Studio della subunità epsilon della DNA polimerasi III di Escherichia coli: stabilità e interazione con la subunità polimerasica

Faithful replication of DNA from one generation to the next is crucial for long-term species survival. Genomic integrity in prokaryotes, archaea and eukaryotes is dependent on efficient and accurate catalysis by multiple DNA polymerases. Escherichia coli possesses five known DNA polymerases (Pol). DNA polymerase III holoenzyme is the major replicative polymerase of the Escherichia coli chromosome (Kornberg, 1982). This enzyme contains two Pol III cores that are held together by a t dimer (Studwell-Vaughan and O’Donnell, 1991). The core is composed of three different proteins named α-, ε- and θ-subunit. The α-subunit, encoded by dnaE, contains the catalytic site for DNA polymerisation (Maki and Kornberg, 1985), the ε-subunit, encoded by dnaQ, contains the 3′→5′ proofreading exonuclease (Scheuermann, et al., 1983) and the θ-subunit, encoded by hole, that has no catalytic activity (Studwell-Vaughan, and O'Donnell, 1983). The three-subunit α–ε–θ DNA pol III complex is the minimal active polymerase form purified from the DNA pol III holoenzyme complex; these three polypeptides are tightly associated in the core (McHenry and Crow, 1979) Despite a wealth of data concerning the properties of DNA polymerase III in vitro, little information is available on the assembly in vivo of this complex enzyme. In this study it is shown that the C-terminal region of the proofreading subunit is labile and that the ClpP protease and the molecular chaperones GroL and DnaK control the overall concentration in vivo of ε. Two α-helices (comprising the residues E311-M335 and G339-D353, respectively) of the N-terminal region of the polymerase subunit were shown to be essential for the binding to ε. These informations could be utilized to produce a conditional mutator strain in which proofreading activity would be titrated by a a variant that can only bind e and that is polymerase-deficient. In this way the replication of DNA made by DNA Pol-III holoenzyme would accordingly become error-prone.

Methane production through anaerobic digestion of dedicated energy crops

Methane yield of ligno-cellulosic substrates (i.e. dedicated energy crops and agricultural residues) may be limited by their composition and structural features. Hence, biomass pre-treatments are envisaged to overcome this constraint. This thesis aimed at: i) assessing biomass and methane yield of dedicated energy crops; ii) evaluating the effects of hydrothermal pre-treatments on methane yield of Arundo; iii) investigating the effects of NaOH pre-treatments and iv) acid pre-treatments on chemical composition, physical structure and methane yield of two dedicated energy crops and one agricultural residue. Three multi-annual species (Arundo, Switchgrass and Sorghum Silk), three sorghum hybrids (Trudan Headless, B133 and S506) and a maize, as reference for AD, were studied in the frame of point i). Results exhibit the remarkable variation in biomass yield, chemical characteristics and potential methane yield. The six species alternative to maize deserve attention in view of a low need of external inputs but necessitate improvements in biodegradability. In the frame of point ii), Arundo was subjected to hydrothermal pre-treatments at different temperature, time and acid catalyst (with and without H2SO4). Pre-treatments determined a variable effect on methane yield: pre-treatments without acid catalyst achieved up to +23% CH4 output, while pre-treatments with H2SO4 catalyst incurred a methanogenic inhibition. Two biomass crops (Arundo and B133) and an agricultural residue (Barley straw) were subject to NaOH and acid pre-treatments, in the frame of point iii) and iv), respectively. Different pre-treatments determined a change of chemical and physical structure and an increase of methane yield: up to +30% and up to +62% CH4 output in Arundo with NaOH and acid pre-treatments, respectively. It is thereby demonstrated that pre-treatments can actually enhance biodegradability and subsequent CH4 output of ligno-cellulosic substrates, although pre-treatment viability needs to be evaluated at the level of full scale biogas plants in a perspective of profitable implementation.