Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure.
T. brucei survival relies on the expression of mitochondrial genes, most of which require RNA editing to become translatable. In trypanosomes, RNA editing involves the insertion and deletion of uridylates, a developmentally regulated process directed by guide RNAs (gRNAs) and catalyzed by the editosome, a complex of proteins. The pathway for mRNA/gRNA complex formation and assembly with the editosome is still unknown. Work from our laboratory has suggested that distinct mRNA/gRNA complexes anneal to form a conserved core structure that may be important for editosome assembly. The secondary structure for the apocytochrome b (CYb) pair has been previously determined and is consistent with our model of a three-helical structure. Here, we used cross-linking and solution structure probing experiments to determine the structure of the ATPase subunit 6 (A6) mRNA hybridized to its cognate gA6-14 gRNA in different stages of editing. Our results indicate that both unedited and partially edited A6/gA6-14 pairs fold into a three-helical structure similar to the previously characterized CYb/gCYb-558 pair. These results lead us to conclude that at least two mRNA/gRNA pairs with distinct editing sites and distinct primary sequences fold to a three-helical secondary configuration that persists through the first few editing events.
Reifur
Larissa
L
Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA.
Koslowsky
Donna J
DJ
D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D045303:Cytochromes b / Q000737:chemistry / Q000378:metabolism; D025261:Mitochondrial Proton-Translocating ATPases / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015800:Protozoan Proteins; D017393:RNA Editing; D017394:RNA, Guide, Kinetoplastida / Q000737:chemistry* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry* / Q000378:metabolism; D014346:Trypanosoma brucei brucei / Q000201:enzymology / Q000235:genetics*
D015800:Protozoan Proteins; D012333:RNA, Messenger; D016053:RNA, Protozoan; D045303:Cytochromes b; C412204:ATP synthase subunit 6; D025261:Mitochondrial Proton-Translocating ATPases; D017394:RNA, Guide, Kinetoplastida
Methods. 1999 May;18(1):51-9
10208816
Nucleic Acids Res. 1987 Nov 11;15(21):8783-98
3684574
Nucleic Acids Res. 1990 Jul 11;18(13):3803-11
2374709
J Biol Chem. 2005 Jan 28;280(4):2429-38
15504736
RNA. 2001 Dec;7(12):1793-802
11780635
Nucleic Acids Res. 2001 Jul 15;29(14):2950-62
11452020
Nucleic Acids Res. 1987 Nov 25;15(22):9109-28
2446263
Cell. 2006 Aug 25;126(4):701-11
16923390
J Mol Biol. 2006 Jun 9;359(3):585-96
16631792
Methods Enzymol. 1989;180:192-212
2482414
J Biol Chem. 1997 Feb 7;272(6):3749-57
9013632
Nat Struct Biol. 1997 Aug;4(8):644-9
9253414
Nucleic Acids Res. 2002 Jan 15;30(2):447-55
11788706
Methods Mol Biol. 2004;265:161-97
15103074
Cell. 1990 Jun 1;61(5):871-8
2160860
Mol Cell Biol. 2000 Nov;20(22):8447-57
11046141
Cell. 1992 Aug 7;70(3):459-67
1379519
RNA. 2006 Jul;12(7):1219-28
16690999
Nucleic Acids Res. 1981 Oct 10;9(19):5125-40
7031604
RNA. 2001 Dec;7(12):1803-16
11780636
J Am Soc Mass Spectrom. 2003 Jul;14(7):728-35
12837594
Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760-4
377283
Int J Parasitol. 2008 Jul;38(8-9):901-12
18295767
Mol Cell Biol. 2001 Feb;21(3):884-92
11154275
J Photochem Photobiol B. 1998 Feb;42(2):109-24
9540218
EMBO J. 1996 Dec 2;15(23):6758-65
8978701
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
15123812
J Mol Biol. 1996 Dec 20;264(5):863-77
9000617
Nucleic Acids Res. 1999 Feb 1;27(3):778-87
9889273
Biochemistry. 2004 Dec 21;43(50):15822-37
15595837
Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22
7524072
J Mol Biol. 1991 Sep 5;221(1):293-308
1717695
Methods Enzymol. 2007;424:3-24
17662834
RNA. 1999 May;5(5):656-69
10334336
Cell. 1988 Oct 21;55(2):267-72
2844415
Mol Cell Biol. 1996 Apr;16(4):1410-8
8657114
EMBO J. 1997 Jul 1;16(13):4069-81
9233816
RNA. 2003 Jan;9(1):62-76
12554877
Cell. 1990 Jul 27;62(2):391-7
1695552
Mol Cell Biol. 1997 Sep;17(9):5377-85
9271415
Cell. 1990 Jun 1;61(5):885-94
2140530
RNA. 2006 Jun;12(6):1038-49
16611942
RNA. 2006 Jul;12(7):1292-303
16691000
RNA. 2006 Jun;12(6):1050-60
16618968
Nucleic Acids Res. 2001 Feb 1;29(3):703-9
11160892
Methods Enzymol. 1989;180:51-62
2482430
EMBO J. 1990 Dec;9(12):4111-8
1701142
Science. 1996 Aug 30;273(5279):1189-95
8703045
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337
Nat Rev Mol Cell Biol. 2004 Nov;5(11):908-19
15520810
Cell. 1991 Nov 1;67(3):537-46
1718605
RNA. 1997 Sep;3(9):1052-67
9292503
Mol Cell Biol. 2008 Jan;28(1):122-30
17954557
Cell. 1990 Jan 26;60(2):189-98
1688737
RNA. 2003 Mar;9(3):265-76
12591999
RNA. 2004 Feb;10(2):159-70
14730014
Proc Natl Acad Sci U S A. 1983 Jul;80(13):3903-7
6306649
J Biol Chem. 1986 Apr 25;261(12):5396-403
2420800
Nucleic Acids Res. 1995 Aug 25;23(16):3093-102
7667084
J Mol Biol. 1989 May 20;207(2):417-31
2754730
Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8901-6
8799125
Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373-7
2432595
Nature. 2005 Mar 17;434(7031):409-13
15772668
Science. 1994 Oct 7;266(5182):114-7
7524149
Nucleic Acids Res. 1997 Jun 15;25(12):2311-8
9171080
EMBO J. 1992 Dec;11(12):4429-38
1330537
Methods Enzymol. 2000;318:136-47
10889985
Cell. 1996 Mar 22;84(6):831-41
8601307
Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1017-22
15657144
RNA. 2008 Jun;14(6):1069-80
18441045
RNA. 1999 Jul;5(7):883-92
10411132
Nucleic Acids Res. 2005 Nov 23;33(20):6610-20
16306234
J Biol Chem. 2007 Feb 16;282(7):4265-4276
17158098
Cell. 2002 Feb 22;108(4):435-8
11909515
RNA Biol. 2004 May;1(1):28-34
17194935
Trends Biochem Sci. 2005 Feb;30(2):97-105
15691655
Biochemistry. 1982 Sep 14;21(19):4700-6
6291588
RNA. 2006 Jan;12(1):83-93
16373494
Mol Biol Rep. 1994 Jul;20(1):35-44
7531281
Nucleic Acids Res. 1991 Jul 11;19(13):3653-60
1712940
Mol Cell. 2003 Aug;12(2):307-19
14536071
Mol Cell Biol. 2002 Mar;22(5):1567-76
11839822
EMBO J. 1997 Dec 15;16(24):7490-9
9405377
Nucleic Acids Res. 1998 Aug 15;26(16):3634-9
9685476