| 1. |
- Melin, Petter, et al.
(författare)
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Characterization of phiA, a gene essential for phialide development in Aspergillus nidulans
- 2003
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Ingår i: Fungal Genetics and Biology. - : Academic Press. - 1087-1845 .- 1096-0937. ; 40:3, s. 234-241
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Tidskriftsartikel (refereegranskat)abstract
- We have previously identified genes and proteins involved in the fungal response to the Streptomyces-produced antibiotics, bafilomycin 131 and concanamycin A, known inhibitors of V-ATPases. Using mRNA differential display we identified an Aspergillus nidulans gene with 30-fold up-regulated expression in the presence of bafilomycin. This gene, here denoted phiA, and its gene product, were further characterized by targeted gene disruption and immunohistochemistry. Phenotypically, the phiA mutation resulted in reduced growth and severely reduced sporulation. The abnormality could be traced to the phialides, which divided several times instead of forming a single flask-shaped cell. The importance of phiA for phialide and conidium development was supported by immunohistochemistry experiments that showed the protein to be mainly present in these two cell types. Attempts to relate phiA to inhibition of V-ATPases did not result in unambiguous conclusions, but suggest the possibility that changed expression of phiA is correlated with growth arrest caused by inhibited V-ATPases.
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| 2. |
- Slagter-Jäger, Jacoba G., et al.
(författare)
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Loop swapping in an antisense RNA/target RNA pair changes directionality of helix progression
- 2003
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 278:37, s. 35558-35563
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Tidskriftsartikel (refereegranskat)abstract
- The binding pathway of the natural antisense RNA CopA to its target CopT proceeds through a hierarchical order of steps. It initiates by reversible loop-loop contacts followed by unidirectional helix progression into the upper stems. This involves extensive breakage of intramolecular base pairs and the subsequent formation of two intermolecular helices, B and B'. Based on the known tRNA anticodon loop structure and on results from the Sok/Hok antisense/target RNA system, it had been suggested that a U-turn (or pi-turn) in the loop of CopT might determine the directionality of helix progression. Data presented here show that the putative U-turn is one of the structural elements of antisense/target RNA pairs required to achieve fast binding kinetics. Swapping of the hypothetical U-turn structure from the target RNA to the antisense RNA retained regulatory performance in vivo and binding rates in vitro but altered the binding pathway by changing the direction in which the initiating helix was extended. In addition, our data indicate that a helical stem immediately adjacent to the target loop sequence is required to provide a scaffold for the U-turn.
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| 3. |
- Vogel, Jörg, et al.
(författare)
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RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
- 2003
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 31:22, s. 6435-6443
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Tidskriftsartikel (refereegranskat)abstract
- Recent bioinformatics‐aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot‐gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co‐expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III‐dependent cleavage. To the best of our knowledge, this represents the first case of two non‐coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half‐lives (<2 to >32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
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| 4. |
- Vogel, Jörg, et al.
(författare)
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The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide
- 2004
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 14:24, s. 2271-2276
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Tidskriftsartikel (refereegranskat)abstract
- More than 60 small RNAs (sRNA) have been identified in E. coli 1, 2, 3, 4, 5, 6 and 7. The functions of the majority of these sRNAs are still unclear. For the few sRNAs characterized, expression and functional studies indicate that they act under stress conditions 8, 9, 10, 11, 12, 13 and 14. Here, we describe a novel E. coli chromosome locus that is part of the SOS response to DNA damage. This locus encodes two sRNAs, IstR-1 and IstR-2, and a toxic peptide, TisB, encoded by tisAB mRNA. Transcription of tisAB and istR-2 is SOS regulated, whereas IstR-1 is present throughout growth. IstR-1 inhibits toxicity by base-pairing to a short region in the tisAB mRNA. This antisense interaction entails RNase III-dependent cleavage, thereby inactivating the mRNA for translation. In the absence of the SOS response, IstR-1 is present in high excess over its target. However, SOS induction leads to depletion of the IstR-1 pool, concomitant with accumulation of tisAB mRNA. Under such conditions, TisB exerts its toxic effect, slowing down growth. We propose that the inhibitory sRNA prevents inadvertent TisB synthesis during normal growth and, possibly, also limits SOS-induced toxicity. Our study adds the SOS regulon to the growing list of global regulatory circuits controlled by sRNA genes.
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| 5. |
- Wagner, Gerhart E. H., et al.
(författare)
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Antisense RNAs everywhere?
- 2002
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Ingår i: Trends in Genetics. - 0168-9525 .- 1362-4555. ; 18:5, s. 223-226
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, systematic searches of both prokaryote and eukaryote genomes have identified a staggering number of small RNAs, the biological functions of which remain unknown. Small RNA-based regulators are well known from bacterial plasmids. They act on target RNAs by sequence complementarity; that is, they are antisense RNAs. Recent findings suggest that many of the novel orphan RNAs encoded by bacterial and eukaryotic chromosomes might also belong to a ubiquitous, heterogeneous class of antisense regulators of gene expression.
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