| 1. |
- Hoffmann, Ute A., et al.
(författare)
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The role of the 5' sensing function of ribonuclease E in cyanobacteria
- 2024
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Ingår i: RNA Biology. - : Informa UK Limited. - 1547-6286 .- 1555-8584. ; 21:1, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologues. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside Escherichia coli.
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| 2. |
- Scholtysek, Peggy, et al.
(författare)
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A T-Shaped Amphiphilic Molecule Forms Closed Vesicles in Water and Bicelles in Mixtures with a Membrane Lipid
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:16, s. 4871-4878
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Tidskriftsartikel (refereegranskat)abstract
- The T-shaped amphiphilic molecule A6/6 forms a columnar hexagonal liquid-crystalline phase between the crystalline and the isotropic liquid when studied in bulk (Chen et al., 2005). Because of the hydrophilic and flexible oligo(oxyethylene) side chain terminated by a 1-acylamino-1-deoxy-d-sorbitol moiety attached to a rigid terphenyl core with terminal hexyloxy alkyl chains, it was expected that also formation of lyotropic phases could be possible. We therefore studied the behavior of A6/6 in water and also in mixtures with bilayer-forming phospholipids, such as dipalmitoyl-phosphatidylcholine (DPPC), using differential scanning calorimetry (DSC), transmission electron microscopy (TEM), cryo-transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), and solid-state nuclear magnetic resonance (ssNMR). DSC showed for the pure A6/6 suspended in water a phase transition at ca. 23 °C. TEM and cryo-TEM showed vesicular as well as layered structures for pure A6/6 in water below and above this phase transition. By atomic force microscopy (AFM), the thickness of the layer was found to be 5?6 nm. This leads to a model for a bilayer formed by A6/6 with the laterally attached polar side chains shielding the hydrophobic layer built up by the terphenyl core with the terminal alkyl chains of the molecules. For DPPC:A6/6 mixtures (10:1), the DSC curves indicated a stabilization of the lamellar gel phase of DPPC. Negative staining TEM and cryo-TEM images showed planar bilayers with hexagonal morphology and diameters between 50 and 200 nm. The hydrodynamic radius of these aggregates in water, investigated by dynamic light scattering (DLS) as a function of time and temperature, did not change indicating a very stable aggregate structure. The findings lead to the proposition of a new bicellar structure formed by A6/6 with DPPC. In this model, the bilayer edges are covered by the T-shaped amphiphilic molecules preventing very effectively the aggregation to larger structures.
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