Minutes Figure S1. HPLC separation of nucleosides from LC/ESI-MS analysis of a total enzymatic Trp
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1 100 A % Relative Abundance m m Ø acp 5 m Øm 5 m m 7 m s * 6 ia m * Minutes Figure S1. HPL separation of nucleosides from L/ESI-MS analysis of a total enzymatic digest of mt trna. V detection at 60 nm. The * denotes non-nucleoside artifacts. ensus of modified nucleosides in L. tarentolae mt trna species Identities of all modified nucleosides were determined by L/ESI-MS analysis of a total nucleoside 1 digest of trna with nuclease P1, phosphodiesterase I and bacterial alkaline phosphatase. Identification of nucleosides was based on mass spectra, V absorbance spectra and relative retention times of standard RNA nucleosides determined in a similar solvent system. Mass spectra consist of protonated + molecule (MH ) ions and protonated base H + ions, with the exception of pseudouridine (Ø) and its '-Omethyl analogue (Øm). Pseudouridine nucleosides do not produce base ions due to presence of the stable - glycosidic bond, but instead undergo extensive fragmentation. ihydrouridine () contains no significant + chromophore and therefore gives no V absorbance signal. Its detection is based on mass response (MH, m/z 47) and HPL elution slightly before Ø. A full listing of nucleoside structures, names and abbreviations can be found in ref. 4 or at References 1. rain, P. F. Preparation and enzymatic hydrolysis of RNA and NA for mass spectrometry. Methods Enzymol. 19, (1990).. Pomerantz, S.. & Mcloskey, J. A. Analysis of RNA hydrolysates by mass spectrometry. Methods Enzymol. 19, (1990).. Felden,., et al. Presence and location of modified nucleotides in E. coli tmrna: structural mimicry with trna acceptor branches. EMO J. 17, (1998). 4. Limbach, P. A., rain, P. F. & Mcloskey, J. A. Summary: the modified nucleosides of RNA. Nucleic Acids Res., (1994).
2 A 60 nm 1,4, ,1 1 acp m or m E 15 m 5 F 17 s 0 i 6 A Minutes Figure S. Reconstructed ion chromatograms from L/ESI-MS of a total RNase T1 digest of L. tarentolae trna. Panel A is an expanded version of Figure 1a (main text). Sequence assignments are given in Table S1. Panels -F : diagnostic ions for the base-modified nucleosides known to be present (data shown in Figure S1). Each trace is individually normalized to the most abundant signal. Elevation of the ion source declustering ( ' cone ') voltage above the optimal value causes fragmentation of the oligonucleotides before the mass analyzer stage. Among the ions generated are those of the base - moiety ( ) and cyclic mononucleotides. All modified nucleosides in trna (except ) generate characteristic ions whose time vs. abundance profiles can be aligned with the V peak and ion current from the - corresponding (normal cone voltage) electrospray ionization mass spectra. The dihydrouridine base moiety is not observed, most likely due to extensive fragmentation; the cyclic nucleotide (M H) ion ( m/ z 07) can be used instead. These data are used to determine which RNase T1-derived oligonucleotide peak in 6 panel a contains the indicated modification. For example, s (panel f) and i A (panel g) are the only basemodified nucleosides present in the ~5 min eluant containing the anticodon stem-loop. These data are used in the sequence assignments shown in Table S1 following Simpson Figure S
3 A s s Minutes Figure S. onfirmation of the identity of -thiouridine (s ) in mitochondrial trna ASL 1-mers by L/ESI-MS analysis using base fragment ions for detection, instead of V absorbance (Fig. S1). Panels A, : s and from mt trna ;, : mixture of authentic s and as retention time markers. The 4 retention times of s and s m are and 4.71 min, respectively.
4 Figure S4. Structure of L. tarentolae mt trna in cloverleaf form, as derived from the gene sequence. Arrows indicate predicted RNase T1 cleavage sites. Table S1. Sequence assignments of RNase T1-derived oligonucleotides from L. tarentolae mitochondrial trna species a Oligonucleotide (peak # in Fig. S) Meas. M r (error ) Modified base ion response b 7-Am p-11 (9) 1-Ap-16 (8) (0.0) (0.0) m/z 164, Fig. Sd 17-mp-19 (5) 0-acp Ap- () -Ap-4 (1) 5-Ap-9 (7) 6 c 1-AØmmAi AAØmAp-4 (1) 6 c 1-AØms mai AAØmAp-4 (1) 7 b 46-m p-49 (6) 50-Ap-5 () 100. (0.1) (0.1) 69. (0.1) (0.0) (0.0) (0.0) 15.8 (0.0) 998. (0.0) m/z 07, Fig. Sc m/z 1, Fig. Sb m/z 0, Fig. Sg m/z 17, Fig. Sf & m/z 0, Fig. Sg m/z 164, Fig. Sd 5 d 54-m AAp-64 + H (11) 495. (0.1) m/z 15, Fig. Se 65-Ap-68 (4) 997. (0.1) 68-AA(OH)-76 (10) 74.6 (0.0) a Measured M r - calculated Mr b Nucleoside isomer or sequence location assigned from principles of conserved sequence location of modified nucleosides; for a summary, see Auffinger, P. & Westhoff, E. in Modification and Editing of RNA (eds rosjean, H. & enne, R.) (ASM Press, Washington, 1998). c This oligonucleotide was directly sequenced by mass spectrometry (see main text). d 5 - The trna contains m (Figure S1). Although no released ion was produced, it is present in other measurements (data not shown ).
