Similarity between the bacterial histone-like protein HU and a protein from spinach chloroplasts

AbstractThe histone-like protein HU isolated from E. coli is well conserved in prokaryotes. We show here that antiserum prepared against bacterial HU cross-reacts with a DNA-binding protein co-sedimenting with the nucleoid of spinach chloroplasts. Antibodies prepared against cyanobacterial HU are more reactive than those raised against E. coli HU. The chloroplast protein resembles HU in that both appear to be composed of two related subunits

Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids

We have investigated the function of one of the six plastid sigma-like transcription factors, sigma 3 (SIG3), by analysing two different Arabidopsis T-DNA insertion lines having disrupted SIG3 genes. Hybridization of wild-type and sig3 plant RNA to a plastid specific microarray revealed a strong reduction of the plastid psbN mRNA. The microarray result has been confirmed by northern blot analysis. The SIG3-specific promoter region has been localized on the DNA by primer extension and mRNA capping experiments. Results suggest tight regulation of psbN gene expression by a SIG3-PEP holoenzyme. The psbN gene is localized on the opposite strand of the psbB operon, between the psbT and psbH genes, and the SIG3-dependent psbN transcription produces antisense RNA to the psbT–psbH intergenic region. We show that this antisense RNA is not limited to the intergenic region, i.e. it does not terminate at the end of the psbN gene but extends as antisense transcript to cover the whole psbT coding region. Thus, by specific transcription initiation at the psbN gene promoter, SIG3-PEP holoenzyme could also influence the expression of the psbB operon by producing psbT antisense RNA

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Pro

Etude du gène nucléaire RPL21 codant la protéine ribosomique plastidiale L21, au cours du développement de la plante

Les chloroplastes sont essentiels au développement de la plante, convertissant l'énergie lumineuse en énergie chimique nécessaire aux différents métabolites. Notre étude s'inscrit dans le cadre de l'intégration du développement chloroplastique dans le développement de la plante. Le choix du gène modèle pour cette étude s'est porté sur le gène RPL21, gène nucléaire codant une protéine de la grande sous-unité du ribosome plastidial. Le gène RPL21, activé durant les premiers stades de la différenciation des proplastes, constitue un gène cible de signaux tissulaires. Nous avons analysé son promoteur, puis étudié en détail l'expression de ce gène nucléaire au cours de la germination et du développement de la plante. Nous avons analysé le core-promoteur de ce gène, comprenant deux départs de transcription alternatifs (P1 et P2). Un complexe protéique constitué d'au moins cinq facteurs a été mis en évidence. Ce complexe interagit au départ de transcription fort et inductible P1. L'étude de l'expression du gène RPL21 au cours de la germination et du développement révèle une forte corrélation entre l'association du complexe protéique au promoteur et l'accumulation des transcrits initiés à P1. Le rôle primordial de ce complexe pour l'activité du gène RPL21 a été testé in planta, au moyen d'un gène rapporteur, la luciférase. Le gène de la luciférase a été fusionné au core-promoteur du gène RPL21 d'épinard et cette construction a été insérée par transformation chez Arabidopsis thaliana. Cette étude menée avec différentes constructions a démontré l'importance du complexe protéique interagissant à P1 pour l'activité du gène RPL21. Etant donné la similitude des promoteurs des gènes nucléaires d'origine procaryotique codant des protéines ribosomiques plastidiales, il est envisageable que ce complexe régule l'ensemble de ces gènes afin d'avoir une synthèse rapide de protéines ribosomiques dans des rapports stoechiométriques au cours du développement et de la croissance de la plante.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Binding of 16S rRNA to chloroplast 30S ribosomal proteins blotted on nitrocellulose

Protein-RNA associations were studied by a method using proteins blotted on a nitrocellulose sheet. This method was assayed with Escherichia Coli 30S ribosomal components. In stringent conditions (300 mM NaCl or 20° C) only 9 E. coli ribosomal proteins strongly bound to the 16S rRNA: S4, S5, S7, S9, S12, S13, S14, S19, S20. 8 of these proteins have been previously found to bind independently to the 16S rRNA. The same method was applied to determine protein-RNA interactions in spinach chloroplast 30S ribosomal subunits. A set of only 7 proteins was bound to chloroplast rRNA in stringent conditions: chloroplast S6, S10, S11, S14, S15, S17 and S22. They also bound to E. coli 16S rRNA. This set includes 4 chloroplast-synthesized proteins: S6, S11, S15 and S22. The core particles obtained after treatment by LiCl of chloroplast 30S ribosomal subunit contained 3 proteins (S6, S10 and S14) which are included in the set of 7 binding proteins. This set of proteins probably play a part in the early steps of the assembly of the chloroplast 30S ribosomal subunit

RECHERCHES METHODOLOGIQUES EN VUE DE L'ISOLEMENT DE MUTANTS D'EXPRESSION DU GENE NUCLEAIRE RPL21

GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene plastids

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