Plant development is complex and highly regulated. Tens of thousands of genes have been sequenced for the model plant <em>Arabidopsis thaliana</em>, yet few have been functionally annotated and characterized. This thesis describes the expression analysis and characterization of four genes in <em>Arabidopsis</em>. Three of these belong to the eukaryotic translation initiation factor 5A (eIF5A) gene family, and the fourth encodes diacylglycerol acyltransferase 1 (DGAT1). Putative roles for these genes in the development of <em>Arabidopsis thaliana</em> are described. <br /><br /> eIF5A is the only known protein to contain the amino acid hypusine. It has been demonstrated previously that eIF5A acts as a shuttle protein, moving specific mRNAs from the nucleus to the cytoplasm for translation. In <em>Arabidopsis thaliana</em> (At), there are three isoforms of eIF5A, and it is clear from the present study that they each have a unique temporal and spatial expression pattern. AteIF5A-1 and -2 are up-regulated during natural senescence and wounding/pathogenesis, respectively, and it is proposed that they regulate the onset of programmed cell death during these events. AteIF5A-3 is up-regulated in elongating meristem of the root, and it is proposed that this isoform is involved in cell growth. <br /><br /> Over-expression of the individual <em>AteIF5A</em> isoforms <em>in planta</em> resulted in pleiotropic phenotypes. When <em>AteIF5A-1</em> or <em>AteIF5A-2</em> was over-expressed, the phenotypes observed were indicative of their putative roles in the translation of proteins required for programmed cell death. When <em>AteIF5A-3</em> was over-expressed, the phenotypes were indicative of a role for this protein in the regulation of cell and tissue elongation. <br /><br /> Lipid analysis of rosette leaves from <em>Arabidopsis thaliana</em> revealed an accumulation of triacylglycerol with advancing leaf senescence coincident with an increase in the abundance and size of plastoglobuli. The terminal step in the biosynthesis of triacylglycerol in <em>Arabidopsis</em> is catalyzed by DGAT1. When gel blots of RNA isolated from rosette leaves at various stages of development were probed with the <em>Arabidopsis</em> EST clone, E6B2T7, which has been annotated as DGAT1, a steep increase in DGAT1 transcript levels was evident in the senescing leaves coincident with the accumulation of triacylglycerol. The increase in DGAT1 transcript correlated temporally with enhanced levels of DGAT1 protein detected immunologically. Two lines of evidence indicated that the triacylglycerol of senescing leaves is synthesized in chloroplasts and sequesters fatty acids released from the catabolism of thylakoid galactolipids. First, triacylglycerol isolated from senescing leaves proved to be enriched in hexadecatrienoic acid (16:3) and linolenic acid (18:3), which are normally present in thylakoid galactolipids. Second, DGAT1 protein in senescing leaves was found to be associated with chloroplast membranes. These findings collectively indicate that DGAT1 plays a role in senescence by sequestering fatty acids de-esterified from galactolipids into triacylglycerol.

In this thesis, an intramolecular Pauson-Khand reaction of chiral enynes derived from homoallyl, allyl and homopropargyl alcohols is described. For this purpose, 2-heteroaryl substituted homoallyl, allyl and homopropargyl alcohols are easily and efficiently resolved through enzymatic resolution in a high ee (91-99%) with a known stereochemistry. Each enantiomerically enriched enyne derived from homoallyl and homopropargyl alcohols affords the conformationally most stable diastereomeric cyclopenta[c]pyran ring system as a sole product, whereas enantiomerically enriched enynes derived from allyl alcohols give the diastereomeric cis:trans mixture of cyclopenta[c]furan ring system. In addition these, an intramolecular Pauson&ndash / Khand reaction of camphor tethered enynes derived from homoallyl, homomethallyl, and homopropargyl alcohols is also described. Accordingly, homoallyl, homomethallyl, and homopropargyl moieties are easily constructed on the camphor carbonyl group with excellent diastereoselectivity due to endo-face selectivity, and with known stereochemistry. Each enantiomerically pure enyne affords the conformationally most stable diastereomeric spirocyclic cyclopenta[c]pyran ring system.

