Architecture of the Trypanosome RNA Editing Accessory Complex, MRB1

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1 Architecture of the Trypanosome RNA Editing Accessory Complex, MRB1 Michelle L. Ammerman, Kurtis M. Downey, Hassan Hashimi, John C. Fisk, Danielle L. Tomasello, Drahomíra Faktorová, Lucie Hanzálková, Tony King, Julius Lukeš, and Laurie K. Read Supplementary Data: Table S1. Primers used in this study Yeast two hybrid primers Name 5' Primer 3' Primer kpap1 GCGCATATGAGAAAGTTTTCAGCTTTT GCGCTGCAGCTCGAGCTACTGATGAT CGGTC TGTCGCATTTTATCC kpap1 GGAGGCCAGTGAATTCATGAGAAAG CGAGCTCGATGGATCCCTACTGATGA TTTTCAGCTTTTCGGTC TTGTCGCATTTTATCC 7510 AAAAGAGATCGAATTCATGCGGCACA TGCAGGTCGACATCGATGTTATTGTC CAATACC ATCAAGTATATCC 0024 AAAAGAGATCGAATTCATGCGGCGTT TGCAGGTCGACATCGATAACCTTGTC GGCACC CTCGTCGTC PPR5 AAAAGAGATCGAATTCATGCTCCGCC TGCAGGTCGACATCGATATATGCAGT GTAGTGA TCCACAAACCT 3180 AAAAGAGATCGAATTCATGCTTCGCT TGCAGGTCGACATCGATATAGGGGCC GCACTGTT ACTCGTC PPR1 TGTATCGCCGGAATTCATGTTCCAAC TGCAGGTCGACATCGATCTAAACATC GCCGGTTAGTGCTG CGCACCGGCAGC MRB0130 AAAAGAGATCGAATTCATGCGGCGG TGCAGGTCGACATCGATCAAACTTAC TGTTCCTTT CTTCCCTACAG 3900 AAAAGAGATCGAATTCATGAATCGTA TGCAGGTCGACATCGATCACCTTCTT CGGGTGGG GATACCCAGT 5120 AAAAGAGATCGAATTCATGACATCTA TGCAGGTCGACATCGATTTTTTTCTTC GCGTAACC CCCTTGTTCTTTCCT GAP1 TGTATCGCCGGAATTCATGCTGCGC TGCAGGTCGACATCGATCTAGTATGC GCGCGCCTG CGAAACGGCAGTC GAP2 AAAAGAGATCGAATTCATGCTTCGCT TGCAGGTCGACATCGATCAACTTCGC TATTGCGG CTCACAGCC Helicase AAAAGAGATCGAATTCATGCGGGCC TGCAGGTCGACATCGATTTACGAGTC ATACGACTAA TCCACCAGCC MRB11870 AAAAGAGATCGAATTCATGCTGCGCC TGCAGGTCGACATCGATTTATTTCTGC ACACATCACG AGTTGATGCGTC MERS1 AAAAGAGATCGAATTCATGCGCAAGC TGCAGGTCGACATCGATTCACGATGC AATTATTTTTC ATCTTCCCCG MRB1820 AAAAGAGATCGAATTCATGCGAACCC TGCAGGTCGACATCGATCTAGCGGGG AAGGATCCTTCG TATTGCCCC MRB2140 CATGGAGGCCGAATTCATGTTCCGCT GCAGGTCGACGGATCCTCAGGTTAAG GGTCGTGGTG GACGCAGAAACA MRB3010 AAAAGAGATCGAATTCATGCGGAGC TGCAGGTCGACATCGATTGCTTGCGG GCGTTGCG TGTAGACC

