE062_1741 BPD_transp_2 PSE_3155 PJE062_1386 BPD_transp_2 PSE_3156 PJE062_1557 ABC_tran PSE_3157 PJE062_1394 ABC_tran Leu/Ile/Val-binding protein homolog High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) PSE_3176 PSE_3177 PSE_3178 PSE_3179 PJE062_1668 PJE062_1420 PJE062_1239 PJE062_1523 SBP_bac_1 BPD_transp_2 BPD_transp_2 ABC_tran Pfam Model Product Gene OpuAC Choline-binding protein Glycine betaine/carnitine/choline transport system permease protein OpuCD Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA Glycine betaine/carnitine/choline transport system permease protein OpuCB opuBC ABC transporter periplasmic binding protein sugar ABC transporter, permease protein sugar ABC transporter, permease protein Ribose import ATP-binding protein RbsA - 19 - Predicted substrate specificity opuCD opuCA Glycine betaine/ carnitine/choline opuCB Ferric anguibactin livH livM Amino acid livG livF Sugar rbsA Table S 4. Continued Locus FO-BEG1 Locus JE062 Pfam Model PSE_3515 PJE062_1371 ABC_tran PSE_3516 PJE062_1361 BPD_transp_1 PSE_3517 ─ BPD_transp_1 PSE_3518 ─ SBP_bac_3 PSE_3627 PSE_3628 PJE062_1374 PJE062_1147 BPD_transp_1 BPD_transp_1 PSE_3629 PJE062_1356 SBP_bac_3 PSE_3630 PJE062_1025 ABC_tran PSE_3640 PSE_3641 PSE_3642 PSE_3644 PJE062_1291 PJE062_983 PJE062_1417 PJE062_1309 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran ABC transporter, substrate binding protein (sugar) ABC transporter, membrane spanning protein (sugar) ABC transporter, membrane spanning protein (sugar) ABC transporter, nucleotide binding/ATPase protein (sugar) PSE_3646 PJE062_1305 Peripla_BP_1 PSE_3647 PJE062_1083 SBP_bac_3 PSE_3648 PJE062_1302 BPD_transp_1 periplasmic binding protein/LacI transcriptional regulator putative amino acid uptake ABC transporter periplasmic solutebinding protein Amino acid uptake ABC transporter permease protein PSE_3653 PSE_3654 PSE_3655 PSE_3656 PJE062_1142 PJE062_1571 PJE062_1526 PJE062_1564 SBP_bac_1 ABC_tran BPD_transp_1 BPD_transp_1 Putrescine-binding periplasmic protein Putrescine transport ATP-binding protein PotG Putrescine transport system permease protein PotH Putrescine transport system permease protein PotI Product Glutamate/glutamine/aspartate/asparagine transport ATP-binding protein BztD Glutamate/glutamine/aspartate/asparagine transport system permease protein BztC Glutamate/glutamine/aspartate/asparagine transport system permease protein BztB Glutamate/glutamine/aspartate/asparagine-binding protein BztA Phosphonates transport system permease protein PhnE Phosphonates transport ATP-binding protein PhnL ABC transporter, phosphonate, periplasmic substrate-binding protein PhnD Phosphonates import ATP-binding protein PhnC - 20 - Gene Predicted substrate specificity bztD bztC Amino acid bztB bztA phnE phnL phnD Phosphonate phnC Sugar Amino acid potF potG potH potI Putrescine/ Spermidine Table S 4. Continued Locus FO-BEG1 Locus JE062 Pfam Model PSE_3671 PJE062_1069 ABC_tran PSE_3672 PJE062_1719 ABC_tran PSE_3673 PJE062_1499 BPD_transp_2 PSE_3674 PJE062_1484 BPD_transp_2 PSE_3675 PJE062_1325 ANF_receptor High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) Leu/Ile/Val-binding protein homolog 4 PSE_3919 PSE_3920 PSE_3921 PSE_3924 ─ ─ ─ ─ BPD_transp_1 BPD_transp_1 SBP_bac_1 ABC_tran Maltose transport system permease protein MalG Maltose transport system permease protein MalF Maltose-binding periplasmic protein Maltose/maltodextrin import ATP-binding protein MalK malG malF malE malK PSE_3948 PSE_3950 PSE_3951 PSE_3953 PJE062_4678 ─ PJE062_5134 PJE062_4603 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran extracellular solute-binding protein, family 1 Multiple sugar-binding transport system permease protein MsmF L-arabinose transport system permease protein AraQ Alpha-glucoside transport ATP-binding protein AglK msmF araQ aglK PSE_4021 PJE062_4745 ANF_receptor PSE_4023 PJE062_44581 ABC_tran PSE_4024 PJE062_4641 ABC_tran PSE_4025 PJE062_4545 BPD_transp_2 PSE_4026 PJE062_5154 BPD_transp_2 Leu/Ile/Val-binding protein homolog High-affinity branched-chain amino acid transport ATP-binding protein LivF (LIV-I protein F) High-affinity branched-chain amino acid transport ATP-binding protein LivG (LIV-I protein G) High-affinity branched-chain amino acid transport system permease protein LivM (LIV-I protein M) High-affinity branched-chain amino acid transport system permease protein LivH (LIV-I protein H) Product - 21 - Gene Predicted substrate specificity livF livG livM Amino acid livH livB Sugar Sugar livB livF livG livM livH Amino acid Table S 4. Continued Locus FO-BEG1 PSE_4503 PSE_4504 PSE_4505 PSE_4506 Locus JE062 PJE062_4774 PJE062_4712 PJE062_5011 PJE062_4906 BPD_transp_1 BPD_transp_1 SBP_bac_1 ABC_tran ABC transporter permease protein spermidine/putrescine ABC transporter membrane component extracellular solute-binding protein family 1 putrescine/spermidine ABC transporter ATPase PSE_4557 PSE_4558 PSE_4559 PSE_4560 PSE_4561 PJE062_4521 PJE062_2508 PJE062_2469 PJE062_2453 PJE062_2480 ABC_tran ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 Dipeptide transport ATP-binding protein DppF Dipeptide transport ATP-binding protein DppD Dipeptide transport system permease protein DppC Dipeptide transport system permease protein DppB Periplasmic dipeptide transport protein dppF dppD dppC dppB dppA PSE_4562 PSE_4564 PSE_4565 PSE_4566 PJE062_2473 PJE062_2457 PJE062_2513 PJE062_2461 ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_1 Maltose/maltodextrin import ATP-binding protein MalK Maltose transport system permease protein MalG Maltose transport system permease protein MalF sugar ABC transporter, periplasmic sugar-binding protein malK malG malF PSE_4804 PJE062_2295 ABC_tran PSE_4805 PJE062_2276 ANF_receptor PSE_4806 PJE062_2012 BPD_transp_2 PSE_4807 PJE062_2240 BPD_transp_2 PSE_4808 PJE062_2180 ABC_tran PSE_4831 PSE_4832 PSE_4833 PSE_4834 PJE062_2307 PJE062_2293 PJE062_2270 PJE062_2181 SBP_bac_5 BPD_transp_1 BPD_transp_1 ABC_tran Pfam Model Product High-affinity branched-chain amino acid transport ATP-binding protein BraG branched-chain amino acid ABC