title: Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure.
abstract: 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.
authors.affiliation: Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA.
authors.forename: Larissa
authors.initials: L
authors.lastname: Reifur
authors.forename: Donna J
authors.initials: DJ
authors.lastname: Koslowsky
mesh_terms: 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*
chemical_list: 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
references.citation: Methods. 1999 May;18(1):51-9
references.pmid: 10208816
references.citation: Nucleic Acids Res. 1987 Nov 11;15(21):8783-98
references.pmid: 3684574
references.citation: Nucleic Acids Res. 1990 Jul 11;18(13):3803-11
references.pmid: 2374709
references.citation: J Biol Chem. 2005 Jan 28;280(4):2429-38
references.pmid: 15504736
references.citation: RNA. 2001 Dec;7(12):1793-802
references.pmid: 11780635
references.citation: Nucleic Acids Res. 2001 Jul 15;29(14):2950-62
references.pmid: 11452020
references.citation: Nucleic Acids Res. 1987 Nov 25;15(22):9109-28
references.pmid: 2446263
references.citation: Cell. 2006 Aug 25;126(4):701-11
references.pmid: 16923390
references.citation: J Mol Biol. 2006 Jun 9;359(3):585-96
references.pmid: 16631792
references.citation: Methods Enzymol. 1989;180:192-212
references.pmid: 2482414
references.citation: J Biol Chem. 1997 Feb 7;272(6):3749-57
references.pmid: 9013632
references.citation: Nat Struct Biol. 1997 Aug;4(8):644-9
references.pmid: 9253414
references.citation: Nucleic Acids Res. 2002 Jan 15;30(2):447-55
references.pmid: 11788706
references.citation: Methods Mol Biol. 2004;265:161-97
references.pmid: 15103074
references.citation: Cell. 1990 Jun 1;61(5):871-8
references.pmid: 2160860
references.citation: Mol Cell Biol. 2000 Nov;20(22):8447-57
references.pmid: 11046141
references.citation: Cell. 1992 Aug 7;70(3):459-67
references.pmid: 1379519
references.citation: RNA. 2006 Jul;12(7):1219-28
references.pmid: 16690999
references.citation: Nucleic Acids Res. 1981 Oct 10;9(19):5125-40
references.pmid: 7031604
references.citation: RNA. 2001 Dec;7(12):1803-16
references.pmid: 11780636
references.citation: J Am Soc Mass Spectrom. 2003 Jul;14(7):728-35
references.pmid: 12837594
references.citation: Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760-4
references.pmid: 377283
references.citation: Int J Parasitol. 2008 Jul;38(8-9):901-12
references.pmid: 18295767
references.citation: Mol Cell Biol. 2001 Feb;21(3):884-92
references.pmid: 11154275
references.citation: J Photochem Photobiol B. 1998 Feb;42(2):109-24
references.pmid: 9540218
references.citation: EMBO J. 1996 Dec 2;15(23):6758-65
references.pmid: 8978701
references.citation: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
references.pmid: 15123812
references.citation: J Mol Biol. 1996 Dec 20;264(5):863-77
references.pmid: 9000617
references.citation: Nucleic Acids Res. 1999 Feb 1;27(3):778-87
references.pmid: 9889273
references.citation: Biochemistry. 2004 Dec 21;43(50):15822-37
references.pmid: 15595837
references.citation: Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22
references.pmid: 7524072
references.citation: J Mol Biol. 1991 Sep 5;221(1):293-308
references.pmid: 1717695
references.citation: Methods Enzymol. 2007;424:3-24
references.pmid: 17662834
references.citation: RNA. 1999 May;5(5):656-69
references.pmid: 10334336
references.citation: Cell. 1988 Oct 21;55(2):267-72
references.pmid: 2844415
references.citation: Mol Cell Biol. 1996 Apr;16(4):1410-8
references.pmid: 8657114
references.citation: EMBO J. 1997 Jul 1;16(13):4069-81
references.pmid: 9233816
references.citation: RNA. 2003 Jan;9(1):62-76
references.pmid: 12554877
references.citation: Cell. 1990 Jul 27;62(2):391-7
