A novel di-acidic motif facilitates ER export of the syntaxin SYP31

It is generally accepted that ER protein export is largely influenced by the transmembrane domain (TMD). The situation is unclear for membrane-anchored proteins such as SNAREs, which are anchored to the membrane by their TMD at the C-terminus. For example, in plants, Sec22 and SYP31 (a yeast Sed5 homologue) have a 17 aa TMD but different locations (ER/Golgi and Golgi), indicating that TMD length alone is not sufficient to explain their targeting. To establish the identity of factors that influence SNARE targeting, mutagenesis and live cell imaging experiments were performed on SYP31. It was found that deletion of the entire N-terminus domain of SYP31 blocked the protein in the ER. Several deletion mutants of different parts of this N-terminus domain indicated that a region between the SNARE helices Hb and Hc is required for Golgi targeting. In this region, replacement of the aa sequence MELAD by GAGAG or MALAG retained the protein in the ER, suggesting that MELAD may function as a di-acidic ER export motif EXXD. This suggestion was further verified by replacing the established di-acidic ER export motif DLE of a type II Golgi protein AtCASP and a membrane-anchored type I chimaera, TMcCCASP, by MELAD or GAGAG. The MELAD motif allowed the proteins to reach the Golgi, whereas the motif GAGAG was found to be insufficient to facilitate ER protein export. Our analyses indicate that we have identified a novel and transplantable di-acidic motif that facilitates ER export of SYP31 and may function for type I and type II proteins in plants

Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches

Background - The major proteins in lupin seeds are conglutins that have primary roles in supplying carbon, sulphur and nitrogen and energy for the germinating seedling. They fall into four families; α, β, γ and δ. Interest in these conglutins is growing as family members have been shown to have beneficial nutritional and pharmaceutical properties. Results - An in-depth transcriptome and draft genome from the narrow-leafed lupin (NLL; Lupinus angustifolius) variety, Tanjil, were examined and 16 conglutin genes were identified. Using RNAseq data sets, the structure and expression of these 16 conglutin genes were analysed across eight lupin varieties from five lupin species. Phylogenic analysis suggest that the α and γ conglutins diverged prior to lupin speciation while β and δ members diverged both prior and after speciation. A comparison of the expression of the 16 conglutin genes was performed, and in general the conglutin genes showed similar levels of RNA expression among varieties within species, but quite distinct expression patterns between lupin species. Antibodies were generated against the specific conglutin families and immunoblot analyses were used to compare the levels of conglutin proteins in various tissues and during different stages of seed development in NLL, Tanjil, confirming the expression in the seed. This analysis showed that the conglutins were expressed highly at the mature seed stage, in all lupin species, and a range of polypeptide sizes were observed for each conglutin family. Conclusions - This study has provided substantial information on the complexity of the four conglutin families in a range of lupin species in terms of their gene structure, phylogenetic relationships as well as their relative RNA and protein abundance during seed development. The results demonstrate that the majority of the heterogeneity of conglutin polypeptides is likely to arise from post-translational modification from a limited number of precursor polypeptides rather than a large number of different genes. Overall, the results demonstrate a high degree of plasticity for conglutin expression during seed development in different lupin species

Glucosylceramide synthesis contributes to the transport of proteins through the plant secretory pathway

