Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism. Although this decision must be made based on multifaceted factors, a major one is the suitability of pathways for the endogenous metabolism of a host organism, in part because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. To address this point, we developed an open-access web server called MRE (metabolic route explorer) that systematically searches for promising heterologous pathways by considering competing endogenous reactions in a given host organism. MRE utilizes reaction Gibbs free energy information. However, 25% of the reactions do not have accurate estimations or cannot be estimated. To address this issue, we developed a method called FC (fingerprint contribution) to provide a more accurate and complete estimation of the reaction free energy. To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. For a given pair of starting and desired compounds in a given chassis organism, MRE ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. Here, we introduce a machine learning method, referred to as fingerprint contribution (FC), with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. FC is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Depuis une cinquantaine d’années, de nombreuses études ont décrit les spongiaires comme de formidables ressources de produits naturels originaux. Ces découvertes ont attisé la curiosité de nombreux scientifiques issus de domaines variés (chimie, biochimie, biologie moléculaire) qui mettent leurs connaissances en commun afin de comprendre le fonctionnement de ces animaux si particuliers. Les travaux envisagés dans ce manuscrit portent sur les éponges du genre Haliclona issu de l’ordre des Haplosclérides. En effet, ce groupe taxonomique révèle des familles de molécules très particulières, notamment les alcaloïdes 3-AP et les polyacétylènes, qui présentent un potentiel pharmacologique à exploiter. En outre la diversité chimique retrouvée au sein de ce genre remet en question la validité de la classification actuelle des Haplosclérides déjà discutée par les données de biologie moléculaire. L’intérêt particulier porté à ces composés originaux concerne également les voies métaboliques permettant d’aboutir à leur biosynthèse. Ainsi les alcaloïdes 3-AP ne trouvant aucun équivalent notamment dans le monde terrestre, la description de leur voie de biosynthèse n’a alors été envisagée que sous forme d’hypothèses. Afin d’éclaircir les différentes problématiques posées par ce groupe de spongiaires, les études menées pendant ce doctorat ont fait appel à des méthodes et techniques variées tels que les méthodes d’extraction et d’analyses de la chimie des produits naturels classique, l’outil récent qu’est la métabolomique ou encore les expériences de « feeding » et l’utilisation de composés radio-marqués / Since about fifty years, several studies described sponges as astounding resources of original natural products. These discoveries aroused scientist’s curiosity in various areas (chemistry, biochemistry, molecular biology) and to understand these animal’s functioning, they share their knowledge. The proposed work in this manuscript, focus on sponges of genus Haliclona from the order Haplosclerida. Indeed, this taxonomic group reveal peculiar chemical families, including 3-AP alkaloids and polyacetylenic compounds, displaying pharmacological potential to be exploited. Besides, chemicalDépôt de thèseDonnées complémentairesdiversity encountered in this genus challenge the actual classification of Haplosclerida group already disputed by biomolecular data. The particular interest in these original compounds also concerns metabolic pathways leading to their biosynthesis. In this way, 3-AP alkaloids, which don’t have any equivalent particularly in terrestrial area, the description of their biosynthesis pathway was only considered by hypothesis. To resolve various problematics proposed by this sponges’ group, studies conducted through this PhD appeal to several methods and technics like usual natural products chemistry extraction and analytical technics, recent tool named metabolomic or feeding experiments with radiolabelled compounds