references.pmid: 1695552
references.citation: Mol Cell Biol. 1997 Sep;17(9):5377-85
references.pmid: 9271415
references.citation: Cell. 1990 Jun 1;61(5):885-94
references.pmid: 2140530
references.citation: RNA. 2006 Jun;12(6):1038-49
references.pmid: 16611942
references.citation: RNA. 2006 Jul;12(7):1292-303
references.pmid: 16691000
references.citation: RNA. 2006 Jun;12(6):1050-60
references.pmid: 16618968
references.citation: Nucleic Acids Res. 2001 Feb 1;29(3):703-9
references.pmid: 11160892
references.citation: Methods Enzymol. 1989;180:51-62
references.pmid: 2482430
references.citation: EMBO J. 1990 Dec;9(12):4111-8
references.pmid: 1701142
references.citation: Science. 1996 Aug 30;273(5279):1189-95
references.pmid: 8703045
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Nat Rev Mol Cell Biol. 2004 Nov;5(11):908-19
references.pmid: 15520810
references.citation: Cell. 1991 Nov 1;67(3):537-46
references.pmid: 1718605
references.citation: RNA. 1997 Sep;3(9):1052-67
references.pmid: 9292503
references.citation: Mol Cell Biol. 2008 Jan;28(1):122-30
references.pmid: 17954557
references.citation: Cell. 1990 Jan 26;60(2):189-98
references.pmid: 1688737
references.citation: RNA. 2003 Mar;9(3):265-76
references.pmid: 12591999
references.citation: RNA. 2004 Feb;10(2):159-70
references.pmid: 14730014
references.citation: Proc Natl Acad Sci U S A. 1983 Jul;80(13):3903-7
references.pmid: 6306649
references.citation: J Biol Chem. 1986 Apr 25;261(12):5396-403
references.pmid: 2420800
references.citation: Nucleic Acids Res. 1995 Aug 25;23(16):3093-102
references.pmid: 7667084
references.citation: J Mol Biol. 1989 May 20;207(2):417-31
references.pmid: 2754730
references.citation: Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8901-6
references.pmid: 8799125
references.citation: Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373-7
references.pmid: 2432595
references.citation: Nature. 2005 Mar 17;434(7031):409-13
references.pmid: 15772668
references.citation: Science. 1994 Oct 7;266(5182):114-7
references.pmid: 7524149
references.citation: Nucleic Acids Res. 1997 Jun 15;25(12):2311-8
references.pmid: 9171080
references.citation: EMBO J. 1992 Dec;11(12):4429-38
references.pmid: 1330537
references.citation: Methods Enzymol. 2000;318:136-47
references.pmid: 10889985
references.citation: Cell. 1996 Mar 22;84(6):831-41
references.pmid: 8601307
references.citation: Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1017-22
references.pmid: 15657144
references.citation: RNA. 2008 Jun;14(6):1069-80
references.pmid: 18441045
references.citation: RNA. 1999 Jul;5(7):883-92
references.pmid: 10411132
references.citation: Nucleic Acids Res. 2005 Nov 23;33(20):6610-20
references.pmid: 16306234
references.citation: J Biol Chem. 2007 Feb 16;282(7):4265-4276
references.pmid: 17158098
references.citation: Cell. 2002 Feb 22;108(4):435-8
references.pmid: 11909515
references.citation: RNA Biol. 2004 May;1(1):28-34
references.pmid: 17194935
references.citation: Trends Biochem Sci. 2005 Feb;30(2):97-105
references.pmid: 15691655
references.citation: Biochemistry. 1982 Sep 14;21(19):4700-6
references.pmid: 6291588
references.citation: RNA. 2006 Jan;12(1):83-93
references.pmid: 16373494
references.citation: Mol Biol Rep. 1994 Jul;20(1):35-44
references.pmid: 7531281
references.citation: Nucleic Acids Res. 1991 Jul 11;19(13):3653-60
references.pmid: 1712940
references.citation: Mol Cell. 2003 Aug;12(2):307-19
references.pmid: 14536071
references.citation: Mol Cell Biol. 2002 Mar;22(5):1567-76
references.pmid: 11839822
references.citation: EMBO J. 1997 Dec 15;16(24):7490-9
references.pmid: 9405377
references.citation: Nucleic Acids Res. 1998 Aug 15;26(16):3634-9
references.pmid: 9685476