Le rôle des lipides comme des acteurs moléculaires de la voie sécrétoire des plantes n'est pas encore complètement élucidé. Le Glucosylceramide (GlcCer) est synthétisé par la Glucosylceramide synthase (GCS) chez les plantes et constitue un des sphingolipides complexes clé dans les membranes, mais on connaît peu les exigences cellulaires pour le GlcCer. Cette étude repose sur le blocage de la biosynthèse de GlcCer, par l'utilisation d'inhibiteurs chez le tabac et l’arabidopsis, et la production de mutants d'Arabidopsis, pour déterminer l'impact de la biosynthèse du GlcCer sur la dynamique endomembranaire des cellules végétales. Dans une approche qui inclue la biochimie des lipides, l'imagerie de cellules vivantes, des études ultrastructurales par microscopie electronique à transmission et des études sur le développement de la plante entière, nous avons acquis une meilleure compréhension de l'impact de la synthèse du GlcCer dans les cellules végétales qui peut être résumée comme suit: (1) Sur la base d’un analyse théorique et de la microscopie de cellules vivantes on a déterminé que la GCS est situé dans le Réticulum Endoplasmique (au début de la voie sécrétoire) dans les cellules végétales, (2) PDMP est un inhibiteur spécifique de GCS chez les plantes, (3) La perturbation de la biosynthèse du GlcCer par le PDMP et par un approche génétique ont montré que le GlcCer est important pour le trafic normale des protéines et pour la dynamique des endomembranes, notamment dans le maintien de la structure de l’appareil de Golgi, (4) La régulation du trafic des protéines mediée par la synthèse du GlcCer pourrait être critique dans l’etablissement et le maintien de la polarité cellulaire, tel qu’il est suggéré par des changements dans la localisation des marqueurs polaires chez l’Arabidopsis traitée avec PDMP, et (5) Un bloc dans la synthèse du GlcCer peut conduire à des défauts importants dans le développement des plantes, comme le montrent des mutants d'Arabidopsis avec une croissance anormale des racines primaires et incapables à se développer jusqu’aux étapes reproductives. Les interactions potentielles entre GlcCer et les machineries de transport sont discutés, ainsi que les mécanismes cellulaires qui sont potentiellement déclenchés dans les cellules végétales pour compenser une perturbation de la biosynthèse du GlcCer.The role of lipids as molecular actors in protein secretion is not well understood in plants. Glucosylceramide (GlcCer) is synthesized by Glucosylceramide Synthase (GCS) in plants and constitutes a key complex sphingolipid in membranes, but little is known about the plant cellular requirements for GlcCer. This study relied upon the block of GlcCer biosynthesis, by the use of inhibitors in tobacco and Arabidopsis, and the production of Arabidopsis mutants, to determine the impact of GlcCer biosynthesis on plant cell endomembrane dynamics. In a comprehensive approach that included lipid biochemistry, live cell imaging, ultrastructural studies by Transmission Electron Microscopy, and whole plant developmental studies, we have gained a better understanding of the impact of GlcCer in plant cells that can be summarised as follows: (1) Based on theoretical analysis and live-cell microscopy the GCS is located to the Endoplasmic Reticulum (at the beginning of the secretory pathway) in plant cells, (2) PDMP is a specific inhibitor of GCS in plants, (3) Disruption of GlcCer biosynthesis using PDMP and genetic approaches showed that GlcCer is important for normal protein trafficking and endomembrane dynamics, notably in the maintenance of Golgi structure, (4) The regulation of protein trafficking by the synthesis of GlcCer could be critical in the establishment and maintenance of cell polarity, as suggested by defects in the localisation of polar markers in Arabidopsis treated with PDMP, and (5) A block in GlcCer synthesis may be conducive to severe defects in plant development, as Arabidopsis mutants showed abnormal primary root growth and inability to develop to reproductive stages. Potential interactions between GlcCer and the transport machineries are discussed, as well as cellular mechanisms that may be set off following a disruption of GlcCer biosynthesis in plant cells

Glucosylceramide synthesis contributes to the transport of proteins through the plant secretory pathway

