| 1. |
- Jöchl, Christoph, et al.
(författare)
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Development-dependent scavenging of nucleic acids in the filamentous fungus Aspergillus fumigatus.
- 2009
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Ingår i: RNA biology. - : Informa UK Limited. - 1555-8584 .- 1547-6286. ; 6:2, s. 179-186
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Tidskriftsartikel (refereegranskat)abstract
- Aspergillus fumigatus is an ubiquitous, filamentous and opportunistic pathogenic fungus which causes fatal invasive aspergillosis among immuno-compromised patients. Since therapeutic strategies are currently limited, the mortality rate of invasive aspergillosis is high and thus, alternative antifungal strategies are required. In this study, we demonstrate that during vegetative growth Aspergillus fumigatus is able to scavenge nucleic acids within its cell wall with accumulation rates of several thousand-fold, compared to the surrounding medium. To investigate, whether nucleic acids, attached to the fungal cell wall, are able to move further into the cytoplasm of fungal cells, we directly applied siRNAs, in the absence of lipo-transfection reagents, to growing A. fumigatus cells. In fact, addition of two 21-nt siRNA duplexes resulted in knock-down of their corresponding target mRNAs, odcA and pyrG, respectively. These findings indicate that RNA interference, mediated by siRNAs, can be used as a fast and efficient tool to investigate the functions of genes within filamentous fungi. In addition, siRNA-based therapies may provide novel approaches for antifungal treatment.
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| 2. |
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| 3. |
- Song, Tianyan, et al.
(författare)
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A novel sRNA that modulates virulence and environmental fitness of Vibrio cholerae
- 2009
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Ingår i: RNA Biology. - : Informa UK Limited. - 1547-6286 .- 1555-8584.
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Tidskriftsartikel (refereegranskat)abstract
- We recently described the discovery and initial functional characterization of a new sRNA, VrrA, in Vibrio cholerae O1 strain A1552. The VrrA homologs were found in all Vibrio strains whose genome sequences were reported at present. In this article, we summarize the multi-functional features of VrrA in V. cholerae pathogenesis and physiology, especially in relation to the regulation of outer membrane vesicle formation and its consequence in environmental adaptation of the bacterium. As the vrrA gene was not predicted by any of the previous bioinformatics-based genome-wide screenings for sRNA, we discuss the reasons and give suggestion on improving current bioinformatics tools.
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| 4. |
- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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Kinship in the SRP RNA family
- 2009
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Ingår i: RNA Biology. - 1547-6286. ; 6:5
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Tidskriftsartikel (refereegranskat)abstract
- The signal recognition particle (SRP) is a ribonucleoprotein complex which participates in the targeting of protein to cellular membranes. The RNA component of the SRP has been found in all domains of life, but the size of the molecule and the number of RNA secondary structure elements vary considerably between the different phylogenetic groups. We continued our efforts to identify new SRP RNAs, compare their sequences, discover new secondary structure elements, conserved motifs, and other properties. We found additional proof for the variability in the apical loop of helix 8, and we identified several bacteria which lack all of their SRP components. Based on the distribution of SRP RNA features within the taxonomy, we suggest seven alignment groups: Bacteria with a small (4.5S) SRP RNA, Bacteria with a large (6S) SRP RNA, Archaea, Fungi (Ascomycota), Metazoa group, Protozoa group, and Plants. The proposed divisions improve the prediction of more distantly related SRP RNAs and provide a more inclusive representation of the SRP RNA family. Updates of the Rfam SRP RNA sequence collection are expected to benefit from the suggested groupings.
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| 5. |
- 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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| 6. |
- Kanduri, Chandrasekhar
(författare)
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Functional insights into long antisense noncoding RNA Kcnq1ot1 mediated bidirectional silencing
- 2008
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Ingår i: RNA biology. - 1547-6286. ; 5:4, s. 208-11
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Tidskriftsartikel (refereegranskat)abstract
- The prevailing view has been that noncoding antisense RNA primarily regulates the transcriptional activity of its sense counterpart, however, a subset of long noncoding antisense RNAs, such as Kcnq1ot1 and Air, have been shown to regulate the transcriptional silencing of multiple genes spread over several hundred kilobases on either side of their promoters. It is however unknown how these long RNAs regulate the transcriptional silencing of multiple genes. Our recent work demonstrated through exploiting an episomal-based system that the Kcnq1ot1 RNA harbors a silencing domain at its 5' end which mediates transcriptional silencing through introducing repressive histone modifications, and by interacting with the chromatin and targeting the associated regions to the perinucleolar space. Based on our current findings as well as previous findings from other labs, we propose a model resembling that of Xist-mediated chromosomal silencing, wherein Kcnq1ot1 RNA initiates transcriptional silencing by coating the flanking chromatin regions and directing the heterochromatin machinery. Maintenance of silencing through subsequent cell divisions would then occur via the targeting of Kcnq1ot1-associated chromatin to the perinucleolar space.
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| 7. |
- Unoson, Cecilia, et al.
(författare)
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Dealing with stable structures at ribosome binding sites : bacterial translation and ribosome standby.
- 2007
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Ingår i: RNA Biology. - 1547-6286. ; 4:3, s. 113-117
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial ribosomes have great difficulties to initiate translation on stable structures within mRNAs. Translational coupling and induced structure changes are strategies to open up inhibitory RNA structures encompassing ribosome binding sites (RBS). There are, however, mRNAs in which stable structures are not unfolded, but that are nevertheless efficiently initiated at high rates. de Smit and van Duin(1) proposed a "ribosome standby" model to theoretically solve this paradox: the 30S ribosome binds nonspecifically to an accessible site on the mRNA (standby site), waiting for a transient opening of a stable RBS hairpin. Upon unfolding, the 30S subunit relocates to form a productive initiation complex. Recent reports have provided experimental support for this model. This review will describe and compare two different flavors of standby sites, their properties, and their likely implications. We also discuss the possibility that ribosome standby may be a more general strategy to obtain high translation rates.
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