| 1. |
- 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. |
- Piccinelli, Paul, 1975
(författare)
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Computational identification of non-coding RNAs
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A large amount of genomic information is now becoming available. Suitable bioinformatic tools to organize and analyze this vast amount of information are therefore important. In the case of protein genes, the majority of these may be correctly identified using standard search methods that are based on sequence alignment. However, a different problem is presented when analysing non-coding RNA genes, since for their identification it is essential to take into consideration secondary structure features. Secondary structure is not only important for non-coding RNA genes, but it is also important in the regulation of gene expression. This work is concerned with the development of methods for ncRNA prediction and the application of these methods to identify specific ncRNA families. In a variety of organisms we report on several ncRNA sequences not previously reported. These novel RNA sequences make it possible to better predict the structure of these RNAs as well as to better understand their evolution and function. To further understand the structure and evolution of the RNases P and MRP we also analyzed the protein composition of these enzymes. Together, these new predictions aid to better understand the structure, function and evolution of RNase P and MRP.
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| 3. |
- Piccinelli, Paul, 1975, et al.
(författare)
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Evolution of the iron-responsive element.
- 2007
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Ingår i: RNA (New York, N.Y.). - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 13:7, s. 952-66
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Tidskriftsartikel (refereegranskat)abstract
- An RNA hairpin structure referred to as the iron-responsive element (IRE) and iron regulatory proteins (IRPs) are key players in the control of iron metabolism in animal cells. They regulate translation initiation or mRNA stability, and the IRE is found in a variety of mRNAs, such as those encoding ferritin, transferrin receptor (Tfr), erythroid aminolevulinic acid synthase (eALAS), mitochondrial aconitase (mACO), ferroportin, and divalent metal transporter 1 (DMT1). We have studied the evolution of the IRE by considering all mRNAs previously known to be associated with this structure and by computationally examining its occurrence in a large variety of eukaryotic organisms. More than 100 novel sequences together with approximately 50 IREs that were previously reported resulted in a comprehensive view of the phylogenetic distribution of this element. A comparison of the different mRNAs shows that the IREs of eALAS and mACO are found in chordates, those of ferroportin and Tfr1 are found in vertebrates, and the IRE of DMT1 is confined to mammals. In contrast, the IRE of ferritin occurs in a majority of metazoa including lower metazoa such as sponges and Nematostella (sea anemone). These findings suggest that the ferritin IRE represents the ancestral version of this type of translational control and that during the evolution of higher animals the IRE structure was adopted by other genes. On the basis of primary sequence comparison between different organisms, we suggest that some of these IREs developed by "convergent evolution" through stepwise changes in sequence, rather than by recombination events.
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| 4. |
- Piccinelli, Paul, 1975, et al.
(författare)
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Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes.
- 2005
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 33:14, s. 4485-95
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Tidskriftsartikel (refereegranskat)abstract
- RNases P and MRP are ribonucleoprotein complexes involved in tRNA and rRNA processing, respectively. The RNA subunits of these two enzymes are structurally related to each other and play an essential role in the enzymatic reaction. Both of the RNAs have a highly conserved helical region, P4, which is important in the catalytic reaction. We have used a bioinformatics approach based on conserved elements to computationally analyze available genomic sequences of eukaryotic organisms and have identified a large number of novel nuclear RNase P and MRP RNA genes. For MRP RNA for instance, this investigation increases the number of known sequences by a factor of three. We present secondary structure models of many of the predicted RNAs. Although all sequences are able to fold into the consensus secondary structure of P and MRP RNAs, a striking variation in size is observed, ranging from a Nosema locustae MRP RNA of 160 nt to much larger RNAs, e.g. a Plasmodium knowlesi P RNA of 696 nt. The P and MRP RNA genes appear in tandem in some protists, further emphasizing the close evolutionary relationship of these RNAs.
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