transporter, periplasmic branchedchain amino acid binding protein High-affinity branched-chain amino acid transport system permease protein BraE High-affinity branched-chain amino acid transport system permease protein BraD High-affinity branched-chain amino acid transport ATP-binding protein BraF Glutathione-binding protein GsiB Dipeptide transport system permease protein DppB Dipeptide transport system permease protein DppC Glutathione import ATP-binding protein GsiA - 22 - Gene Predicted substrate specificity Putrescine/ Spermidine Oligopeptide Sugar braG braE Amino acid braD braF gsiB dppB dppC gsiA Oligopeptide Table S 4. Continued Locus FO-BEG1 PSE_4895 PSE_4896 PSE_4897 Locus JE062 PJE062_2134 PJE062_2061 PJE062_2075 Gene Predicted substrate specificity ABC_tran BPD_transp_1 SBP_bac_3 amino-acid ABC transporter ATP-binding protein YecC amino-acid ABC transporter permease protein PatM amino-acid ABC transporter-binding protein PatH yecC patM patH Amino acid PSE_4935 PSE_4936 PSE_4937 PJE062_2212 PJE062_2256 PJE062_2348 ABC_tran BPD_transp_1 SBP_bac_1 Molybdenum import ATP-binding protein ModC Molybdenum transport system permease protein ModB Molybdate-binding periplasmic protein modC modB modA Molybdenum PSE_4960 PSE_4961 PSE_4962 PJE062_2103 PJE062_2002 PJE062_2254 BioY CbiQ ABC_tran BioY protein Cobalt transport protein Cobalt import ATP-binding protein CbiO 1 bioY cbiQ cbiO Cobalt PSE_5060 PSE_5062 PSE_5063 PSE_5064 PSE_5065 PJE062_4022 PJE062_4017 PJE062_3999 PJE062_3997 PJE062_4020 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran ABC_tran ABC-type sugar transport system, periplasmic component sn-glycerol-3-phosphate transport system permease protein UgpE sn-glycerol-3-phosphate transport system permease protein UgpA sn-glycerol-3-phosphate import ATP-binding protein UgpC sn-glycerol-3-phosphate import ATP-binding protein UgpC ugpE ugpA ugpC ugpC PSE_p0066 PJE062_3787 Peripla_BP_1 PSE_p0067 PJE062_3695 ABC_tran rgmG PSE_p0068 PJE062_3689 BPD_transp_2 D-ribose-binding protein Putative ribose/galactose/methyl galactoside import ATP-binding protein Galactoside transport system permease protein MglC PSE_p0070 PSE_p0071 PSE_p0072 PSE_p0073 PJE062_3838 PJE062_3875 PJE062_3669 PJE062_3794 ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_1 sn-glycerol-3-phosphate import ATP-binding protein UgpC sn-glycerol-3-phosphate transport system permease protein UgpE sn-glycerol-3-phosphate transport system permease protein UgpA sn-glycerol-3-phosphate-binding periplasmic protein UgpB ugpC upgE upgA upgB Pfam Model Product - 23 - Glycerol-3-phosphate rbsB Sugar mglC Glycerol-3-phosphate Table S 4. Continued Locus FO-BEG1 PSE_p0079 PSE_p0080 PSE_p0081 PSE_p0082 Locus JE062 PJE062_3869 ─ ─ PJE062_3781 SBP_bac_1 BPD_transp_1 BPD_transp_1 ABC_tran ABC transporter, periplasmic binding-protein Lactose transport system permease protein LacF Multiple sugar-binding transport system permease protein MsmG Maltose/maltodextrin import ATP-binding protein MalK PSE_p0179 PSE_p0180 PSE_p0181 PSE_p0182 PJE062_3795 PJE062_3917 PJE062_3909 PJE062_3834 BPD_transp_1 BPD_transp_1 SBP_bac_1 ABC_tran Spermidine/putrescine transport system permease protein PotB Putrescine transport system permease protein PotH ABC transporter, periplasmic substrate-binding protein Spermidine/putrescine import ATP-binding protein PotA PSE_p0206 PSE_p0210 PJE062_3717 PJE062_3844 ABC_tran BPD_transp_1 PSE_p0211 PJE062_3654 BPD_transp_1 PSE_p0212 PJE062_3625 SBP_bac_1 sugar ABC transporter, ATP-binding protein L-arabinose transport system permease protein AraQ starch degradation products transport system permease protein AmyD ABC-type sugar transport system, periplasmic component PSE_p0237 PSE_p0238 PSE_p0239 PSE_p0240 PJE062_3796 PJE062_3619 PJE062_3887 PJE062_3972 ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 Oligopeptide transport ATP-binding protein AppF Oligopeptide transport system permease protein AppC Oligopeptide transport system permease protein AppB Periplasmic dipeptide transport protein appF appC appB dppA Oligopeptide PSE_p0350 PSE_p0351 PSE_p0352 PSE_p0353 PSE_p0354 PJE062_3636 ─ PJE062_3745 PJE062_3770 PJE062_3690 ABC_tran ABC_tran BPD_transp_1 BPD_transp_1 SBP_bac_5 Oligopeptide transport ATP-binding protein AppF Oligopeptide transport ATP-binding protein OppD Probable D,D-dipeptide transport system permease protein DdpC Glutathione transport system permease protein GsiC Periplasmic dipeptide transport protein appF oppD dppC gsiC dppA Oligopeptide Pfam Model Product - 24 - Gene lacF msmG malK potB potH Predicted substrate specificity Sugar Putrescine/ Spermidine potA araQ amyD Sugar Table S 5. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted peptidases/proteases and proteins involved in protection against reactive oxygen species (ROS). Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Absence of a gene name or an EC number indicates that no assignment was made due to missing of these parameters for the respective genes. Locus FO-BEG1 Locus JE062 PSE_0001 PSE_0229 PSE_0251 PSE_0273 PSE_0434 PSE_0464 PSE_0466 PSE_0494 PSE_0563 PSE_0669 PSE_0709 PSE_0710 PSE_0811 PSE_0812 PJE062_3184 PJE062_3278 PJE062_3407 PJE062_3414 ─ ─ PJE062_2551 PJE062_2791 PJE062_2577 PJE062_2688 PJE062_2578 PJE062_2576 PJE062_2788 PJE062_2571 PSE_0992 PJE062_2365 PSE_1070 PJE062_4381 PSE_1080 PJE062_4511 PSE_1106 PSE_1182 PSE_1188 PSE_1495 PSE_1496 PSE_1498 PSE_1533 PSE_1565 PSE_1568 PSE_1618 PSE_1833 PSE_1842 PSE_2257 PSE_2285 PSE_2356 PSE_2396 PSE_2422 PSE_2435 PSE_2461 PSE_2472 PJE062_4512 ─ ─ PJE062_5268 PJE062_5323 PJE062_5212 PJE062_182 PJE062_241 PJE062_410 PJE062_92 ─ ─ PJE062_671 PJE062_817 PJE062_223 PJE062_57 PJE062_398 PJE062_293 PJE062_207 PJE062_117 PSE_2490 PJE062_382 PSE_2733 PJE062_4294 Product Peptidases /Proteases Peptidase M23/M37 family protein Peptidase family M48 Peptidase family S41 D-alanyl-D-alanine carboxypeptidase Peptidase family M48 Peptidase M75, Imelysin Peptidase M75, Imelysin Peptidase M22, glycoprotease Pyrrolidone-carboxylate peptidase Peptidase family S49 Peptidase family S41 Peptidase M23 Peptidase family U32 Peptidase family U32 Penicillin-insensitive murein endopeptidase precursor/D-alanyl-D-alanine-endopeptidase Type IV leader peptidase family Cytosol aminopeptidase/leucine aminopeptidase Peptidase M19, renal dipeptidase Dipeptidase 1/Microsomal dipeptidase Metallopeptidase family M24 Peptidase M16 family protein Peptidase M16 family protein Lipoprotein signal peptidase Peptidase U62, modulator of DNA gyrase Peptidase M16 family protein D-alanyl-D-alanine carboxypeptidase Peptidase family S49 Peptidase M24 Peptidase M24 Peptidase M23B Peptidase family M20/M25/M40 Peptidase family M20/M25/M40 Peptidase M19, renal dipeptidase Peptidase family M20/M25/M40 Protease 2/Oligopeptidase B Peptidase U35, phage prohead HK97 Phage cell wall peptidase, NlpC/P60 Aminopeptidase N (Alpha-aminoacylpeptide hydrolase) Cytosol aminopeptidase/Leucine aminopeptidase - 25 - Gene EC dacC pcp 3.4.19.3 mepA 3.4.24.