5 % Relative Abundance A 84 Ømpp (M-H) m/z Figure S6. Product ion spectrum from collision-induced dissociation of m/z 64 from an RNase T digest (alkaline phosphatase omitted) of gel-purified RNase T1-derived trna ASL 1-mers. Similar to the arguments given previously (Figure S5), the structure corresponding to the 18. min HPL eluant (Figs. a & d) is derived from the I mass spectrum to be Ømpp, thus accounting for Øm-9 present in all trna species. The relative molecular mass (M M r 64) of the NmpMp dimer requires presence of the equivalent of cytidine, uridine and one methyl. Placement of as the ' residue is dictated by mz m/z / 40, the pp ion. The absence of any uracil-ribose bond cleavage products, including uracil base (m/z mz 111) reflects presence of pseudouridine in the 5' position, with ribose methylation confirmed by comparison of ions mz m/z / and 7/19. Simple elimination pathways are as noted in Figure S5: loss of cytosine: (path A), H O (), HPO () and H PO (). 4
6 Table S Sequence ions assigned from the collision-induced dissociation mass spectra of anticodon stem-loop 1-mers Ion assignment (charge) m/z (error) a Synthetic A A A A A p a n - (1-) d n -H O (1-) w n (1-) b 44.1(0.0.) b 748.(-0.1) 1054.(-0.1) 159.(0.1) 679.1(0.1) 81.7(0.1) 996.(0.1) c (0.1) 8.1(0.0) 64.1(0.1) 940.(0.1) 6.1(0.0) 774.6(0.1) 99.(0.1) 110.7(0.0) 168.(0.0) 16.7(0.1) 890.8(0.1) 196.7(0.1) 864.1(0.0) 947.1(0.1) 117.(0.0) (0.1) 84.1(0.1) 11.(0.1) 967.7(0.1) 80.(0.1) 181.(0.1) 690.1(0.0) 101.(0.1) 650.1(0.0) (0.1) 57.6(0.1) 771.1(0.1) 44.1(0.1) b 996.(0.1) c 691.(0.1) 6.1(0.0) t precursor A Ψ A i 6 A A Ψm A p a n - (1-) d n -H O (1-) w n (1-) 554.(0.0) d 748.1(0.0) (0.0) 159.(0.0) 679.1(0.0) 81.6(0.0) 995.9(0.) c (0.1) 8.0(0.0) 64.1(0.0) 940.1(0.0) 469.6(0.0) 145.1(0.0) 6.0(0.0) 1550.(0.0) 774.6(0.0) 99.1(0.0) 117.7(0.0) 10.(0.0) 150.(0.0) (0.0) 177.6(0.0) 918.1(0.0) 17.7(0.0) 891.5(0.0) 11.1(0.0) (0.0) 850.1(0.0) 117.(0.0) 974.6(0.0) 810.1(0.0) 181.1(0.0) 690.1(0.0) 101.(0.0) 650.1(0.0) (0.0) 57.5(0.0) 771.7(0.0) 44.0(0.0) 996.1(0.0) c 691.1(0.0) 6.0(0.0) nedited mito A Ψm m A i 6 A A Ψm A p a n - (1-) d n -H O (1-) 568.1(0.0) d 76.1(0.0) 108.(0.0) 187.(0.0) 845.6(0.0) (0.0) 108.7(0.0) 15.(0.0) 101.8(0.0) 8.0(0.0) 648.1(0.0) 954.1(0.0) 17.(0.0) 1578.(0.1) 788.6(0.0) 95.1(0.0) (0.0) 116.(0.0) w n (1-) (0.0) 918.1(0.0) 17.7(0.0) 891.5(0.0) 11.(0.0) (0.0) 850.1(0.0) 117.(0.0) 974.6(0.0) 810.1(0.0) 181.1(0.0) 690.1(0.0) (0.0) 57.5(0.0) 101.(0.0) 996.1(0.0) 691.1(0.0) 6.0(0.0) 771.1(0.0) 44.0(0.0) Edited mito A Ψm s m A i 6 A A Ψm A p a n - (1-) 568.1(0.0) d 76.1(0.0) 701.6(0.0) 854.1(0.0) d n -H O (1-) 8.0(0.0) 648.1(0.0) 970.1(0.0) 644.6(0.0) 797.1(0.0) 961.6(0.0) 1160.(0.0) 14.7(0.0) 989.5(0.0) w n (1-) 177.7(0.0) 918.1(0.0) 11.(0.0) 676.1(0.0) 850.1(0.0) 690.1(0.0) 57.6(0.0) 771.1(0.0) 44.0(0.0) 117.(0.0) 891.5(0.0) 974.6(0.0) 810.1(0.0) a Measured m/z minus calculated m/z for the assignment shown. b Ions w 1 and (a ) differ in mass by 0.06 a, but can be distinguished by isotope spacing if both are present. c y and (a 7 ) have same mass, but isotope pattern indicates both are present. d When pseudouridine is present, (a ) is replaced by a, a simple cleavage equivalent to (d phosphate). 101.(0.0) 996.1(0.0) 691.1(0.0) 6.0(0.0)
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