<p>Recombinant Candida antarctica lipase B was successfullyproduced in the methylotropic yeast Pichia pastoris. Thespecific activities of Candida antarctica lipase B produced inPichia pastoris and commercial Candida antarctica lipase B fromNovozymes were the same. In shake-flask cultivations theexpression levels were about 25 mg L-1. Production levels couldbe increased to 1.5 g L-1, using a fermentor. A model tosimulate growth and oxygen consumption was described. The highcell density growth could be explained by the low maintenancecoefficient of Pichia pastoris. Enrichment of the aeration withoxygen increased the recombinant protein production. The lipasewas also produced as a fusion to a cellulose binding module.The cellulose binding module did not interfere with thespecific activity of the lipase. With this fusion proteincatalytic reactions can be performed in close proximity to acellulose surface. The binding module can also function as anaffinity tag for purification. Establishment of the Candidaantarctica lipase B production system allowed the engineeringof Candida antarctica lipase B variants. Four differentvariants were produced in order to investigate if electrostaticinteractions contributed to enantioselectivity. Theenantioselectivity of two halogenated secondary alcohols wasdoubled for the Ser47Ala variant. Thisimplied thatelectrostatic interactions are important forenantioselectivity. The Trp104His variant showed a decrease inenantioselectivity for all tested substrates. This was causedby an increase in the size of the stereoselectivity pocket.Symmetrical secondary alcohols of different size were used tomap the stereoselectivity pocket. A substituent as large as apropyl or isopropyl could be accommodated in the pocket of theTrp104His variant. In the wild-type lipase thestereoselectivity pocket was estimated to fit an ethyl group.The enzyme variants were subjected to a thermodynamic study, toelucidate changes in the enthalpic and entropic contributionsto enantioselectivity. The enthalpic and entropic contributionschanged for the different lipase variants and werecompensatory. The compensation was not perfect, allowing forchanges in enantioselectivity.</p><p>In general one can conclude that rational design of newenzyme properties, in order to change the substrateselectivity, is feasible if based on a thorough model ofsubstrate enzyme interactions.</p><p><b>Key words:</b>Protein expression, Candida antarctica lipaseB, Pichia pastoris, sitedirected mutagenesis, fermentation,selectivity</p>

<p>The recent development of methods for constructing andhandling large collections (libraries) of proteins, from whichvariants with desired traits can be isolated, hasrevolutionized the field of protein engineering. Key elementsof such methods are the various ways in which the genotypes(the genes) and the phenotypes (the encoded proteins) arephysically linked during the process. In one section of thework underlying this thesis, one such technique (phagedisplay), was used to isolateand identify protein librarymembers based on their catalytic or target molecule-bindingproperties.</p><p>In a first study, phage display libraries of the lipolyticenzyme Lipolase from Thermomyces lanuginosa were constructed,the objective being to identify variants with improvedcatalytic efficiency in the presence of detergents. Toconstruct the libraries, nine positions were targeted for codonrandomization, all of which are thought to be involved in theconformational change-dependent enzyme activation that occursat water-lipid interfaces. The aim was to introduce two tothree amino acid mutations at these positions per lipase gene.After confirming that the wt enzyme could be functionallydisplayed on phage, selections with the library were performedutilizing a mechanism-based biotinylated inhibitor in thepresence of a detergent formulation. According to rhodamineB-based activity assays, the fraction of active clonesincreased from 0.2 to 90 % over three rounds of selection.Although none of the variants selected using this approachshowed increased activity, in either the presence or absence ofdetergent compared to the wild type enzyme, the resultsdemonstrated the possibility of selecting variants of theenzyme based on catalytic activity.</p><p>In the following work, phage libraries of the StaphylococcalProtein A (SPA)-derived Z-domain, constructed by randomizationof 13 surface-located positions, were used to isolate Z domainvariants (affibodies) with novel binding specificities. Astargets for selections, the parental SPA domains as well as twopreviously selected affibodies directed against two unrelatedtarget proteins were used. Binders of all three targets wereisolated with affinities (KD) in the range of 2-0.5 µM.One SPA binding affibody (Z_SPA-1) was shown to bind to each of the fivehomologous native IgG-binding domains of SPA, as well as theZdomain used as the scaffold for library constructions.Furthermore, the Z_SPA-1affibody was shown to compete with one of thenative domains of SPA for binding to the Fc part of humanantibodies, suggesting that the Z_SPA-1affibody bound to the Fc-binding surface ofthe Z domain. The majority of the affibodies isolated in theother two selections using two different affibodies as targets,showed very little or no binding to unrelated affibodies,indicating that the binding was directed to the randomizedsurface of their respective targets, analogously toanti-idiotypic antibodies.</p><p>The structure of the wild type Z domain/Z_SPA-1affibody co-complex was determined by x-raycrystallography, which confirmed the earlier findings in thatthe affibody Z_SPA-1affibody was shown to bind to the Fc bindingsurface of the Z domain. Further, both the Z domain and the Z_SPA-1affibody had very similar three helix-bundletopologies, and the interaction surface involved ten out of thethirteen randomized residues, with a central hydrophobic patchsurrounded by polar residues. In addition, the interactionsurface showed a surprisingly high shape complementarity, giventhe limited size of the library used for selections. The Z_SPA-1affibody was further investigated for use invarious biotechnological applications. In one study, the Z_SPA-1affibody was successfully recruited as a novelaffinity gene fusion partner for production, purification anddetection of cDNA-encoded recombinant proteins using anSPA-based medium for affinity chromatography. Further, the SPAbinding capability of the Z_SPA-1affibody was employed for site-specific andreversible docking of Z_SPA-1affibody-tagged reporter proteins onto an SPAfusion protein anchored to a cellulose surface via acellulose-binding moiety. These generated protein complexesresembles the architecture of so-called cellulosomes observedin cellulolytic bacteria. The results suggest it may bepossible to use anti-idiotypic affibody-binding protein pairsas modules to build other self-assembling types of proteinnetworks.</p><p><b>Keywords:</b>phage display, selection, mechanism-basedinhibitor, affinity domains, crystal structure, Staphylococcusaureus protein A, affinity chromatography, anti-idiotypicbinding pairs, affibody, combinatorial, protein engineering,lipase, cellulosome, assembly.</p>

