RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

Grosjean, Henri; Gaspin, Christine; Marck, Christian; Decatur, Wayne A; de Crécy-Lagard, Valérie

doi:10.1186/1471-2164-9-470

BMC Genomics

Table 1 Predictions of H. volcanii tRNA modifications genes

From: RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

Pos.	Mod.	tRNA (see Additional file 1)	Prediction method	Hv orf^a	COG	Comments^b
10	m²G/m²₂G	G1-4/R1, D1, Q1, E1-2, H1, P1-3	Homology with P. abyssi PAB1283*[177]	HVO_0156	1041
13	Ψ	R1, D1, Q1, E1-2, G1-2, H1, Me, Mi, P1-3, S1,T1,V1-2	Homology with E. coli TruD*[178]	HVO_0658	0585	1Z2Z
15	G⁺	R2-3, N1, C1, I2, L1-5, K1-2, Me, Mi, F1, P1, P3, S1-3,T1-2, W1, Y1, V2	Homology with M. jannaschii MJ0436*[87]	HVO_2001	0343	1IQ8
22	Ψ	Me	Cbf5 without Guide RNA?			See text
26	m²G m²₂G	A3, R3, L4/A2,R2,I1-2, L1-3,L5,K1-2,S1-3,T1-2, W1	Homology with P. furiosus protein PF1871*[179]	HVO_0236	1867	2DUL
28	Ψ	I1	Cbf5 without Guide RNA?			See Text
32	Cm	K1-2,W1, Y1	Homology with E. coli protein TrmH*[91].	HVO_2906	0565
34	Cm	Me,W1	aFib +sRNA* [75]			See Additional files 4 and 5
	?mcm ⁵ s ² U?	R3, E2, G2, K2, L5	Homology with yeast Trm9* [180], Elp3* [125]. Tuc1* [123]	HVO_0574 + HVO_2888 + HVO_0580	2226 1243 0037	See text
	cmo ⁵ U	?		?	?	see text
	C*	I2	Prediction this work	HVO_0339 or HVO_0697	1571 or 2047	See text
	ac⁴C	Q1, E1, K1,P1, S1	Prediction this work	HVO_2736	1444	See text
37	t⁶A	N1,I1-2, K1-2, Me not Mi, S3, T1-2	Homology M. maripaludis protein MMP0186*[181]	HVO_0253	0009	2EQA
	m¹G	R1-3, C1, Q1, E2, H1, L1-5, F1, P1-3, W1, Y1	Homology with M. jannaschii MJ0883*[182]	HVO_0929	0336	2FRN
38-40	Ψ₃₈,Ψ₃₉	38 = P1/39 = L2, L4, K1, Me, F1, S1, Y1	Homology with Yeast Pus3* [101]	HVO_1852	0101
39	Um	W1	aFib + sRNA [75]			See Additional file 4
39-40	m⁵C	39 = L1/40 = I1	Homology with P. abyssi PAB1947* [110]	HVO_1594	0144
48,49	m⁵C	Almost all except L4, D1, Q1, H1, Mi	Homology with P. abyssi PAB1947* [110]	HVO_1594	0144
52	Ψ	K1	Cbf5 without sRNA?			See text
54 and 55	Ψ	All	Cbf5 without sRNA? and/or homology to P. furiosus PF1139 (PsuX) [98]	HVO_2493 HVO_1979	0103 1258	See text 2V9K
	m¹Ψ	all except Q1,H1	Prediction [93]	HVO_1989	1901	See text 2QMM
56	Cm	All	Homology with P. abyssi PAB1040* [94]	HVO_1173	1303	2O3A
57	m¹A		Homology with P. abyssi PAB0283* [111]	HVO_1383	2519	1YB2
	m¹I	All harboring A57 except H1	Prediction this work	HVO_2747	1491	See text; 2I5H

^aRefSeq annotation in archaea.ucsc.edu/; ^bif the structure of an Archaeal member of the family is available the PDB code is given ; *Experimentally verified.

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ISSN: 1471-2164

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