Table S1 PCR Primers Used in This Study

1SUPPLEMENTARY MATERIALS 2 3Table S1 PCR primers used in this study 4 5 Target gene and primer Sequence (from 5' to 3')a 6 7 Downstream region of dfdC for Rhodococcus sp. YK2 8 up GTGCTTGCCTTCGGAAGGCCC 9 down CAGGGTCCCGGAACGGGAA 10 Coding region of luxAB 11 luxAB-5' w/StuI-KpnI-PmaCI AGGCCTTGGTACCCACGTGAAATTTGGAAACTTCCTTC 12 luxAB-3' w/StuI-XbaI AGGCCTTCTAGATTACGAGTGGTATTTGACGATG 13 Chloramphenicol-resistance gene of pRF30 14 RfCm-5' w/NcoI CCATGGGTGCTCTCTGCACATCGTTAGC 15 RfCm-3' w/NcoI CCATGGCTTCGCGGTGACGGCGGATCG 16 dfdR-disruption 17 ORF4 single-5' GGAGTCGAGTCGAGAAGGA 18 ORF4 single-3' GGCATTGTAATATCCGCGTATC 19 dfdR 20 ORF4-5' upstream w/SpeI GGACTAGTAATATATGCCCTGACCTCACGG- 21 TCAGGGGTCATTTAATTCCCGGTTTTCATGCAC 22 ORF4-3' w/SpeI GGACTAGTTCATGCCAGCCATTTGG 23 dfdR-ORF 24 dfdR-ORF-5' w/PmaCI CACGTGAGTGAGGTGGCAACCTCCAGTA 25 dfdR-ORF-3' w/XbaI TCTAGAATCATGCCAGCCATTTGGCGACTG

26 PdfdA1 27 PdfdA1(-481)-5' w/KpnI GGGTACCGGGTCCTCGCGAT 28 PdfdA1-3' w/SfoI CGGCGCCCATTGTTGCCTCCATTCCTA

29 PdfdA1-upstream probe for EMSA 30 Ap-5' (-180) CCTTCGGTGGTGAGCGA 31 Ap-3' (+1) TGCGTTGAGTGTTACATCA

32 PdfdA1-downstream probe for EMSA 33 Ap-5' (-34) CACGACGGCTGCGGTGTGAT 34 Ap-3' (+172) TGTTGCCTCCATTCCTAGCTTCAGTT

35 PdfdB-promoter cassette (5'-with SpeI and 3'-with PmaCI, XbaI, EcoRV, and SpeI) 36 PdfdB-5' w/SpeI GGACTAGTAATATATGCCCTGACCTCACGG- 37 TCAGGGGTCATTTCGTCAGGGGCTTCCGAAC 38 PdfdB-3' w/SpeI GGACTAGTATAGGTCACTCGCGAGTGAAAA- 39 GAAGATATCTCTAGACACGTGGGCCTCCCCTTTC 40 Primer extension analysis of dfdA1 41 RTdfdA1-5'-Texas Red CTCACCAGTTGACCACTGTCATTCA 42 43a Restriction endonuclease recognition sequences and ribosomal RNA gene terminator sequences 44introduced in the primers are indicated by underlines and dotted underlines, respectively.

1 1 1 2Table S2 Characterization of deduced ORFs of dfd-gene cluster in dibenzofuran-utilizing 3actinomycetes 4 5 6 Gene Lengtha Relative gene and its function Source microorganismb %-Identityc Accession number 7 8 Terrabacter sp. YK3 9 orf1 179 probable integrase/recombinase Rhodococcus sp. RHA1 73 (107/145) ABH00294 10 dfdA1 474 Alpha subunit of DF dioxygenase, dfdA1 Terrabacter sp. YK3 100 (474/474) BAC06602 11 dfdA2 179 Beta subunit of DF dioxygenase, dfdA2 Terrabacter sp. YK3 100 (179/179) BAC06603 12 dfdA3 123 Ferredoxin component of DF dioxygenase, dfdA3 Terrabacter sp. YK3 100 (123/123) BAC06604 13 dfdA4 407 Ferredoxin reductase component of 14 DF dioxygenase, dfdA4 Terrabacter sp. YK3 100 (407/407) BAC06605 15 orf6 429 ISMsm4, transposase M. smegmatis MC2 155 36 (159/433) ABK69943 16 orf7 473 conserved hypothetical protein, Tfu 1701 Thermobifida fusca YX 31 (142/452) AAZ55736 17 orf8 245 regulatory protein Janthinobacterium sp. J3 31 (76/239) BAC56739 18 orf9 507 hypothetical protein Nocardioides sp. DF412 64 (323/504) BAG06222 19 orf10 309 Putative transposase (Fragment) Rhodococcus sp. YK2 100 (225/225) BAC00788 20 dfdB 308 Extradiol dioxygenase, dfdB Rhodococcus sp. YK2 100 (308/308) BAC00789 21 dfdC 280 Hydroxylase, dfdC Rhodococcus sp. YK2 100 (280/280) BAC00790 22 orf13 402 putative GAF sensor protein, Mvan_3991 M. vanbaalenii PYR-1 36 (106/291) ABM14768 23 24 Rhodococcus sp. YK2 25 orf0 172 probable integrase/recombinase Rhodococcus sp. RHA1 73 (101/138) ABH00294 26 dfdA1 474 Alpha subunit of DF dioxygenase, dfdA1 Nocardioides sp. DF412 98 (468/474) BAG06223 27 dfdA2 179 Beta subunit of DF dioxygenase, dfdA2 Terrabacter sp. YK3 100 (179/179) BAC06603 28 dfdA3 123 Ferredoxin component of DF dioxygenase, dfdA3 Terrabacter sp. YK3 100 (123/123) BAC06604 29 dfdA4 407 Ferredoxin reductase component of 30 DF dioxygenase, dfdA4 Terrabacter sp. YK3 100 (407/407) BAC06605

31 orf1YK2 225 Putative transposase (Fragment) Rhodococcus sp. YK2 100 (225/225) BAC00788 32 dfdB 308 Extradiol dioxygenase, dfdB Rhodococcus sp. YK2 100 (308/308) BAC00789 33 dfdC 280 Hydroxylase, dfdC Rhodococcus sp. YK2 100 (280/280) BAC00790

34 orf4YK2 402 putative GAF sensor protein, Mvan_3991 M. vanbaalenii PYR-1 36 (106/291) ABM14768 35 36a Number of amino acids in the deduced ORF. 37b Organism abbreviations: M. smegmatis, Mycobacterium smegmatic and M. vanbaalenii, 38Mycobacterium vanbaalenii. 39c Identity obtained by BLASTP analysis. 40 41

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