Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.Comment: 4 pages, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014

Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

Explorative analysis of the mechanisms of Phaeocystis globosa blooms in the Beibu Gulf using amplicon sequencing data

Phaeocystis is an ecologically important cosmopolitan genus with several species that form harmful algal blooms. Previous studies of the mechanisms of Phaeocystis blooms have been hindered by the small size of Phaeocystis cells and the complex Phaeocystis life cycle, which includes multiple free-living stages and a colonial stage that dominates during blooms. In this thesis, I apply 16S amplicon sequencing to explore the mechanisms underlying a P. globosa bloom in the Beibu Gulf. Using the spatial-temporal dynamics of P. globosa, bacteria, archaea, phytoplankton and environmental variables, I develop a model for the development and progression of the P. globosa bloom. After, I identify bacteria that interact with P. globosa during the bloom by studying the P. globosa colony microbiome. While P. globosa colonies had different bacterial compositions compared to seawater samples collected from the same locations, I did not find evidence for a core P. globosa colony microbiome

Two-component signalling systems of chloroplasts: function, distribution and evolution

PhD 2008 QMTwo-component signal transduction, comprising sensor kinases and response regulators, is the predominant signalling mechanism in prokaryotes. This signalling system originated in bacteria, and has spread to the eukaryotic domain of life through symbiotic, lateral gene transfer from the bacterial ancestors of chloroplasts and mitochondria. During the course of their evolution, chloroplasts, with the exception of a few instances in non-green algae, appear to have relinquished all genes encoding two-component systems to their eukaryotic host cell nuclei. In green algae and plants, chloroplast genes for two-component systems were neither known nor were chloroplast two-component proteins shown to exist as products of nuclear genes prior to the work described here. This thesis describes the identification and characterisation of a novel two-component sensor kinase in chloroplasts. This Chloroplast Sensor Kinase (CSK) is the product of a nuclear gene in algae and plants. CSK is synthesised in the cytosol of Arabidopsis thaliana and imported into the chloroplast as a protein precursor. CSK is autophosphorylated and couples photosynthetic electron transport to gene transcription in chloroplasts. The identity of the response regulator partner of CSK reveals an unexpected phylogenetic and functional relatedness of CSK with chloroplast two-component systems of non-green algae. Chloroplast two-component systems are likely to be universal in photosynthetic eukaryotes and they persist in chloroplasts as products of nuclear genes even where chloroplast genomes no longer encode them. Chloroplast twocomponent systems have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. The persistence of cyanobacterial two-component systems in chloroplasts and their function in coupling photosynthesis with chloroplast gene expression are central to the premise that chloroplasts retain genes whose expression is regulated by the activity of the photosynthetic electron transport chain, using a mechanism conserved from their cyanobacterial ancestors.Queen Mary University of London Postgraduate Research Studentshi

Control of plastidial metabolism by the Clp protease complex

Plant metabolism is strongly dependent on plastids. Besides hosting the photosynthetic machinery, these endosymbiotic organelles synthesize starch, fatty acids, amino acids, nucleotides, tetrapyrroles, and isoprenoids. Virtually all enzymes involved in plastid-localized metabolic pathways are encoded by the nuclear genome and imported into plastids. Once there, protein quality control systems ensure proper folding of the mature forms and remove irreversibly damaged proteins. The Clp protease is the main machinery for protein degradation in the plastid stroma. Recent work has unveiled an increasing number of client proteins of this proteolytic complex in plants. Notably, a substantial proportion of these substrates are required for normal chloroplast metabolism, including enzymes involved in the production of essential tetrapyrroles and isoprenoids such as chlorophylls and carotenoids. The Clp protease complex acts in coordination with nuclear-encoded plastidial chaperones for the control of both enzyme levels and proper folding (i.e. activity). This communication involves a retrograde signaling pathway, similarly to the unfolded protein response previously characterized in mitochondria and endoplasmic reticulum. Coordinated Clp protease and chaperone activities appear to further influence other plastid processes, such as the differentiation of chloroplasts into carotenoid-accumulating chromoplasts during fruit ripening

Characterization of six Arabidopsis AROGENATE DEHYDRATASE promoters

Phenylalanine is an important aromatic amino acid synthesized by higher plants, and is a major component of numerous specialized metabolites including structural components, pigments, and defense compounds. The last step in the synthesis of phenylalanine is catalyzed by an enzyme called AROGENATE DEHYDRATASE, of which there are six different isoenzymes encoded by the Arabidopsis genome. All six have specialized roles within the plant, and are differentially expressed during development and under stressful conditions. To deduce the specialized role of each ADT, unique patterns of regulatory motifs were identified for all six ADT promoters, as well as corresponding transcription factors with similar expression profiles to each enzyme. Seven stable transgenic Arabidopsis lines were also generated using ADT promoter-eGFP/GUS constructs to test expression in all tissues during development, and under stressful conditions