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- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.
- 2006
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 34:18, s. 5145-56
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Tidskriftsartikel (refereegranskat)abstract
- The RNases P and MRP are involved in tRNA and rRNA processing, respectively. Both enzymes in eukaryotes are composed of an RNA molecule and 9-12 protein subunits. Most of the protein subunits are shared between RNases P and MRP. We have here performed a computational analysis of the protein subunits in a broad range of eukaryotic organisms using profile-based searches and phylogenetic methods. A number of novel homologues were identified, giving rise to a more complete inventory of RNase P/MRP proteins. We present evidence of a relationship between fungal Pop8 and the protein subunit families Rpp14/Pop5 as well as between fungal Pop6 and metazoan Rpp25. These relationships further emphasize a structural and functional similarity between the yeast and human P/MRP complexes. We have also identified novel P and MRP RNAs and analysis of all available sequences revealed a K-turn motif in a large number of these RNAs. We suggest that this motif is a binding site for the Pop3/Rpp38 proteins and we discuss other structural features of the RNA subunit and possible relationships to the protein subunit repertoire.
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| 2. |
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| 3. |
- Davila Lopez, Marcela, et al.
(författare)
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Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of the major and minor spliceosomal components
- 2008
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Ingår i: RNA Society Meeting 2008.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- An essential step of gene expression is the removal of non-coding sequences (introns) from the pre-mRNA and the ligation of coding sequences (exons) to form the mature RNA (mRNA). It is known that the pre-mRNA splicing occurs by two sequential trans-esterification reactions and is catalyzed by a multicomponent complex, the spliceosome. Its assembly involves five small nuclear ribonucleoprotein particles (snRNPs) as well as an array of protein factors, which are determined by the class of intron to be spliced1. To date, two intron classes are known, U2- and U12-type introns. The U2-dependent spliceosome (panel a) is formed by the interaction of the U1, U2, U4/U6 and U5 snRNPs and numerous non-snRNP proteins with the pre-mRNA. The U12-dependent spliceosome (also referred to as the minor spliceosome, panel b), in contrast, consists of the U11, U12, U4atac/U6atac and U5 snRNPs with an unknown number of non-snRNP proteins. Thus, of the main spliceosomal subunits, only the U5 snRNA is common to both spliceosomes2.
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| 4. |
- Davila Lopez, Marcela, et al.
(författare)
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Conserved and variable domains of RNase MRP RNA
- 2009
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Ingår i: RNA Biology. - 1547-6286. ; 6:3, s. 208-221
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Tidskriftsartikel (refereegranskat)abstract
- Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.
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| 5. |
- Davila Lopez, Marcela, et al.
(författare)
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Early evolution of histone mRNA 3' end processing.
- 2008
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 14:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- The replication-dependent histone mRNAs in metazoa are not polyadenylated, in contrast to the bulk of mRNA. Instead, they contain an RNA stem-loop (SL) structure close to the 3' end of the mature RNA, and this 3' end is generated by cleavage using a machinery involving the U7 snRNP and protein factors such as the stem-loop binding protein (SLBP). This machinery of 3' end processing is related to that of polyadenylation as protein components are shared between the systems. It is commonly believed that histone 3' end processing is restricted to metazoa and green algae. In contrast, polyadenylation is ubiquitous in Eukarya. However, using computational approaches, we have now identified components of histone 3' end processing in a number of protozoa. Thus, the histone mRNA stem-loop structure as well as the SLBP protein are present in many different protozoa, including Dictyostelium, alveolates, Trypanosoma, and Trichomonas. These results show that the histone 3' end processing machinery is more ancient than previously anticipated and can be traced to the root of the eukaryotic phylogenetic tree. We also identified histone mRNAs from both metazoa and protozoa that are polyadenylated but also contain the signals characteristic of histone 3' end processing. These results provide further evidence that some histone genes are regulated at the level of 3' end processing to produce either polyadenylated RNAs or RNAs with the 3' end characteristic of replication-dependent histone mRNAs.
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| 6. |
- Samuelsson, Tore, 1951, et al.
(författare)
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A histone 3' end processing machinery in protozoa
- 2007
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Ingår i: 5th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB).
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In metazoa replication-dependent histone mRNAs are not polyadenylated. At the 3' end of these mRNAs there is a conserved sequence that contains a 16 nucleotide stem loop (SL) besides a purine rich sequences, called the histone downstream element (HDE) located several nucleotides downstream. This is necessary for endonucleolytic cleavage of pre-mRNA to release the mature mRNA. For this task also trans-acting factors are needed, such as a U7 snRNP, a stem loop binding protein (SLBP) and a subunit of the cleavage/polyadenylation specificity factor (CPSF-73)1,2. In order to understand the evolutionary origin of this molecular machinery we have computationally searched for all the transacting factors as well as the histone mRNA stem-loop structure in histone mRNAs in a range of eukaryotic species. We have used profile HMMs and covariance models to identify SL motifs as well as U7 RNA homologues in lower metazoa. Profile-based searches were used to identify proteins homologous to the mammalian SLBP. Surprisingly, a number of protozoan species seem to have the histone 3' end processing machinery characteristic of metazoa. These results show that this machinery is more ancient than previously anticipated.
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