Trypanosome H/ACA box snoRNAs

Non-coding RNAs (ncRNA) are RNA molecules that have a function but are not translated into proteins. Small nucleolar RNAs (snoRNAs), one of the largest classes of ncRNA, are further subdivided into the two major C/D and H/ACA snoRNA families. snoRNA serve as guide RNAs for 2'-O-methylation and pseudouridylation of specific nucleotides and indicate the site of modification by direct base pairing with the target RNA. The majority of these snoRNAs are responsible for the post-transcriptional modification of ribosomal RNAs (rRNA) and in some cases of small nuclear RNAs (sRNAs). These post-transcriptional modifications are crucial for rRNA processing, stability and maturation.[1]

H/ACA with pseudouridylation pocket

The H/ACA snoRNAs that guide pseudouridylation in Trypanosomes consist of a single-hairpin followed by an AGA-box.[1] These H/ACA snoRNA contain a pseudouridylation pocket that guides the H/ACA snoRNA to the correct region of its target rRNA. The pseudouridylation pocket ensures modification of the correct uridine, as it contains two short sequences that are complementary to the target RNA. In addition it is able to basepair with the regions flanking the uridine in need of modification. Trypanosomal snoRNAs differ in both sequence and structure to eukaryotic snoRNAs as they contain one stem loop and an AGA-box at the 3' end. Despite these differences, trypanosomal snoRNAs function identically to eukaryotic snoRNAs and since the discovery of single stem H/ACA snoRNAs in Trypanosomes, similar single hairpin ncRNAs have been discovered in Archea and Euglena.[2][3][4] The table below summarizes the H/ACA snoRNAs and the corresponding target sites identified in Trypanosomes.[5]

H/ACA snoRNAs identified in Trypanosomes

H/ACA ID Target Reference
TB3Cs2H1 ?308-L5 Myslyuk et al. 2008 [6]
TB3Cs2H2 ?1658-L5 Myslyuk et al. 2008 [6]
TB8Cs4H1 ?358-L3 Myslyuk et al. 2008 [6]
TB8Cs4H2 ?141-L3 Myslyuk et al. 2008[6]
TB9Cs6H1 ?199-L5, ?29-5.8S Myslyuk et al. 2008[6]
TB9Cs6H2 ?1653-L5 Myslyuk et al. 2008[6]
TB10Cs5H1 ?1254-L3 Myslyuk et al. 2008[6]
TB10Cs5H2 ?131-S Myslyuk et al. 2008[6]
TB10Cs5H3 ?1276-S Myslyuk et al. 2008[6]
TB11Cs5H1 ?1710-S Myslyuk et al. 2008[6]
TB11Cs5H2 ?176-L3 Myslyuk et al. 2008[6]
TB11Cs5H3 ?1314-L3 Myslyuk et al. 2008[6]
TB6Cs1H1 ?380-L3 Liang et al. 2005[7]
TB6Cs1H2 Liang et al. 2005[7]
TB6Cs1H3 ?662-S Liang et al. 2005[7]
TB6Cs1H4 ?824-L5 Liang et al. 2005[7]
TB6Cs2H1 ?1001-SSU Liang et al. 2005[7]
TB8Cs2H1 ?1113-S Liang et al. 2005[7]
TB8Cs3H1 ?1423-S Liang et al. 2005[7]
TB9Cs1H1 ?1088-S,?1272-L3 Liang et al. 2005[7]
TB9Cs1H2 ?1619-S Liang et al. 2005[7]
TB9Cs1H3 ?1250-L5 Liang et al. 2005[7]
TB9Cs2H1 ?617-L3 Liang et al. 2005[7]
TB9Cs2H2 ?1412-L5 Liang et al. 2005[7]
TB9Cs3H1 ?1208-L3 Liang et al. 2005[7]
TB9Cs3H2 ?1103-L5 Liang et al. 2005[7]
TB9Cs4H1 ?2123-S Liang et al. 2005[7]
TB9Cs4H2 ?1336-L3 Liang et al. 2005[7]
TB9Cs4H3 Liang et al. 2005[7]
TB10Cs1H1 ?659-L3 Liang et al. 2005[7]
TB10Cs1H2 ?901-L5 Liang et al. 2005[7]
TB10Cs1H3 ?40-S Liang et al. 2005[7]
TB10Cs2H1 ?1167-L3 Liang et al. 2005[7]
TB10Cs2H2 ?1173-L5 Liang et al. 2005[7]
TB10Cs3H1 ?263-S Liang et al. 2005[7]
TB10Cs3H2 ?397-L3 Liang et al. 2005[7]
TB10Cs4H1 ?2248-L5 Liang et al. 2005[7]
TB10Cs4H2 ?1186-S Liang et al. 2005[7]
TB10Cs4H3 ?1773-L5 Liang et al. 2005[7]
TB10Cs4H4 ?505-S Liang et al. 2005[7]
TB11Cs2H1 ?28 SL Liang et al. 2005[7]
TB11Cs3H1 ?1308-L3 Liang et al. 2005[7]
TB11Cs3H2 ?475-L3 Liang et al. 2005[7]
TB11Cs4H1 ?1357-L3 Liang et al. 2005[7]
TB11Cs4H2 ?566-L3 Liang et al. 2005[7]
TB11Cs4H3 ?61-S Liang et al. 2005[7]

References
  1. Liang XH, Liu L, Michaeli S (October 2001). "Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNA". J. Biol. Chem. 276 (43): 40313–8. doi:10.1074/jbc.M104488200. PMID 11483606.
  2. Tang TH, Bachellerie JP, Rozhdestvensky T, et al. (May 2002). "Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus". Proc. Natl. Acad. Sci. U.S.A. 99 (11): 7536–41. doi:10.1073/pnas.112047299. PMC 124276. PMID 12032318.
  3. Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, Hüttenhofer A (February 2003). "Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Res. 31 (3): 869–77. doi:10.1093/nar/gkg175. PMC 149196. PMID 12560482. Retrieved 2010-07-12.
  4. Russell AG, Schnare MN, Gray MW (July 2004). "Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis". RNA. 10 (7): 1034–46. doi:10.1261/rna.7300804. PMC 1370595. PMID 15208440.
  5. Doniger T, Michaeli S, Unger R (2009). "Families of H/ACA ncRNA molecules in trypanosomatids". RNA Biol. 6 (4): 370–4. doi:10.4161/rna.6.4.9270. PMID 19652533. Retrieved 2010-07-12.
  6. Myslyuk I, Doniger T, Horesh Y, et al. (2008). "Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes". BMC Bioinformatics. 9: 471. doi:10.1186/1471-2105-9-471. PMC 2613932. PMID 18986541.
  7. Liang XH, Uliel S, Hury A, et al. (May 2005). "A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification". RNA. 11 (5): 619–45. doi:10.1261/rna.7174805. PMC 1370750. PMID 15840815.
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