- pepA 3.4.11.1 lspA 3.4.23.36 ptrB 3.4.21.83 ampN 3.4.11.2 ampA 3.4.11.1 Table S 5. Continued Locus FO-BEG1 PSE_2795 PSE_2941 PSE_2997 PSE_3040 PSE_3062 PSE_3141 PSE_3234 PSE_3404 PSE_3468 PSE_3475 Locus JE062 PJE062_1383 PJE062_1153 PJE062_1623 ─ ─ PJE062_1066 PJE062_1678 PJE062_1716 PJE062_1772 ─ PSE_3524 ─ PSE_3609 PSE_3808 PSE_3821 PSE_3979 PJE062_1430 PJE062_3548 ─ PJE062_5150 PSE_3998 PJE062_4868 PSE_4028 PSE_4247 PSE_4285 PSE_4388 PSE_4435 PSE_4669 PSE_4674 PSE_4759 PSE_4873 PJE062_4576 PJE062_5063 PJE062_5046 PJE062_5031 PJE062_4791 PJE062_2225 PJE062_2053 PJE062_2089 PJE062_2076 PSE_4884 PJE062_2338 PSE_4893 PSE_4926 PSE_5035 PSE_0055 PSE_0097 PSE_0489 PJE062_1994 PJE062_2084 PJE062_4092 PJE062_3479 PJE062_3209 PJE062_2770 PSE_0491 PJE062_2610 PSE_0494 PSE_0709 PSE_0869 PSE_0880 PSE_2435 PSE_2484 PSE_2726 PSE_3446 PJE062_2791 PJE062_2578 PJE062_2969 PJE062_3017 PJE062_293 PJE062_401 PJE062_4115 PJE062_1826 PSE_3447 PJE062_1775 PSE_3448 PJE062_1602 PSE_3805 PJE062_3583 Product Peptidase family M20/M25/M40 Peptidase family M20/M25/M40 Prolyl oligopeptidase family Clp protease Peptidase M15 D-alanyl-D-alanine carboxypeptidase Peptidase M23B Peptidase family M50 Peptidase M23B Peptidase family M48 Peptidyl-dipeptidase dcp (Dipeptidyl carboxypeptidase) Signal peptidase I D-alanyl-D-alanine carboxypeptidase Clp protease Transglutaminase-like cysteine peptidase Methionine aminopeptidase (MAP) (Peptidase M) Peptidase S58, DmpA Xaa-Pro aminopeptidase 1 Peptidase T Prolyl oligopeptidase family Xaa-Pro dipeptidase M42 glutamyl aminopeptidase Cell division protease FtsH homolog Oligoendopeptidase F homolog Peptidase family M48 O-sialoglycoprotein endopeptidase (Glycoprotease) Peptidase family M20/M25/M40 Peptidase U32 Peptidase S58, DmpA CAAX protease family protein ATP-dependent protease La, LON ATP-dependent protease peptidase subunit ATP-dependent hsl protease ATP-binding subunit HslU Peptidase M22, glycoprotease Peptidase family S41 Serralysin zinc protease pqqL Protease 2/Oligopeptidase B Serine protease Serine protease ATP-dependent protease La ATP-dependent Clp protease ATP-binding subunit clpX ATP-dependent Clp protease proteolytic subunit (Endopeptidase Clp) ATP-dependent Clp protease ATP-binding subunit clpA Gene EC dacA 3.4.16.4 3.4.24.- dcp 3.4.15.5 lepB dacF 3.4.21.89 3.4.16.4 3.4.21.92 map 3.4.11.18 xpp1 pepT 3.4.11.9 3.4.11.4 pepQ 3.4.13.9 ftsH 3.6.4.3 gcp 3.4.24.57 hslV 3.4.25.- hslU pqqL ptrB degP1 3.4.24.40 3.4.99.3.4.21.83 3.4.21.- lon 3.4.21.53 clpX clpP clpA 3.4.21.92 Table S 5. Continued Locus FO-BEG1 Locus JE062 PSE_3806 PJE062_3584 PSE_3852 PJE062_4839 PSE_4208 PJE062_5075 PSE_4228 PSE_4718 PJE062_4726 PJE062_1984 PSE_4884 PJE062_2338 PSE_0143 PSE_2428 PJE062_3455 PJE062_90 PSE_1899 PSE_4005 PJE062_693 PJE062_4983 PSE_0100 PJE062_3343 PSE_0180 PSE_0181 PSE_0722 PJE062_3475 PJE062_3303 ─ PSE_1918 PJE062_770 PSE_1949 PSE_2025 PJE062_923 PJE062_566 PSE_2156 PJE062_603 PSE_2209 PJE062_579 PSE_2511 PJE062_470 PSE_2926 PJE062_1164 PSE_3314 ─ PSE_3466 PJE062_1662 PSE_3521 PJE062_1626 PSE_3918 ─ PSE_4045 PJE062_4776 PSE_4466 PSE_5045 PSE_5046 PSE_p0159 PSE_p0165 PSE_p0321 PJE062_4550 PJE062_4053 PJE062_4061 PJE062_3672 PJE062_3748 PJE062_3655 Product ATP-dependent Clp protease adapter protein clpS 1 Serine protease Intracellular protease 1 (Intracellular protease I) Trypsin-like serine protease Zinc protease O-sialoglycoprotein endopeptidase (Glycoprotease) Protection against reactive oxygen species Copper/zinc superoxide dismutase Manganese/iron superoxide dismutase Catalase Peroxidase/catalase (Catalase-peroxidase) Catalase Cytochrome c551 peroxidase (Cytochrome c peroxidase) (CCP) Thioredoxin peroxidase Alkylhydroperoxidase AhpD Peroxiredoxin, OsmC-like protein Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Di-heme cytochrome c peroxidase Alkylhydroperoxidase AhpD Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Di-heme cytochrome c peroxidase Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Phosphatidic acid phosphatase type 2/haloperoxidase Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen Organic hydroperoxide resistance protein Di-heme cytochrome c peroxidase Di-heme cytochrome c peroxidase Di-heme cytochrome c peroxidase Alkylhydroperoxidase AhpD Alkylhydroperoxidase AhpD - 27 - Gene EC ClpS pfpI gcp 3.4.24.57 sodC sodF 1.15.1.1 1.15.1.1 catA catA 1.11.1.6 1.11.1.6 ccpR tdx ahpD osmC Table S 6. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted proteins involved vitamin synthesis. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Absence of a gene name or an EC number indicates that no assignment was made due to missing of these parameters for the respective genes. Locus FO-BEG1 Locus JE062 PSE_0621 PSE_0622 PSE_0906 PSE_0907 PSE_0908 PSE_0909 PSE_0910 PSE_0911 PSE_3819 PSE_4137 PSE_4138 PSE_4699 PSE_1900 PJE062_2616 PJE062_2638 PJE062_2968 PJE062_2761 PJE062_2880 PJE062_2900 PJE062_2986 PJE062_2936 PJE062_5088 PJE062_5017 PJE062_4585 PJE062_2332 PJE062_4447 PSE_1901 PJE062_4491 PSE_1902 PSE_3582 PSE_2998 PSE_1658 PSE_3005 PSE_4898 PJE062_4514 PJE062_1837 PJE062_1279 PJE062_60 PJE062_1473 PJE062_2346 PSE_1646 PJE062_256 PSE_0835 PJE062_3009 PSE_3584 PSE_3585 PJE062_1363 ─ PSE_3586 PJE062_977 PSE_1503 PJE062_5201 PSE_0236 PSE_3972 PSE_2813 PSE_5052 PSE_3836 PJE062_3408 PJE062_4864 PJE062_994 PJE062_3977 PJE062_4956 Product Vitamin B1 Thiaminea) Thiamine-phosphate pyrophosphorylase Hydroxyethylthiazole kinase Thiamine biosynthesis protein ThiF Thiamine-phosphate pyrophosphorylase Thiazole biosynthesis protein ThiG ThiS, thiamine-biosynthesis Thiamine biosynthesis oxidoreductase ThiO Thiamine biosynthesis protein ThiC Thiamine-phosphate pyrophosphorylase Phosphomethylpyrimidine kinase Hydroxyethylthiazole kinase Thiamine-phosphate pyrophosphorylase Thiamine-binding periplasmic protein Thiamine transport system permease protein ThiP Thiamine import ATP-binding protein ThiQ Thiamine-monophosphate kinase Cysteine desulfurase, NifS 1-deoxy-D-xylulose-5-phosphate synthase TENA/THI-4/PQQC family TENA/THI-4/PQQC family Vitamin B2 Riboflavinb) Riboflavin biosynthesis protein RibBA (3,4dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase-2) Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimi dine deaminase/5-amino-6-(5phosphoribosylamino)uracil reductase) Riboflavin synthase beta chain Riboflavin synthase alpha chain Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimi dine deaminase/5-amino-6-(5phosphoribosylamino)uracil reductase) Riboflavin biosynthesis protein ribF (Riboflavin kinase/ FMN adenylyltransferase) Vitamin B9 Folic acidc) GTP cyclohydrolase 1 GTP cyclohydrolase 1 Alkaline phosphatase Alkaline phosphatase Dihydroneopterin aldolase (DHNA) Gene EC thiE thiM thiF thiE thiG thiS thiO thiC thiE thiD thiM thiE thiB 2.5.1.3 2.7.1.50 2.7.7.2.5.1.3 1.4.3.19 2.5.1.3 2.7.4.7 2.7.1.50 2.5.1.3 thiP thiQ thiL nifS/iscS dxpS tenA tenA 2.8.1.7 2.2.1.7 3.5.99.2 3.5.99.2 ribBA 3.5.4.25/ 4.1.99.12 ribD 3.5.4.26/ 1.1.1.93 risB risA 2.5.1.9 ribD 3.5.4.26/ 1.1.1.193 ribF 2.7.1.26/ 2.7.7.2 folE folE folB 3.5.4.16 3.5.4.16 3.1.3.1 3.1.3.1 4.1.2.25 Table S 6. Continued Locus FO-BEG1 Locus JE062 PSE_0133 PJE062_3459 PSE_0134 PJE062_3328 PSE_0339 PJE062_3466 PSE_4234 ─ Product 2-amino-4-hydroxy-6hydroxymethyldihydropteridine pyrophosphokinase Dihydropteroate synthase (DHPS) Bifunctional protein folC (Folylpolyglutamate synthase/Dihydrofolate synthase) Dihydrofolate reductase type III DHFR PSE_0073 PSE_0074 PJE062_3117 PJE062_3423 PSE_0272 PJE062_3130 PSE_0298 PSE_0823 PJE062_3171 PJE062_2890 PSE_0824 PJE062_2592 PSE_0825 PJE062_2904 PSE_0826 PJE062_3055 PSE_0827 PJE062_3024 PSE_0828 PJE062_2713 PSE_0829 PJE062_2999 PSE_0830 PSE_0832 PSE_0833 PJE062_2731 PJE062_2996 PJE062_2650 PSE_2555 PJE062_4304 PSE_2556 PJE062_4127 PSE_3492 PJE062_1509 Vitamin B12 Cobalamind) Aerobic cobaltochelatase subunit CobS Aerobic cobaltochelatase subunit CobT Cobalamin (vitamin B12) biosynthesis CobWlike Cobyrinic acid a,c-diamide synthase Sirohydrochlorin cobaltochelatase (CbiX) Precorrin-8X methylmutase/Precorrin isomerase CobH/CbiC Precorrin-6Y C(5,15)-methyltransferase CobL/CbiE/CbiT Precorrin-2 C(20)-methyltransferase CobI/CbiL Precorrin-3B C(17)-methyltransferase CobJ/CibH/GbiG Precorrin-4 C(11)-methyltransferase CobM/CbiF Cobyrinic acid A,C-diamide synthase CobB/CbiA Uroporphyrinogen-III C-methyltransferase Cobalt-precorrin-6A synthase Precorrin-6A reductase CobK/CbiJ Cobalamin (5'-phosphate) synthase CobS/CobV Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT/CobU) Cobalamin biosynthesis protein CobD/CbiB PSE_3493 PJE062_1793 Cobyric acid synthase CobQ/CobB PSE_3494 PJE062_1191 PSE_3495 PSE_3496 PJE062_1559 PJE062_1259 PSE_3497 PJE062_1011 PSE_4445 PJE062_4542 PSE_4713 ─ PSE_4818 PJE062_2023 PSE_3491 PJE062_1667 PSE_4671 PJE062_1992 Cob(I)yrinic acid a,c-diamide adenosyltransferase (CobA/CobO) Aerobic cobaltochelatase subunit cobN Cobalamin (vitamin B12) biosynthesis CobW Bifunctional adenosylcobalamin biosynthesis protein CobP/CobU (Adenosylcobinamide kinase/Adenosylcobinamide-phosphate guanylyltransferase) Cob(II)yrinic acid a,c-diamide reductase Cobyrinic acid a,c-diamide synthase CobQ/CobB Cobalamin (vitamin B12) biosynthesis CobW Threonine-phosphate decarboxylase CobC/CobD Vitamin B6 Pyridoxinee) Phosphoserine aminotransferase (PdxF) - 29 - Gene EC folK 2.7.6.3 folP folA 2.5.1.15 6.3.2.12/ 6.3.2.17 1.5.1.3 cobS cobT 6.6.1.2 6.6.1.2 folC cobW cbiX cobH/cbi C cobL/cbiE /cbiT cobI/cbiL cobJ/cibH /cbiG cobM/cbi F 4.99.1.3 1.7.7.1/ 5.4.1.2 2.1.1.132 2.1.1.130 2.1.1.131 2.1.1.133 cobB/cbiA 6.3.5.9 cobA cbiD cobK/cbiJ 2.1.1.107 cobS/cobV 2.7.8.26 cobT/cob U cobD/cbiB cobQ/cob B cobA/cob O cobN cobW 1.3.1.54 2.4.2.21 6.3.1.10 6.3.5.10 2.5.1.17 6.6.1.2 cobP/cob U 2.7.1.156/ 2.7.7.62 bluB cobQ/cob B cobW cobC/cob D 1.16.8.1 serC/pdxF 2.6.1.52 4.1.1.81 Table S 6. Continued Locus FO-BEG1 PSE_1564 Locus JE062 PJE062_153 PSE_2728 PJE062_4225 PSE_4205 PSE_p0050 PJE062_4768 PJE062_3885 PSE_0084 ─ PSE_1669 PJE062_333 PSE_1658 PJE062_60 PSE_3083 PSE_3084 PSE_3085 PJE062_1792 PJE062_1708 PJE062_1407 PSE_3086 PJE062_1813 PSE_3087 PJE062_1055 Product Threonine synthase 4-hydroxythreonine-4-phosphate dehydrogenase Pyridoxine 5'-phosphate synthase Pyridoxamine kinase Pyridoxine kinase/Pyridoxal kinase/Pyridoxamine kinase Pyridoxine/pyridoxamine 5'-phosphate oxidase 1-deoxy-D-xylulose-5-phosphate synthase Vitamin H Biotinf) Biotin synthase 8-amino-7-oxononanoate synthase Dethiobiotin synthetase Adenosylmethionine-8-amino-7oxononanoate aminotransferase 3-oxoacyl-[acyl-carrier-protein] synthase 3 Gene EC thrC 4.2.3.1 pdxA 1.1.1.262 pdxJ pdxY 2.6.99.2 2.7.1.35 pdxK 2.7.1.35 pdxH 1.4.3.5 dxpS 2.2.1.7 bioB bioF bioD 2.8.1.6 2.3.1.47 6.3.3.3 bioA 2.6.1.62 bioZ 2.3.1.180 lipA lipB 2.8.1.8 2.3.1.181 Lipoic acidg) PSE_3289 PSE_3828 a) Thiamin PJE062_975 PJE062_4856 Lipoyl synthase Octanoyltransferase (Vitamin B1) For the biosynthesis of vitamin B1, thiazole and pyrimidine must be synthesized via different pathways and then combined to thiamin phosphate (Begley et al., 1999; Jurgenson et al., 2009). We identified genes coding for the enzymes of the pyrimidine branch as well as the proteins responsible for the formation of thiazole, including ThiO for the aerobic formation of dehydroglycine