Trypanosome H/ACA box snoRNAs

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.{{cite journal |vauthors=Liang XH, Liu L, Michaeli S |title=Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNA |journal=J. Biol. Chem. |volume=276 |issue=43 |pages=40313–8 |date=October 2001 |pmid=11483606 |doi=10.1074/jbc.M104488200 |doi-access=free }}

Image:Haca w pocket.JPG

The H/ACA snoRNAs that guide pseudouridylation in Trypanosomes consist of a single-hairpin followed by an AGA-box. 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.{{cite journal |vauthors=Tang TH, Bachellerie JP, Rozhdestvensky T, etal |title=Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue=11 |pages=7536–41 |date=May 2002 |pmid=12032318 |pmc=124276 |doi=10.1073/pnas.112047299 |bibcode=2002PNAS...99.7536T |doi-access=free }}{{cite journal |vauthors=Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, Hüttenhofer A |title=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 |journal=Nucleic Acids Res. |volume=31 |issue=3 |pages=869–77 |date=February 2003 |pmid=12560482 |pmc=149196 |doi= 10.1093/nar/gkg175|url=}}{{cite journal |vauthors=Russell AG, Schnare MN, Gray MW |title=Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis |journal=RNA |volume=10 |issue=7 |pages=1034–46 |date=July 2004 |pmid=15208440 |pmc=1370595 |doi=10.1261/rna.7300804 }} The table below summarizes the H/ACA snoRNAs and the corresponding target sites identified in Trypanosomes.{{cite journal |vauthors=Doniger T, Michaeli S, Unger R |title=Families of H/ACA ncRNA molecules in trypanosomatids |journal=RNA Biol |volume=6 |issue=4 |pages=370–4 |year=2009 |pmid=19652533 |doi= 10.4161/rna.6.4.9270|url=http://www.landesbioscience.com/journals/rna/abstract.php?id=9270 |access-date=2010-07-12|doi-access=free }}

H/ACA snoRNAs identified in Trypanosomes

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H/ACA ID ! Target ! Reference
TB3Cs2H1 | ?308-L5 | Myslyuk et al. 2008 {{cite journal |vauthors=Myslyuk I, Doniger T, Horesh Y, etal |title=Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes |journal=BMC Bioinformatics |volume=9|pages=471 |year=2008 |pmid=18986541 |pmc=2613932 |doi=10.1186/1471-2105-9-471 |doi-access=free }}
TB3Cs2H2 | ?1658-L5 | Myslyuk et al. 2008
TB8Cs4H1 | ?358-L3 | Myslyuk et al. 2008
TB8Cs4H2 | ?141-L3 | Myslyuk et al. 2008
TB9Cs6H1 | ?199-L5, ?29-5.8S | Myslyuk et al. 2008
TB9Cs6H2 | ?1653-L5 | Myslyuk et al. 2008
TB10Cs5H1 | ?1254-L3 | Myslyuk et al. 2008
TB10Cs5H2 | ?131-S | Myslyuk et al. 2008
TB10Cs5H3 | ?1276-S | Myslyuk et al. 2008
TB11Cs5H1 | ?1710-S | Myslyuk et al. 2008
TB11Cs5H2 | ?176-L3 | Myslyuk et al. 2008
TB11Cs5H3 | ?1314-L3 | Myslyuk et al. 2008
TB6Cs1H1 | ?380-L3 | Liang et al. 2005{{cite journal |vauthors=Liang XH, Uliel S, Hury A, etal |title=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 |journal=RNA |volume=11 |issue=5 |pages=619–45 |date=May 2005 |pmid=15840815 |pmc=1370750 |doi=10.1261/rna.7174805 }}
TB6Cs1H2 | | Liang et al. 2005
TB6Cs1H3 | ?662-S | Liang et al. 2005
TB6Cs1H4 | ?824-L5 | Liang et al. 2005
TB6Cs2H1 | ?1001-SSU | Liang et al. 2005
TB8Cs2H1 | ?1113-S | Liang et al. 2005
TB8Cs3H1 | ?1423-S | Liang et al. 2005
TB9Cs1H1 | ?1088-S,?1272-L3 | Liang et al. 2005
TB9Cs1H2 | ?1619-S | Liang et al. 2005
TB9Cs1H3 | ?1250-L5 | Liang et al. 2005
TB9Cs2H1 | ?617-L3 | Liang et al. 2005
TB9Cs2H2 | ?1412-L5 | Liang et al. 2005
TB9Cs3H1 | ?1208-L3 | Liang et al. 2005
TB9Cs3H2 | ?1103-L5 | Liang et al. 2005
TB9Cs4H1 | ?2123-S | Liang et al. 2005
TB9Cs4H2 | ?1336-L3 | Liang et al. 2005
TB9Cs4H3 | | Liang et al. 2005
TB10Cs1H1 | ?659-L3 | Liang et al. 2005
TB10Cs1H2 | ?901-L5 | Liang et al. 2005
TB10Cs1H3 | ?40-S | Liang et al. 2005
TB10Cs2H1 | ?1167-L3 | Liang et al. 2005
TB10Cs2H2 | ?1173-L5 | Liang et al. 2005
TB10Cs3H1 | ?263-S | Liang et al. 2005
TB10Cs3H2 | ?397-L3 | Liang et al. 2005
TB10Cs4H1 | ?2248-L5 | Liang et al. 2005
TB10Cs4H2 | ?1186-S | Liang et al. 2005
TB10Cs4H3 | ?1773-L5 | Liang et al. 2005
TB10Cs4H4 | ?505-S | Liang et al. 2005
TB11Cs2H1 | ?28 SL | Liang et al. 2005
TB11Cs3H1 | ?1308-L3 | Liang et al. 2005
TB11Cs3H2 | ?475-L3 | Liang et al. 2005
TB11Cs4H1 | ?1357-L3 | Liang et al. 2005
TB11Cs4H2 | ?566-L3 | Liang et al. 2005
TB11Cs4H3 | ?61-S | Liang et al. 2005