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

BMC Genomics

Table 3 Type and location of tRNA modifications of representative organisms belonging to the three domains of life Archaea (A), Eubacteria (B) and Eukarya (E)

Kingdom Position	A	B	B	E	E (B)
	H. volcanii	M. capricolum.	E. coli	S. cerevisiae	S. cer (mito)
10	m²G/m²₂G			m²G	-
12	-			ac⁴C	-
13	Ψ		Ψ	Ψ	-
15	G+				-
17/20	-	D	D	D	D
22	Ψ				-
26	m²G/m²₂G			m²G/m²₂G, Ψ	m²G/m²₂G
28	Ψ			Ψ	Ψ
31	-			Ψ	Ψ
32	-		Ψ	Ψ	Ψ
32	Cm		Cm, Um	Cm, Ψ, m3C	-
34	Cm, ?s ² U	Cm, Um, s²U	Um, s ² U	Cm,Um,Gm,s ² U	-
34	?mc m⁵U	cmn m⁵U	mn m⁵U	mc m⁵U	cmn m⁵U
34	C, U	k²C	k²C, cmo⁵U	cm⁵U, m⁵C	U*?
34	ac⁴C	I	ac⁴C, I	I	-?
37	-	m⁶A	m⁶A, ms²i⁶A	i⁶A	i⁶A
37	m ¹ G, t ⁶ A	m ¹ G, t ⁶ A	m ¹ G, t ⁶ A, m ⁶ t ⁶ A	m ¹ G, t ⁶ A	m ¹ G, t ⁶ A
37	-			m¹I, yW	-
38	Ψ		Ψ	Ψ	Ψ
39	Ψ	Ψ	Ψ	Ψ	Ψ
39	m ⁵ C, U _m				-
40	m⁵C		Ψ	m⁵C	-
47	-		acp³U	D	-
48	m⁵C			m⁵C	-
49	m⁵C			m⁵C	-
52	Ψ				-
54	Ψ, m ¹ Ψ		m⁵U	m⁵U	m⁵U
55	Ψ	Ψ	Ψ	Ψ	Ψ
56	C _m				-
57	m ¹ I				-
58	-			m¹A	-
72	-				Ψ

For H. volcanii and yeast mitochondria [S. cer(mito)] all modifications are listed whereas for E. coli, M. capricolum and yeast cytoplasm those that are relevant for the comparison are indicated (for more details see [4]); modifications present in A,B,E are in bold; modification that appear specific to H. volcanii (and most certainly to Archaea) are in underlined bold and.

ISSN: 1471-2164