2 MRB5390 MRB4160 MRB8620 MRB8170 TbRGG2 TbRGG1 MRB1860 MRB6070 MRB6070 MRB800 MRB10130 MRB8180 MRB1680 MRB1590 MRB0880 AAAAGAGATCGAATTCATGAATGGGA GGCTGTACT AAAAGAGATCGAATTCATGTACCCTT TCATAGAACCTCG CGCGAATTCATGAGTAACCCTTTTGA GAAAGTTGC TGTATCGCCGGAATTCATGCGACGG CTAAGCCTTCTT AAAAGAGATCGAATTCATGAAGCGCA CACCTGTT AAAAGAGATCGAATTCATGGTGTGTA GCACCATC GCGCATATGCTGCTGCCCACTCTCG AGCG TGTATCGCCGGAATTCGATGTAAACC TAAAGTTGTGTGG CGCGAATTCATGTTCAGCGGGCTTCA GCGTGC TGTATCGCCGGAATTCATGCGACGTC GGGTAGTTTTATG GCGCATATGCTCAACGTTCTCTCGAG CACAGC GGAGGCCAGTGAATTCATGTACCGT CTTTATCGTCGGACTGTAG AAAAGAGATCGAATTCATGTGTACAC ACGCGCTCATATC CATGGAGGCCGAATTCATGTACCATC GTGGCTACGGC CGCGAATTCATGAGGAGTAGCCGGG GTATTTTG TGCAGGTCGACATCGATGCGTCTCAA TAGAAGCTG TGCAGGTCGACATCGATCTAATAAAG CACCTTCGCTAACAT CGCGGATCCCTACTTACCACCATCTT GCGACAAC TGCAGGTCGACATCGATCTAACAAAA TACCTTCGCTAACAT TGCAGGTCGACATCGATCACCTTCTG ACTGGCATC TGCAGGTCGACATCGATCTTTCCCAC CAAACTAGG GCGAGATCTATCGATTCACACCAGCT GTAAAGGCGGATTATTCAC TGCAGGTCGACATCGATCTAAGAATC TGATTCTTTAGAGGCTC CGCGGATCCCTAAGAATCTGATTCTTT AGAGGCTC TGCAGGTCGACATCGATCTAAAGCGA TGCTTCGTCAGGT CGCGTCGACTCACATAACTCCGGGAG CAGCTCC CGAGCTCGATGGATCCCTAAACTGCT GTGGCCAG TGCAGGTCGACATCGATTTACGACGT CACCTCACTTACCT GCAGGTCGACGGATCCTCATCTTTTC GCAGTAACGGTCC CGCGGATCCTTACTGTGTACCGTGTT CACCCGC PTP construct primers MRB6070 GAGGGCCCGTTCCAGTAGGGGTGGA GAGCGGCCGCGAATCTGATTCTTTAG MRB5390 GAGGGCCCTGAACGACCAACTGTAC GAGCGGCCGCCGTCTCAATAGAAGC MRB10130 GGAAGCTTCATCCGATCACCTCATGA GAGCGGCCGCCTAACTCCGGGAGCA MRB11870 GAGGGCCCCATAGCAGTTGGCCACG GAGCGGCCGCTTCTGCAGTTGATGC RGG2 3'UTR RNAi construct primers TbRGG2 GAGGATCCAACCCTATTTACGGGAAT GACTCGAGCCCAAAGACAATACGGT TbRGG2 addback construct primers TbRGG2 GGAAGCTTATGAAGCGCACACCTGTT GTCTAGACACCTTCTGACTGGCATC

3 Supplementary Table S2. Likely contaminants associated with MRB1 components identified by LC-MS/MS. MRB10130 likely Unique Amino acid contaminants peptides coverage Tb , % Kinetoplastid membrane protein 11 (KMP-11) Tb , Tb % Tubulin alpha chain Tb , % 40S ribosomal protein S15a, putative Tb % Tubulin beta chain (Beta tubulin) Tb % translation elongation factor eef-1 alpha chain Tb , % RPS3 40S ribosomal protein S3, putative Tb Tb % 28G S acidic ribosomal protein, putative Tb , % ribosomal protein L3, mitochondrial, putative Tb Tb , % 60S ribosomal protein L21E, putative Tb , Tb Tb % enolase Tb , % 60S ribosomal subunit protein L31, putative Tb Tb , % 60S ribosomal protein L18a, putative Tb Tb10.6k , % 60S ribosomal protein L18 Tb Tb , % 60S ribosomal protein L10a Tb Tb , % 60S ribosomal protein L10, putative Tb Tb % heat shock protein 83 Tb , % mitochondrial carrier protein, putative Tb , Tb Tb % mmdh mitochondrial malate dehydrogenase

4 Tb , Tb % Guanine nucleotide-binding protein subunit b- like protein Tb , % 60S ribosomal protein L5, putative Tb Tb % 60S ribosomal protein L4 Tb , Tb , Tb MRB5390 likely contaminants % retrotransposon hot spot (RHS) protein, putative Unique peptides Amino acid coverage % Tubulin beta chain (Beta tubulin) Tb % translation elongation factor eef-1 alpha chain % Tubulin alpha chain Tb % mitochondrial carrier protein, putative Tb , % GAPDH glyceraldehyde 3-phosphate Tb dehydrogenase Tb % short-chain dehydrogenase, putative Tb % mmdh mitochondrial malate dehydrogenase MRB6070 likely Unique Amino acid contaminants peptides coverage Tb % DRBD2 Tb % poly(a)-binding protein % Tubulin alpha chain Tb % expression site-associated gene, putative Tb , % TEF1 elongation factor 1-alpha Tb , Tb % HSP60 chaperonin Hsp60, mitochondrial precursor Tb % putative uncharacterized protein

5 MRB11870 likely Unique Amino Acid containants peptides coverage % Tubulin alpha chain % Tubulin beta chain (Beta tubulin) Tb , % TEF1 elongation factor 1-alpha Tb % hypothetical protein, conserved