<p>Enzymes as tools in organic synthesis have provided enormous advantages. This thesis deals with the applications of enzymes in the kinetic resolutions of racemic compounds. The stereochemistry of chiral compounds and the kinetics of α/β hydrolase lipases are presented. From a practical point of view, the handling of a large number of parameters that influences the kinetic resolutions, especially enantioselectivity (E-value) are systematically described. A variety of approaches employed for raising the yields to over 50% are additionally discussed.</p><p>Methods for the preparation of synthetically useful chiral building blocks were developed in this thesis. Thus, resolution of secondary alcohols bearing two vicinal stereocentres are studied. These building blocks can serve as starting materials for the synthesis of various enantiomerically pure compounds for agrochemistry, pharmaceuticals, chemical industry, and particularly for the total synthesis of pheromones.</p><p>Racemic 3-substitued 2-hydroxybutane derivatives were produced in fairly high diastereomeric purities by a variety of chemical approaches, such as epimerization, metal-catalysed asymmetric addition etc. Kinetic resolution of these racemates was achieved by enzyme-catalysed reactions. Two lipases, Candida antarctica lipase B and Pseudomonas cepacia lipase were found to be useful in acylations as well as hydrolyses. In the biotransformations studied, the presence and nature of the second vicinal stereocentre in the chiral secondary alcohols investigated seemed to be important, e.g. in terms of the efficiencies of sequential kinetic resolutions, and altering the selectivities as well.</p>

New catalytic synthetic methods in organic chemistry that satisfy increasingly stringent environmental constraints are in great demand by the pharmaceutical and chemical industries. Studies over last 15 years have revealed that activity of enzymes can be increased in organic solvents rather than their natural aqueous environment. Because of their ease of use, high selectivity and environment friendliness, enzymes are enjoying increasing popularity in today's synthesis world. Chapter 1 describes chemo-enzymatic synthesis of various glycolipid analogs. A highly regioselective macrolactonization was achieved using lipase from Candida antarctica as a catalyst. It also describes evaluation of lipases from different source and their efficiency in catalyzing the macrolactonization reaction. These analogs were synthesized using commercially available agriculture based disaccharides (maltose, lactose, cellobiose, melibiose). These glycolipid analogues have potential applications in the cosmetic industry, formulation, food production, and pharmaceutical industry.In Chapter 2, ring opening polymerization of epsilon-caprolactone in ionic liquid, [bmim][PF6] was investigated. A comparative study of ROP in different solvents (toluene, Ionic liquid, and bulk condition) was conducted. Effect of time and enzyme concentration on molecular weight and % yield was investigated. It was concluded that enzymatic ring opening polymerization of epsilon-caprolactone in ionic liquid, [bmim][PF6 ] is a very competitive and environmental friendly way of synthesizing high molecular weight polyesters.