Le rôle des lipides comme des acteurs moléculaires de la voie sécrétoire des plantes n'est pas encore complètement élucidé. Le Glucosylceramide (GlcCer) est synthétisé par la Glucosylceramide synthase (GCS) chez les plantes et constitue un des sphingolipides complexes clé dans les membranes, mais on connaît peu les exigences cellulaires pour le GlcCer. Cette étude repose sur le blocage de la biosynthèse de GlcCer, par l'utilisation d'inhibiteurs chez le tabac et l’arabidopsis, et la production de mutants d'Arabidopsis, pour déterminer l'impact de la biosynthèse du GlcCer sur la dynamique endomembranaire des cellules végétales. Dans une approche qui inclue la biochimie des lipides, l'imagerie de cellules vivantes, des études ultrastructurales par microscopie electronique à transmission et des études sur le développement de la plante entière, nous avons acquis une meilleure compréhension de l'impact de la synthèse du GlcCer dans les cellules végétales qui peut être résumée comme suit: (1) Sur la base d’un analyse théorique et de la microscopie de cellules vivantes on a déterminé que la GCS est situé dans le Réticulum Endoplasmique (au début de la voie sécrétoire) dans les cellules végétales, (2) PDMP est un inhibiteur spécifique de GCS chez les plantes, (3) La perturbation de la biosynthèse du GlcCer par le PDMP et par un approche génétique ont montré que le GlcCer est important pour le trafic normale des protéines et pour la dynamique des endomembranes, notamment dans le maintien de la structure de l’appareil de Golgi, (4) La régulation du trafic des protéines mediée par la synthèse du GlcCer pourrait être critique dans l’etablissement et le maintien de la polarité cellulaire, tel qu’il est suggéré par des changements dans la localisation des marqueurs polaires chez l’Arabidopsis traitée avec PDMP, et (5) Un bloc dans la synthèse du GlcCer peut conduire à des défauts importants dans le développement des plantes, comme le montrent des mutants d'Arabidopsis avec une croissance anormale des racines primaires et incapables à se développer jusqu’aux étapes reproductives. Les interactions potentielles entre GlcCer et les machineries de transport sont discutés, ainsi que les mécanismes cellulaires qui sont potentiellement déclenchés dans les cellules végétales pour compenser une perturbation de la biosynthèse du GlcCer.The role of lipids as molecular actors in protein secretion is not well understood in plants. Glucosylceramide (GlcCer) is synthesized by Glucosylceramide Synthase (GCS) in plants and constitutes a key complex sphingolipid in membranes, but little is known about the plant cellular requirements for GlcCer. This study relied upon the block of GlcCer biosynthesis, by the use of inhibitors in tobacco and Arabidopsis, and the production of Arabidopsis mutants, to determine the impact of GlcCer biosynthesis on plant cell endomembrane dynamics. In a comprehensive approach that included lipid biochemistry, live cell imaging, ultrastructural studies by Transmission Electron Microscopy, and whole plant developmental studies, we have gained a better understanding of the impact of GlcCer in plant cells that can be summarised as follows: (1) Based on theoretical analysis and live-cell microscopy the GCS is located to the Endoplasmic Reticulum (at the beginning of the secretory pathway) in plant cells, (2) PDMP is a specific inhibitor of GCS in plants, (3) Disruption of GlcCer biosynthesis using PDMP and genetic approaches showed that GlcCer is important for normal protein trafficking and endomembrane dynamics, notably in the maintenance of Golgi structure, (4) The regulation of protein trafficking by the synthesis of GlcCer could be critical in the establishment and maintenance of cell polarity, as suggested by defects in the localisation of polar markers in Arabidopsis treated with PDMP, and (5) A block in GlcCer synthesis may be conducive to severe defects in plant development, as Arabidopsis mutants showed abnormal primary root growth and inability to develop to reproductive stages. Potential interactions between GlcCer and the transport machineries are discussed, as well as cellular mechanisms that may be set off following a disruption of GlcCer biosynthesis in plant cells

siRNA-mediated silencing of mgfp5-ER in GFP-expressing protoplasts

RNA-mediated gene silencing is a highly conserved cellular mechanism induced by the intracellular presence of double-stranded RNA (dsRNA). Small interfering RNA duplexes (siRNA) are produced after enzymatic cleavage of dsRNA and induce the degradation of homologous RNA. siRNA-mediated silencing appears to be an RNA based system for counteraction of virus infections in plants and it could be used in specific silencing of genes for genomic studies involving gene characterization. This thesis explores the use of multiple siRNAs for silencing of the mgfp5-ER gene in protoplasts expressing the Green Fluorescent Protein (GFP). To investigate this, hairy roots expressing GFP were produced by Agrobacterium-mediated transformation. Nicotiana tabacum cv. Petit Havana SR1 (tobacco), Solanum tuberosum cv. Iwa (potato), rapid-cycling Brassica oleracea, and B. campestris var. pekinensis cv. Wong Bok (Chinese cabbage) explants were co-cultivated with Agrobacterium strain A4T. Hairy roots were produced in tobacco and Chinese cabbage; the efficiency of transformation was 33% and 7% respectively. The hairy roots were selected on the basis of their uniform expression of GFP and their characteristic hairy root phenotype. PCR was used to confirm the presence of the GFP gene. Additionally, seeds were obtained from rapid-cycling B. oleracea plants stably expressing GFP. Chinese cabbage hairy roots and hypocotyls from etiolated rapid-cycling B. oleracea seedlings were subsequently used as source material for protoplast isolation. Yields of 3-5x10⁵ protoplasts per gram of Chinese cabbage hairy roots and a mean yield of 1.2x10⁶ protoplasts per gram of etiolated hypocotyls were obtained. A mixture of multiple siRNA was produced to target silencing of GFP in the protoplasts by transfection. Delivery of the siRNA was confirmed by observing the fate of control Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) siRNA labelled with Cy3 fluorescent dye. As performed in this study, transfection of siRNA using a combination of polyethylene glycol (PEG) and Lipofectamine™ 2000 was not successful in delivering the siRNA into the protoplasts. Image analysis was used to measure GFP levels in this experiment. Successful transfection was achieved using Lipofectamine™ 2000 alone. Control Cy3-labeled GAPDH siRNA was observed in the protoplasts transfected, which confirmed transfection. Approximately 30% of the protoplasts showed red-fluorescent spots consistent with fluorescence of the dye. However, Lipofectamine™ 2000 was toxic and protoplast viability was reduced to approximately 50% when measured 48 h after transfection. Silencing of GFP was measured by qualitative RT-PCR. Preliminary studies were carried out to partly optimise qualitative RT-PCR analysis for confirmation of GFP silencing. Much work needs to be done before gene silencing in protoplasts using transfection of siRNA becomes efficient but this study has set the basis for future research on transfection of siRNA into protoplasts to reduce gene expression

