Project description:Using NanoPore Technology and universal primers to amplify and assemble complete chloroplasts from tree and shrub species that have naturalized in Britain
Project description:The experiment was conducted to examine the influence of non-chloroplast genomes rearangements on chloroplast transcription in cucumber
Project description:The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition.
Project description:ngs2014_07_hevea-hevea_tpd-seq-RNAseq analysis of latex samples from healthy and Tapping Panel Dryness-affected trees.-Identification of Tapping Panel Dryness (TPD)-affected trees in a polyclonal trials grown under standard condition. Trees were tapped since November 2010 every 2 days. Latex yield and TPD occurrence were monitored as well as latex RNA samples were collected twice a year for further analysis. At the end of the experiment, gene expression in latex of healthy and TPD trees were compared.
Project description:In this study we used metaproteomics to discern the metabolism and physiology of the microorganisms occurring in the phototrophic mats of four soda lakes in the interior of British Columbia, Canada. Binned and assembled metagenomes were used as the database for protein identification.
Project description:The paired-end Illumina sequencing of total genomic DNA from Arabidopsis were performed to detect unique breakpoints consistent with rearrangements of chloroplast DNA.
Project description:Devastating citrus disease Huanglongbing (HLB) is without existing cures. Herein, we present results demonstrating the possible mechanisms (hypoxia stress) behind HLB-triggered shoot dieback by comparing the transcriptomes, hormone profiles, and key enzyme activities in buds of severely and mildly symptomatic ‘Hamlin’ sweet orange (Citrus sinensis). Within six months (October – May) in field conditions, severe trees had 23% bud dieback, greater than mild trees (11%), with a concomitant reduction in canopy density. In February, differentially expressed genes (DEGs) associated with responses to osmotic stress, low oxygen levels, and cell death were upregulated, with those for photosynthesis and cell cycle downregulated in severe versus mild trees. For severe trees, not only were the key markers for hypoxia, including anaerobic fermentation, reactive oxygen species (ROS) production, and lipid oxidation, transcriptionally upregulated, but also alcohol dehydrogenase activity was significantly greater compared to mild trees, indicating a link between bud dieback and hypoxia. Tricarboxylic acid cycle revival, given the upregulation of glutamate dehydrogenase and alanine aminotransferase DEGs, suggests that ROS may also be generated during hypoxiareoxygenation. Greater (hormonal) ratios of abscisic acid to cytokinins and jasmonates and upregulated DEGs encoding NADPH oxidases in severe versus mild trees indicate additional ROS production under limited oxygen availability due to stomata closure. Altogether, our results provided evidence that as HLB progresses, excessive ROS produced in response to hypoxia and during hypoxia-reoxygenation likely intensify the oxidative stress in buds leading to cell death, contributing to marked bud and shoot dieback and decline of the severely symptomatic sweet orange trees.
Project description:A transcription factor CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1) regulates chloroplast development in rice (Oryza sativa) through modifying the expression of important nuclear expressed, chloroplast localized genes. A transcriptome analysis was done in wild type plants and transgenic rice over-expressing this OsCGA1 to identify the set of genes with altered expression.
Project description:Protein N-termini are prone to post translational modification and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information and the N-termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N-termini using terminal amine isotopic labeling of substrates (TAILS). Many nuclear-encoded plastid proteins accumulated with two or three different N-termini; we evaluated the significance of these different proteoforms. Ala, Val, Thr (often in N-Î? acetylated form) and Ser were the most frequently observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly under-represented. Plastid-encoded proteins showed a similar distribution of N-terminal residues, but with a higher frequency of Met. Infrequent residues such as Ile, Arg, Cys, Pro, Asp and Glu were observed for several abundant proteins likely reflecting functional regulation through their N-termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (Asp, Glu, Leu, Phe). We propose that after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed. This work provides a baseline for understanding N-terminal processing and maturation of chloroplast proteins.