Les enzymes pancréatiques de remplacement sont les plus utilisées dans le but d'améliorer la qualité de vie des personnes ayant un problème d'insuffisance pancréatique exocrine (IPE) relié aux maladies comme la pancréatite, la fibrose kystique et la stéatorrhée. Les enzymes pancréatiques de remplacement ont différentes origines et les plus utilisées proviennent du pancréas d'origine porcine (EPP), étudiées dans le présent travail. Dans le commerce on peut trouver des comprimés d'enzymes avec enrobages entériques. En effet, il y a plusieurs formes commerciales d'enzymes pancréatiques disponibles sur le marché et telles compositions peuvent être résistantes au milieu gastrique, mais le profil de libération n'est pas toujours satisfaisant. Comme un exemple, chez les patients atteints d'IPE la région supérieure du petit intestin est généralement acide ce qui a comme résultat que les préparations entériques normalement soient dissoutes trop tard dans l'intestin ce qui rendre indisponibles les enzymes dans le site approprié. Suite à la découverte de la capacité des comprimés faits d'enzymes pancréatiques de former une couche externe en milieu acide (FGS), l'objectif du présent travail a été d'élaborer des comprimés d'enzymes sans excipients additionnés et sans enrobage, capables de se protéger dans un milieu gastrique et de libérer son contenu dans l'intestin. Il semble que les enzymes ont une plus grande force de cohésion inter particulaire après leur compression et peuvent aussi être auto-assemblés en comprimés monolithiques. L'auto-assemblage est le résultat de plusieurs sortes d'interactions entre les chaines de protéines, comme les associations d'hydrogène (ex : entre lysine, histidine, tyrosine et sérine) et les interactions ioniques (ex : entre les -COO- et NH3+ impliquant glutamate-lysine et aspartate-lysine). Dans les comprimés obtenus, les protéines peuvent agir comme des tampons et de cette manière augmentent la stabilité gastrique. Dans le milieu intestinal, les groupes carboxyliques sont déprotonés et ionisés provoquant aussi l'hydratation, l'érosion et la désintégration des comprimés et la libération des enzymes thérapeutiques. Des études de stabilisation et de dissolution des comprimés d'EPP (lipase, amylase et protéase) ont été faites dans des milieux FGS et FIS. Suite aux résultats prometteurs du brevet « Compositions pharmaceutiques gastro-résistantes à base d'enzymes », le travail est approfondi sur des aspects structuraux en utilisant une préparation commerciale d'alpha-amylase. Les profiles FTIR et SDS/PAGE ont été utilisés pour étudier les interactions protéine-protéine dans des comprimés d'alpha-amylase et l'effet de la pression et du milieu gastrique sur la structure de cette enzyme. La nouveauté du concept est que les enzymes pancréatiques en plus d'être les principes actifs, agissent comme liants et comme agents chargés de générer et stabiliser une couche externe sensible au pH. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : enzyme, gastro-résistance, comprimés, pancréas, FTIR, alpha-amylase, lipase, protéase.

No description available.

<p>The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity (&gt / 1%) was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study.</p>

Pseudozyma (Candida) antarctica lipase B (PalB) was expressed in Escherichia coli facilitating protein engineering. The lack of glycosylation was evaluated for a deeper understanding of the difficulties in expressing PalB in E. coli. Different systems were tested: periplasmic expression in Rosetta (DE3), cytosolic expression in Rosetta-gami 2(DE3), Origami 2(DE3), and coexpression of groES and groEL. Periplasmic expression resulted 5.2 mg/L active PalB at 16 °C in shake flasks. This expression level was improved by using the EnBase technology, enabling fed-batch cultivation in 24-deep well scale. The feed rate was titrated with the addition of α-amylase, which slowly releases glucose as energy source. Different media were evaluated where the EnBase mineral salt medium resulted in 7.0 mg/L of active PalB. Protein secreted directly into the media was obtained using the constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter for screening and production of PalB in P. pastoris. A protease sensitive fusion protein CBM-PalB (cellulose-binding module) was used as a model system. When optimised, the expression system resulted in 46 mg/L lipase in 72 hours in shake flask, 37 mg/L lipase in 28 hours in 96-deep-well plate format, and 2.9 g PalB per 10 L bioreactor cultivation. The E. coli expression system was used to express a small focused library of PalB variants, designed to prevent water from entering the active site through a hypothesised tunnel. Screening of the library was performed with a developed assay, allowing for simultaneous detection of both transacylation and hydrolytic activity. From the library a mutant S47L, in which the inner part of the tunnel was blocked, was found to catalyse transacylation of vinyl butyrate in 20 mM butanol 14 times faster than hydrolysis. Water tunnels, assisting water in reaching the active sites, were furthermore found by molecular modelling in many hydrolases. Molecular modelling showed a specific water tunnel in PalB. This was supported by experimental data, where the double mutant Q46A S47L catalysed transacylation faster than hydrolysis compared to the wild type PalB. / <p>QC 20100818</p>