Trypanosome H/ACA box snoRNAs

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In molecular biology, 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 Haca w pocket.JPG
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 IDTargetReference
TB3Cs2H1 ?308-L5Myslyuk et al. 2008 [6]
TB3Cs2H2 ?1658-L5Myslyuk et al. 2008 [6]
TB8Cs4H1 ?358-L3Myslyuk et al. 2008 [6]
TB8Cs4H2 ?141-L3Myslyuk et al. 2008 [6]
TB9Cs6H1 ?199-L5, ?29-5.8SMyslyuk et al. 2008 [6]
TB9Cs6H2 ?1653-L5Myslyuk et al. 2008 [6]
TB10Cs5H1 ?1254-L3Myslyuk et al. 2008 [6]
TB10Cs5H2 ?131-SMyslyuk et al. 2008 [6]
TB10Cs5H3 ?1276-SMyslyuk et al. 2008 [6]
TB11Cs5H1 ?1710-SMyslyuk et al. 2008 [6]
TB11Cs5H2 ?176-L3Myslyuk et al. 2008 [6]
TB11Cs5H3 ?1314-L3Myslyuk et al. 2008 [6]
TB6Cs1H1 ?380-L3Liang et al. 2005 [7]
TB6Cs1H2 Liang et al. 2005 [7]
TB6Cs1H3 ?662-SLiang et al. 2005 [7]
TB6Cs1H4 ?824-L5Liang et al. 2005 [7]
TB6Cs2H1 ?1001-SSULiang et al. 2005 [7]
TB8Cs2H1 ?1113-SLiang et al. 2005 [7]
TB8Cs3H1?1423-SLiang et al. 2005 [7]
TB9Cs1H1 ?1088-S,?1272-L3Liang et al. 2005 [7]
TB9Cs1H2 ?1619-SLiang et al. 2005 [7]
TB9Cs1H3 ?1250-L5Liang et al. 2005 [7]
TB9Cs2H1 ?617-L3Liang et al. 2005 [7]
TB9Cs2H2 ?1412-L5Liang et al. 2005 [7]
TB9Cs3H1 ?1208-L3Liang et al. 2005 [7]
TB9Cs3H2 ?1103-L5Liang et al. 2005 [7]
TB9Cs4H1 ?2123-SLiang et al. 2005 [7]
TB9Cs4H2 ?1336-L3Liang et al. 2005 [7]
TB9Cs4H3Liang et al. 2005 [7]
TB10Cs1H1 ?659-L3Liang et al. 2005 [7]
TB10Cs1H2 ?901-L5Liang et al. 2005 [7]
TB10Cs1H3?40-SLiang et al. 2005 [7]
TB10Cs2H1 ?1167-L3Liang et al. 2005 [7]
TB10Cs2H2 ?1173-L5Liang et al. 2005 [7]
TB10Cs3H1 ?263-SLiang et al. 2005 [7]
TB10Cs3H2 ?397-L3Liang et al. 2005 [7]
TB10Cs4H1?2248-L5Liang et al. 2005 [7]
TB10Cs4H2 ?1186-SLiang et al. 2005 [7]
TB10Cs4H3 ?1773-L5Liang et al. 2005 [7]
TB10Cs4H4 ?505-SLiang et al. 2005 [7]
TB11Cs2H1 ?28 SLLiang et al. 2005 [7]
TB11Cs3H1 ?1308-L3Liang et al. 2005 [7]
TB11Cs3H2?475-L3Liang et al. 2005 [7]
TB11Cs4H1 ?1357-L3Liang et al. 2005 [7]
TB11Cs4H2 ?566-L3Liang et al. 2005 [7]
TB11Cs4H3 ?61-SLiang et al. 2005 [7]

Related Research Articles

<span class="mw-page-title-main">TB9Cs3H2 snoRNA</span>

TB9Cs3H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB9Cs3H2 is predicted to guide the pseudouridylation of LSU5 ribosomal RNA (rRNA) at residue Ψ1103.

<span class="mw-page-title-main">TB6Cs1H1 snoRNA</span>

TB6Cs1H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB6Cs1H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ380.

<span class="mw-page-title-main">TB6Cs1H3 snoRNA</span>

TB6Cs1H3 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB6Cs1H3 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ662.

<span class="mw-page-title-main">TB10Cs1H1 snoRNA</span>

TB10Cs1H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs1H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ659.

<span class="mw-page-title-main">TB9Cs2H1 snoRNA</span>

TB9Cs2H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB9Cs2H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ617.

<span class="mw-page-title-main">TB10Cs2H1 snoRNA</span> Class of RNA

TB10Cs2H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs2H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ1167.

<span class="mw-page-title-main">TB10Cs3H2 snoRNA</span>

TB10Cs3H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs3H2 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ397.

<span class="mw-page-title-main">TB8Cs2H1 snoRNA</span>

TB8Cs2H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB8Cs2H1 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ1113.

<span class="mw-page-title-main">TB10Cs4H4 snoRNA</span>

TB10Cs4H4 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs4H4 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ505.

<span class="mw-page-title-main">TB11Cs4H3 snoRNA</span>

TB11Cs4H3 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB11Cs4H3 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ566.

<span class="mw-page-title-main">TB6Cs1H4 snoRNA</span>

TB6Cs1H4 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB6Cs1H4 is predicted to guide the pseudouridylation of LSU5 ribosomal RNA (rRNA) at residue Ψ824.

TB9Cs1H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB9Cs1H2 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ1619.

<span class="mw-page-title-main">TB8Cs4H2 snoRNA</span>

TB8Cs4H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB8Cs4H2 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ141.

<span class="mw-page-title-main">TB10Cs4H2 snoRNA</span>

TB10Cs4H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs4H2 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ1186.

<span class="mw-page-title-main">TB10Cs5H3 snoRNA</span>

TB10Cs5H3 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs5H3 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ1276.

<span class="mw-page-title-main">TB10Cs5H2 snoRNA</span>

TB10Cs5H2 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs5H2 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ131.

TB6Cs2H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB6Cs2H1 is predicted to guide the pseudouridylation of SSU ribosomal RNA (rRNA) at residue Ψ1101.

TB9Cs1H3 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB9Cs1H3 is predicted to guide the pseudouridylation of LSU5 ribosomal RNA (rRNA) at residue Ψ1250.

TB11Cs3H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB11Cs3H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ1308.

TB10Cs5H1 is a member of the H/ACA-like class of non-coding RNA (ncRNA) molecule that guide the sites of modification of uridines to pseudouridines of substrate RNAs. It is known as a small nucleolar RNA (snoRNA) thus named because of its cellular localization in the nucleolus of the eukaryotic cell. TB10Cs5H1 is predicted to guide the pseudouridylation of LSU3 ribosomal RNA (rRNA) at residue Ψ1254.

References

  1. 1 2 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. Bibcode:2002PNAS...99.7536T. 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.
  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. 1 2 3 4 5 6 7 8 9 10 11 12 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. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 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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