as the final step of the thiazole synthesis. We also identified the key enzyme ThiE, performing the linkage of thiazole and pyrimidine to thiamin phosphate and its subsequent phosphorylation to the vitamin thiamin pyrophosphate via ThiL (Jurgenson et al., 2009). b) Riboflavin (Vitamin B2) Vitamin B2 is required for numerous reactions and processes and is produced by plants and microorganisms, but must be taken up by animals (Fischer and Bacher, 2005). We identified the key enzyme GTP cyclohydrolase II, which is required for the conversion of GTP as the first step of the pathway, in the genomes of FO-BEG1 and JE062. Furthermore, riboflavin synthase and lumazine synthase, catalyzing the formation of riboflavin and the reutilization of the by-product 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedion, respectively, as well as other enzymes described to be required for this de novo synthesis pathway (Fischer and Bacher, 2005), were found in both genomes (in strain JE062, only the alpha subunit of the riboflavin synthase was missing), indicating the capability of both strains to produce vitamin B2. c) Folic acid (Vitamin B9) Tetrahydrofolate, a biochemical derivate of the folic acid, serves as a donor and acceptor of one-carbon units in a number of anabolic and catabolic processes (Bermingham and Derrick, 2002). All enzymes reported to be required for the formation of folate have been detected in strain FO-BEG1 (in JE062, the dehydrofolate reductase is missing), except for DHNE and DHPP. The roles of 7,8-dihydoneopterin triphosphate epimerase (DHNE) and 7,8dihydroneopterin triphosphate pyrophosphohydrolase (DHPP) are not clarified yet (Bermingham and Derrick, 2002) and it is questionable, whether they at all are involved in the de novo synthesis of folic acid. The capability of the strains FO-BEG1 and JE062 to grow without the external supply of vitamins implies that folate is synthesized in these strains. d) Cobalamin (Vitamin B12) The de novo synthesis of cobalamin is restricted to prokaryotes. All other living organisms must take up this vitamin to ensure the function of several enzymes, like the methionine synthase and the methylmalony-CoA mutase (Martens et al., 2002). The biosynthesis of vitamin B12 is a complex process that requires an array of enzymes. Two pathways exist for the de novo synthesis of cobalamin – the aerobic synthesis, in which cobalt is inserted into the molecule via the proteins CobN, CobS and CobT, and the anaerobic pathway with CbiX as the enzyme responsible for the insertion of cobalt. Genes for both pathways are present in the analyzed genomes of Pseudovibrio sp. FO-BEG1 and JE062, CobG, however, a key enzyme in the oxygen-dependent pathway, seems to be missing. A cobalamin biosynthesis pathway of similar structure has been reported for the Roseobacter clade already, and vitamin B12 production has indeed been shown in Dinoroseobacter shibae DFL12, a symbiont of marine algae (Wagner-Döbler et al., 2010). e) Pyridoxine (Vitamin B6) Only prokaryotes and plants can de novo synthesize vitamin B6. It is a cofactor of over 100 enzymatic reactions, predominantly in the amino acid metabolism (Fitzpatrick et al., 2007). In both genomes we could identify genes pdxA, pdxJ and dxpS coding for the key enzymes of the so-called DXP-dependent pathway, which leads to the condensation of the - 31 - vitamer pyridoxine 5´-phosphate (PNP) (Fitzpatrick et al., 2007). Furthermore, the synthesized PNP can be interconverted via the salvage pathway, which is completely present in both genomes, into the other vitamer forms of vitamin B6 (Mooney et al., 2009). f) Biotin (Vitamin H) A complete operon for the synthesis of biotin consisting of bioB, bioF, bioD, bioA and bioZ was identified in the genomes of Pseudovibrio sp. FO-BEG1 and JE062. The arrangement of the genes is identical with the described operon of Mesorhizobium sp. (Sullivan et al., 2001), a symbiotic alphaproteobacterium found in the soil. This bacterium contains the unique gene bioZ, which is proposed to be involved in the pimeloyl-CoA synthesis in the first steps of biotin formation (Guillén-Navarro et al., 2005; Streit and Entcheva, 2003). Importantly, in Mesorhizobium, the operon is functional and has been proven to produce biotin, if expressed. g) Lipoic acid For the endogenous synthesis of lipoic acid, which is a branch of the fatty acid biosynthesis, LipB and LipA are required, a lipoyl (octanoyl)-transferase and an enzyme catalyzing the sulfur insertion into the molecule, respectively (Booker, 2004). Genes encoding both proteins were identified in both genomes. References Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon APGM, Taylor S et al. (1999). Thiamin biosynthesis in prokaryotes. Arch Microbiol 171: 293–300. Bermingham A, Derrick JP. (2002). The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery. BioEssays 24: 637–648. Booker SJ. (2004). Unraveling the pathway of lipoic acid biosynthesis. Chem Biol 11: 10–12. Fischer M, Bacher A. (2005). Biosynthesis of flavocoenzymes. Nat Prod Rep 22: 324–350. Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T. (2007). Two independent routes of de novo vitamin B6 biosynthesis: not that different after all. Biochem J 407: 1–13. Guillén-Navarro K, Encarnación S, Dunn MF. (2005). Biotin biosynthesis, transport and utilization in rhizobia. FEMS Microbiol Lett 246: 1591–1565. Jurgenson CT, Begley TP, Ealick SE. (2009). The structural and biochemical foundations of thiamin biosynthesis. Annu Rev Biochem 78: 569–603. Martens JH, Barg H, Warren MJ, Jahn D. (2002). Microbial production of vitamin B12. Appl Microbiol Biotechnol 58: 275–285. Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. (2009). Vitamin B6: a long known compound of surprising complexity. Molecules 14: 329–351. Streit WR, Entcheva P. (2003). Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production. Appl Microbiol Biotechnol 61: 21–31. Sullivan JT, Brown SD, Yocum RR, Ronson CW. (2001). The bio operon on the acquired symbiosis island of Mesorhizobium sp. strain R7A includes a novel gene involved in pimeloyl-CoA synthesis. Microbiol-SGM 147: 1315–1322. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B et al. (2010). The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4: 61–77. - 33 - Table S 7. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted integrases, transposases, subunits of the gene transfer agent (GTA) and genes of the NRPS/PKS cluster as well as the tdaA-tdaF locus involved in tropodithietic acid (TDA) synthesis. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Absence of a gene name indicates that no assignment was made due to missing of this parameter for the respective genes. For the NRPS/PKS cluster, sequence similarity to the genes of the colibactin producing E. coli CFT073 strain is given. Locus FO-BEG1 Locus JE062 PSE_2457 PSE_2458 PSE_2459 PSE_2460 PSE_2461 PSE_2462 PJE062_203 PJE062_274 PJE062_167 PJE062_351 PJE062_207 PJE062_422 PSE_2463 ─ PSE_2464 PSE_2465 PSE_2466 PSE_2467 PSE_2468 PSE_2469 PSE_2470 ─ PJE062_282 PJE062_363 ─ ─ PJE062_443 PJE062_201 PSE_2471 PJE062_275 PSE_2472 PJE062_117 PSE_2473 PJE062_155 PSE_0066 PSE_0453 PSE_0457 PSE_0623 PSE_0748 PSE_1819 PSE_3013 PSE_3106 PSE_3107 PSE_3108 PSE_3364 PSE_3365 PSE_3929 PSE_4169 ─ ─ ─ ─ PJE062_3298 PJE062_3485 ─ PJE062_2786 PJE062_2951 ─ PJE062_3594 ─ ─ ─ ─ ─ PJE062_5158 PJE062_1148 PJE062_1677 PJE062_1028 PJE062_507 PJE062_4173 Product GTA Phage DNA Packaging Protein Phage portal protein, HK97 hypothetical protein hypothetical protein Peptidase U35, phage prohead HK97 Phage major capsid protein, HK97 family Phage conserved hypothetical protein, phiE125 gp8 Phage head-tail adaptor conserved hypothetical protein Phage major tail protein, TP901-1 family Gene transfer agent (GTA) like protein Conserved hypothetical phage protein Phage minor tail protein Gene transfer agent protein Phage conserved hypothetical protein BR0599 Phage cell wall peptidase, NlpC/P60 Gene transfer agent (GTA) orfg15, like protein Integrases Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Phage integrase family Gene Table S 7. Continued Locus FO-BEG1 Locus JE062 PSE_1176 PSE_1177 PSE_1204 PSE_1205 PSE_2059 PSE_2315 PSE_2316 PSE_3120 PSE_3121 PSE_3337 PSE_3338 PSE_3339 ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ PSE_3340 ─ PSE_3341 ─ PSE_3342 ─ PSE_3344 ─ PSE_3345 ─ PSE_3361 PSE_3362 PSE_4189 PSE_p0146 ─ ─ ─ ─ ─ PJE062_3174 Locus FO-BEG1 Locus JE062 PSE_3317 PSE_3318 PSE_3319 PSE_3320 ─ ─ ─ ─ PSE_3321 PJE062_617* PSE_3322 PJE062_571* PSE_3323 PJE062_611* PSE_3324 PSE_3325 ─ ─ PSE_3326 ─ PSE_3327 ─ PSE_3328 PSE_3329 PSE_3330 ─ ─ ─ Product Gene Transposases ISCc3, transposase OrfA ISCc3, transposase OrfB ISCc3, transposase OrfB ISCc3, transposase OrfA Transposase ISCc3, transposase OrfA ISCc3, transposase OrfB ISCc3, transposase OrfA ISCc3, transposase OrfB ISCc3, transposase OrfA ISCc3, transposase OrfB ISCc3, transposase OrfB Transposon Tn7 transposition protein TnsE Transposon Tn7 transposition protein TnsD Transposon Tn7 transposition protein TnsC Transposon Tn7 transposition protein TnsB Transposon Tn7 transposition protein TnsA ISCc3, transposase OrfA ISCc3, transposase OrfB Transposase Transposase IS4 family protein Transposase Product NRPS-PKS 4'-phosphopantetheinyl transferase Cadicidin biosynthesis thioesterase Beta-lactamase class C Polyketide synthase Protein containing DUF214, permase predicted Protein containing DUF214, permase predicted Lipoprotein-releasing system ATP-binding protein LolD Secretion protein HlyD Non-ribosomal peptide synthetase Multi antimicrobial extrusion protein MatE Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit Peptide synthetase Non-ribosomal peptide synthetase Polyketide synthase - 35 - tnsE tnsD tnsC tnsB tnsA Gene hetI Evalue / identity [%] to E. coli CFT073 ─ 8.0E-56 / 44% 1.0E-53 / 34% 4.0E-103 / 43% ─ ─ lolD hlyD ─ ─ 2.0E-145 / 34% 4.0E-78 / 49% 2.0E-89 / 43% 0.0 / 43% 0.0 / 38% 0.0 / 51% Table S 7. Continued Locus FO-BEG1 Locus JE062 Product PSE_3331 PSE_3332 PSE_3333 PSE_3334 PSE_3335 PSE_3336 ─ ─ ─ ─ ─ ─ Non-ribosomal peptide synthase Acyl-CoA dehydrogenase domain protein Hypothetical protein 3-hydroxybutyryl-CoA dehydrogenase Polyketide synthase Polyketide synthase PSE_p0217 PJE062_3951 Gene hbd Evalue / identity [%] to E. coli CFT073 0.0 / 39% 3.0E-79 / 50% 2.0E-12 / 56% 1.0E-85 / 64% 1.0E-178 / 44% 0.0 / 40% ─ Type I polyketide synthase Genes marked with * encode an ABC transporter PSE_2264 PJE062_934 PSE_2263 PSE_2261 PSE_2260 PSE_2259 PSE_2247 PJE062_697 PJE062_802 PJE062_828 PJE062_841 PJE062_775 PSE_1790 PJE062_343 PSE_1788 PJE062_430 PSE_1798 PJE062_190 PSE_1673 PSE_4373 PSE_1234 PJE062_253 PJE062_4989 PJE062_4367 a)Genes Genes presumably involved in TDA biosynthesisa) Transcriptional regulator, LysR family protein Glutathione S-transferase domain YwfB thioesterase superfamily protein acyl-CoA dehydrogenase domain protein Flavoprotein phenylacetic acid degradation oxidoreductase PaaK phenylacetate-CoA oxygenase, PaaI subunit Phenylacetate-CoA oxygenase, PaaJ subunit betaC-S lyase sulfite oxidase subunit YedY sulfite reductase (NADPH) protein tdaA tdaB tdaC tdaD tdaE tdaF paaK paaI paaJ malY tdaH cysI ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ presumably involved in the production of tropodithietic acid (TDA) Information about the involved genes was taken from Geng and Belas (2010) and Geng et al. (2008) References Geng HF, Belas R. (2010). Expression of tropodithietic acid biosynthesis is controlled by a novel autoinducer. J Bacteriol 192: 4377–4387. Geng HF, Bruhn JB, Nielsen KF, Gram L, Belas R. (2008). Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. Appl Environ Microbiol 74: 1535–1545. Table S 8. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted proteins presumably involved in attachment, protein-protein interactions and predicted LuxR transcriptional regulators. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. For luxR homologues, the presence of an amino-terminal autoinducer-binding or response regulatory domain is indicated with a ‘+’. Absence of a gene name or an EC number indicates that no assignment was made due to missing of these parameters for the respective genes. Locus FO-BEG1 PSE_0544 PSE_2079 PSE_3116 Locus JE062 PJE062_2814 ─ ─ PSE_0098 PSE_0865 PSE_1079 PSE_1686 PJE062_3465 PJE062_3032 PJE062_4509 PJE062_118 PSE_2479 PJE062_323 PSE_2694 PSE_3163 PSE_3476 PJE062_4181 PJE062_1441 ─ PSE_3705 PJE062_1339 PSE_4003 PSE_4676 PSE_4741 PSE_4770 PSE_4880 PSE_p0011 PJE062_4620 PJE062_2205 PJE062_2047 PJE062_2250 PJE062_2166 PJE062_3638 PSE_0262 PJE062_3497 PSE_1737 PJE062_108 PSE_1793 PJE062_380 PSE_2549 PJE062_4185 PSE_3010 PJE062_1367 PSE_4219 PJE062_4679 PSE_4221 PJE062_5026 PSE_4700 PJE062_2257 Product Gene EC ORFs containing ankyrin repeat domainsa) ankyrin repeat protein ankyrin repeat protein ankyrin repeat protein ORFs containing tetratricopeptide repeat domainsa) Thioredoxin Methyltransferase type 12 Tetratricopeptide repeat protein Tetratricopeptide repeat protein Cytochrome c-type biogenesis protein CycH Tetratricopeptide repeat protein Tetratricopeptide repeat protein peptidase M48, Ste24p type III secretion system chaperone protein B Tetratricopeptide repeat protein Tol-Pal system YbgF Tetratricopeptide repeat protein Tetratricopeptide repeat protein HemY domain protein Methyltransferase type 12 ORFs containing Sel1 domainsa) Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein Sel1 domain protein repeat-containing protein - 37 - 2.1.1.- cycH hemY 2.1.1.- Table S 8. Continued Locus FO-BEG1 PSE_1550 PSE_1999 PSE_2098 PSE_2110 PSE_3194 Locus JE062 PJE062_305 PJE062_658 PJE062_650 PJE062_550 PJE062_1243 PSE_4342 PSE_4343 PSE_4344 PJE062_4994 PJE062_4861 PJE062_5083 PSE_4345 PJE062_4741 PSE_4346 PJE062_4746 PSE_1070 PSE_1071 PSE_1072 PSE_1074 PSE_1075 PJE062_4381 PJE062_4395 PJE062_4414 PJE062_4427 PJE062_4478 PSE_1076 PJE062_4469 PSE_2099 PJE062_871 PSE_2111 PJE062_850 PSE_1084 PSE_1085 PJE062_4462 PJE062_4380 Locus FO-BEG1 Locus JE062 PSE_1326 PJE062_1887 PSE_1528 PJE062_237 PSE_1752 PJE062_454 PSE_1756 PJE062_469 PSE_2176 PJE062_945 Product Gene Invasion associated locus Ba) Invasion associated locus B Invasion associated locus B Invasion associated locus B Invasion associated locus B Invasion associated locus B Genes associated with amyloid production Curlin associated repeat Curlin associated repeat Curlin associated repeat Curli production assembly/transport component CsgG Curli production assembly/transport component CsgF tda/cpa locus Type IV leader peptidase family Pilus assembly, Flp-type CpaB bacterial type II/III secretion system protein pilus assembly protein CpaD response regulator receiver protein type II/IV secretion system protein, TadA subfamily EC ialB ialB ialB ialB ialB csgG csgF cpaA cpaB cpaC cpaD cpaE cpaF Genes containing YadA domainsa) protein containing YadA-like, C-terminal domain protein containing YadA-like, C-terminal domain Genes containing TadE-like domainsa) TadE-like protein TadE-like protein Product LuxR transcriptional regulator transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein tadE tadE Gene Presence of a response regulatory domain luxR + luxR Presence of an autoinducer domain + luxR + luxR + luxR + Table S 8. Continued Locus FO-BEG1 Locus JE062 PSE_2420 PJE062_63 PSE_4321 PJE062_5001 PSE_4867 PJE062_2072 PSE_4891 ─ PSE_4980 PJE062_4013 PSE_4981 PJE062_3991 PSE_4982 PJE062_4089 PSE_p0305 PJE062_3930 a) Homologues Product transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein transcriptional regulator, LuxR family protein Gene Presence of a response regulatory domain Presence of an autoinducer domain luxR luxR luxR + luxR luxR luxR luxR luxR of genes presumably involved in attachment and prokaryote-eukaryote interactions Genomes of sponge-associated microorganisms often show an overrepresentation of eukaryotic domains mediating protein-protein interactions, especially ankyrin repeat and tetratricopeptide repeat (TPR) domains containing genes, which are thought to play a role in bacteria-host interactions (Liu et al., 2011; Siegl et al., 2011; Thomas et al., 2010). Genes containing ankyrin or TPR repeat domains could also be identified in the genome of both Pseudovibrio strains. Additionally, we found genes containing YadA and TadE domains, known to be required for binding to host tissue (Hoiczyk et al., 2000) and adherence to surfaces (Kachlany et al., 2001), respectively. Open reading frames containing Sel1 repeats were detected in both Pseudovibrio genomes. Those repeats were found in great abundance in an amoeba symbiont (Schmitz-Esser et al., 2010) and are thought to mediate prokaryoteeukaryote interactions (Mittl and Schneider-Brachert, 2007). We also identified five homologues of “invasion-associated locus B” genes in genomes of strain FO-BEG1 and JE062. In Bartonella bacilliformis the invasion-associated locus B gene (ialB) was shown to have a direct role in human erythrocyte parasitism and was needed for adherence and invasion of the erythrocytes by the bacterium (Coleman and Minnick, 2001). In summary, we identified a number of different protein homologues and genes with repeat motifs assumed to be involved in prokaryote-eukaryote interactions, supporting the proposed role of Pseudovibrio as a symbiont with possibilities to attach, invade and interact with the host organism. - 39 - References Coleman SA, Minnick MF. (2001). Establishing a direct role for the Bartonella bacilliformis invasion-associated locus B (IalB) protein in human erythrocyte parasitism. Infect Immun 69: 4373–4381. Hoiczyk E, Roggenkamp A, Reichenbecher M, Lupas A, Heesemann J. (2000). Structure and sequence analysis of Yersinia YadA and Moraxella UspAs reveal a novel class of adhesins. EMBO J 19: 5989–5999. Kachlany SC, Planet PJ, DeSalle R, Fine DH, Figurski DH. (2001). Genes for tight adherence of Actinobacillus actinomycetemcomitans: from plaque to plague to pond scum. Trends Microbiol 9: 429–437. Liu MY, Kjelleberg S, Thomas T. (2011). Functional genomic analysis of an uncultured δproteobacterium in the sponge Cymbastela concentrica. ISME J 5: 427–435. Mittl PRE, Schneider-Brachert W. (2007). Sel1-like repeat proteins in signal transduction. Cell Signal 19: 20–31. Schmitz-Esser S, Tischler P, Arnold R, Montanaro J, Wagner M, Rattei T et al. (2010). The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J Bacteriol 192: 1045–1057. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang CG et al. (2011). Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5: 61–70. Thomas T, Rusch D, DeMaere MZ, Yung PY, Lewis M, Halpern A et al. (2010). Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J 4: 1557–1567. Table S 9. Genes detected in the genomes of Pseudovibrio sp. FO-BEG1 and JE062 coding for predicted subunits of the type III and type VI secretion systems. Genes that could not be detected in the not closed genome of strain JE062 are indicated with ‘─’. Absence of a gene name indicates that no assignment was made due to missing of this parameter for the respective genes. For the type III secretion system, sequence similarity to the best SwissProt hit is given. Locus FO-BEG1 Locus JE062 PSE_2750 PSE_3453 PSE_3455 PSE_3456 PJE062_4298 PJE062_1387 PJE062_1601 PJE062_1751 PSE_3677 PJE062_1314 PSE_3678 PSE_3679 PSE_3680 PSE_3681 PSE_3682 PSE_3683 PSE_3684 PSE_3685 PSE_3686 PSE_3687 PSE_3688 PSE_3689 PSE_3690 PSE_3691 PSE_3692 PSE_3693 PSE_3694 PSE_3695 PSE_3696 PSE_3697 PSE_3698 PSE_3699 PSE_3700 PSE_3701 PSE_3702 PSE_3703 PSE_3704 ─ PJE062_1029 PJE062_1817 PJE062_1687 PJE062_1490 PJE062_1016 PJE062_1246 PJE062_1406 PJE062_1474 PJE062_1036 PJE062_1156 PJE062_996 PJE062_1724 PJE062_1825 PJE062_1134 PJE062_1461 PJE062_969 PJE062_1844 PJE062_1796 PJE062_1006 PJE062_1665 PJE062_991 PJE062_1656 PJE062_1486 PJE062_1647 PJE062_962 PJE062_1171 PSE_3705 PJE062_1339 PSE_3706 PSE_3707 PSE_3708 PSE_3709 PJE062_1315 ─ PJE062_1165 PJE062_1353 PSE_3710 ─ Product Type III secretion system Inositol phosphate phosphatase IpgD Protein kinase YpkA Protein kinase YpkA Protein kinase YpkA Low calcium response locus protein D (LcrD) hypothetical protein dienelactone hydrolase and related enzymes Yop proteins translocation protein U Yop proteins translocation protein T Yop proteins translocation protein S Yop proteins translocation protein R Yop proteins translocation protein Q hypothetical protein hypothetical protein Yop proteins secretion ATPase Yop proteins translocation protein L hypothetical protein Yop proteins translocation J hypothetical protein hypothetical protein hypothetical protein hypothetical protein hypothetical protein hypothetical protein Yop proteins translocation protein C hypothetical protein hypothetical protein hypothetical protein Tetratricopeptide region hypothetical protein hypothetical protein hypothetical protein type III secretion system chaperone protein B hypothetical protein hypothetical protein hypothetical protein hypothetical protein membrane-bound Yop targeting protein YopN - 41 - Gene Evalue / identity [%] to SwissProt Hit ipgD ypkA ypkA ypkA 5.0E-18 / 27% 5.0E-11 / 26% 4.0E-10 / 26% 2.0E-12 / 28% yscV 0.0 / 54% yscU yscT yscS yscR yscQ 4.0E-62 / 41% 8.0E-22 / 38% 2.0E-5 / 52% 8.0E-49 / 57% 0.0060 / 30% yscN yscL 2.0E-147 / 66% 8.0E-9 / 26% yscJ 1.0E-42 / 47% yscC 1.0E-8 / 24% escB *1.0E-5 / 27% yopN *6.0E-14 / 25% Table S 9. Continued Locus FO-BEG1 Locus JE062 PSE_3711 PSE_3712 PSE_3713 PSE_3714 PSE_3715 ─ PJE062_1659 PJE062_1450 PJE062_1254 PJE062_1816 PSE_4190 ─ Product hypothetical protein Cyclic nucleotide-binding domain hypothetical protein hypothetical protein Yop proteins translocation protein D Effector protein YopJ (Virulence factor YopJ) Gene Evalue / identity [%] to SwissProt Hit yscD 0.045 / 21% yopJ 6.0E-22 / 29% * No SwissProt Hit, BlastP Hit instead PSE_1854 PSE_1855 PJE062_773 PJE062_714 PSE_1856 PJE062_893 PSE_1857 PJE062_506 PSE_1858 PJE062_730 PSE_1859 PJE062_884 PSE_1860 PJE062_596 PSE_1861 PJE062_492 PSE_1862 PJE062_933 PSE_1863 PJE062_502 PSE_1864 PSE_1865 PJE062_588 PJE062_641 Type VI secretion system cluster I ImpA domain protein Type VI secretion protein IcmF type VI secretion protein, VC_A0107 family type VI secretion protein EvpB type VI secretion system, lysozyme-related protein type VI secretion protein, VC_A0110 family type VI secretion protein, VC_A0111 family FHA domain protein type VI secretion lipoprotein, VC_A0113 family type VI secretion protein, VC_A0114 family type IV / VI secretion system DotU ATPase, type VI secretion system ClpV1 PSE_2844 PJE062_1121 Type VI secretion system cluster II Type VI secretion protein IcmF PSE_2845 PJE062_1271 PSE_2846 PJE062_1112 PSE_2847 PJE062_1027 PSE_2848 PSE_2849 PSE_2850 PSE_2851 PSE_2852 PJE062_1673 PJE062_1460 PJE062_1178 PJE062_1054 PJE062_1408 PSE_2853 PJE062_1012 PSE_2854 PSE_2855 PJE062_1728 PJE062_1703 PSE_2856 PJE062_1167 PSE_2857 PJE062_1049 Type IV / VI secretion system, DotU/OmpA/MotB type VI secretion protein, VC_A0114 family type VI secretion lipoprotein, VC_A0113 family FHA domain protein hypothetical protein hypothetical protein Rhs element Vgr protein hypothetical protein type VI secretion protein, EvpB/VC_A0108 family voltage-gated sodium channel ATPase, type VI secretion system ClpV1 type VI secretion protein, VC_A0111 family type VI secretion protein, VC_A0110 family impA icmF evpB fha dotU clpV1 icmF dotU/o mpA/mo tB fha clpV1 Table S 9. Continued Locus FO-BEG1 Locus JE062 PSE_2858 PJE062_1774 PSE_2859 PSE_2860 PSE_2861 PSE_2862 PSE_2863 PJE062_1348 PJE062_988 PJE062_1094 PJE062_1199 PJE062_1550 PSE_p0119 PSE_p0120 PSE_p0121 ─ ─ ─ PSE_p0122 ─ PSE_p0123 PSE_p0124 ─ ─ PSE_1192 PJE062_748 PSE_1193 PSE_1194 PSE_1195 ─ ─ PJE062_528 PSE_1196 PJE062_779 Product Gene type VI secretion system lysozyme-related protein virulence protein, SciE type SciM protein Cytoplasmic protein SciI Cytoplasmic protein SciH ImpA domain protein sciE sciM sciI sciH impA Rhs-family protein hypothetical protein FHA domain protein type VI secretion system Vgr family protein hypothetical protein Type VI secretion system effector, Hcp1 Type VI secretion system effector, Hcp1 family ypothetical protein hypothetical protein hypothetical protein Type VI secretion system Vgr family protein - 43 - rhs fha vgr hcp1 hcp1 vgr Evalue / identity [%] to SwissProt Hit