Rapid nanoscale quantitative analysis of plant sphingolipid long-chain bases by GC-MS

International audienceIn eukaryotic organisms, sphingolipids are major structural lipids of biological membranes and perform additional essential functions as signalling molecules. While long-chain bases (LCB), the common precursor to all sphingolipid classes, is represented by only one major molecular species in animals and fungi, up to nine LCB have been found in plants. In the absence of genuine plant sphingolipid references required for proper quantification, we have reinvestigated and optimized a protocol destined to the quantification of total plant LCB that relies on the use of gas chromatography-mass spectrometry (GC-MS). This rapid three-step protocol sequentially involves (1) the release of LCB from biological samples using barium hydroxide solution, (2) their oxidation into aldehydes by metaperiodate, and (3) the subsequent identification/quantification of these aldehydes by GC-MS. It is simple and reliable and enables separation of aldehydes upon their stero-specificity. It further enables the quantification of total LCB from a wide variety of samples including yeast and animal cell culturesIn eukaryotic organisms, sphingolipids are major structural lipids of biological membranes and perform additional essential functions as signalling molecules. While long-chain bases (LCB), the common precursor to all sphingolipid classes, is represented by only one major molecular species in animals and fungi, up to nine LCB have been found in plants. In the absence of genuine plant sphingolipid references required for proper quantification, we have reinvestigated and optimized a protocol destined to the quantification of total plant LCB that relies on the use of gas chromatography-mass spectrometry (GC-MS). This rapid three-step protocol sequentially involves (1) the release of LCB from biological samples using barium hydroxide solution, (2) their oxidation into aldehydes by metaperiodate, and (3) the subsequent identification/quantification of these aldehydes by GC-MS. It is simple and reliable and enables separation of aldehydes upon their stero-specificity. It further enables the quantification of total LCB from a wide variety of samples including yeast and animal cell culture

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

Abstract Background Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. Results By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5′ RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. Conclusion This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development

Doxorubicin Inhibits Phosphatidylserine Decarboxylase and Modifies Mitochondrial Membrane Composition in HeLa Cells

Doxorubicin (DXR) is a drug widely used in chemotherapy. Its mode of action is based on its intercalation properties, involving the inhibition of topoisomerase II. However, few studies have reported the mitochondrial effects of DXR while investigating cardiac toxicity induced by the treatment, mostly in pediatric cases. Here, we demonstrate that DXR alters the mitochondrial membrane composition associated with bioenergetic impairment and cell death in human cancer cells. The remodeling of the mitochondrial membrane was explained by phosphatidylserine decarboxylase (PSD) inhibition by DXR. PSD catalyzes phosphatidylethanolamine (PE) synthesis from phosphatidylserine (PS), and DXR altered the PS/PE ratio in the mitochondrial membrane. Moreover, we observed that DXR localized to the mitochondrial compartment and drug uptake was rapid. Evaluation of other topoisomerase II inhibitors did not show any impact on the mitochondrial membrane composition, indicating that the DXR effect was specific. Therefore, our findings revealed a side molecular target for DXR and PSD, potentially involved in DXR anti-cancer properties and the associated toxicity

Erratum to "Links between lipid homeostasis, organelle morphodynamics and protein trafficking in eukaryotic and plant secretory pathways" [Plant Cell Rep. 30 (2011) 177-193]

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