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. 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. <b>Key words:</b>Protein expression, Candida antarctica lipaseB, Pichia pastoris, sitedirected mutagenesis, fermentation,selectivity

Initiation is the first step in protein biosynthesis representing a fundamental event in cell life which determines fidelity, efficiency and regulation of gene expression. In addition to the ribosome and mRNA, three protein factors IF1, IF2 and IF3 are involved in the initiation of translation in prokaryotes. Several minor functions have been attributed to the smallest of these factors, IF1. However, the main function of IF1 remains to be elucidated. In order to investigate the role of this protein in the initiation process we have mutated the corresponding gene infA. Using a high-copy plasmid and site-directed mutagenesis, the six arginine residues of IF1 were separately altered to leucine or aspartate. Another set of plasmid-encoded IF1 mutants with a cold-sensitive phenotype was collected using localized random mutagenesis. This strategy was followed by deletion of the chromosomal infA gene. All variants with a mutated infA gene on a plasmid and a deletion of the chromosomal infA copy were viable, except for an R65D alteration. Several of the mutated infA genes were successfully recombined into the chromosome thereby replacing the wild-type allele. Some of these mutants displayed reduced growth rates and a partial cold-sensitive phenotype. The influence of the leucine group of mutants in IF1 on the expression of two reporter genes with different initiation and/or +2 codons has been investigated. Our results do not indicate any involvement of IF1 in recognition of the +2 codon immediately following the start codon, thus representing the A-site. In addition, this group of mutants has no changed efficiency of decoding at the near-cognate initiation codons UUG and GUG. However, one cold-sensitive IF1 mutant shows a general overexpression of both reporter genes, in particular at low temperatures. Overall, the results do not support the hypothesis that IF1 could possess codon discriminatory functions while blocking the A-site of the ribosome. In this study we also identify that IF1 has RNA chaperone activity both in vitro and in vivo. The chaperone assays are based on splicing of the group I intron in the thymidylate synthase gene (td) from phage T4. Some of the IF1 mutant variants are more active as RNA chaperones than the wild-type. Both wild-type IF1 and mutant variants bind with high affinity to RNA in a band-shift assay. It is suggested that the RNA chaperone activity of IF1 contributes to RNA rearrangements during the early phase of translation initiation.

Mushrooms are believed to have a great potential for production of bioactive metabolites e. g. terpenes, a group of interesting compounds with diverse chemical properties such as antitumour and antibacterial activity. Cop6 is a terpene cyclase isolated from the mushroom Coprinus cinereus that catalyzes the cyclization of farnesyl diphosphate (FPP) to mainly α-cuprenene. In this study gas chromatography combined with mass spectroscopy (GC-MS) is used to analyze the product profile of Cop6 mutants created by PCR based site directed mutagenesis. The goal is to produce trichodiene, the parent hydrocarbon in the biosynthesis of trichothecene antibiotics and mycotoxins. Valine instead of tyrosine in amino acid position 195 resulted in cyclisation of (E)-β-Farnesene and (3Z,6E)-α-Farnesene besides the products of the wild type enzyme. Another mutant with aspartic acid instead of asparagine in position 224 resulted in the synthesis of β-Bisabolene except for α-cuprenene and methionine in position 74 instead of isoleucine killed the activity of the cyclase. Furthermore, an attempt to saturation of position 98 was made, resulting in four mutants. Two of them essentially killed the activity of the cyclase whereas two had minor effect of the product profile compared to the wild type.

B cells produce a diverse array of antibody specificities that are of low affinity during the initial phase of a humoral immune response. However, somatic hypermutation of the rearranged V region in the immunoglobulin locus generates new antibody affinities, accompanied by the selection of B cells that produce superior antibody affinities. Somatic hypermutation is initiated by the conversion of G:C base pairs to G:U lesions by the enzyme activation induced cytosine deaminase. Left unrepaired, G:U lesions will give rise to transition mutations at G:C base pairs, but are converted to transition and transversion mutations at G:C and A:T base pairs by the paradoxical participation of the base excision repair and mismatch repair pathways. The mismatch repair pathway, which evolved to correct errors produced during DNA replication, is co-opted by hypermutating B cells to produce A:T mutations via the processing of G:U lesions. This process requires the mismatch repair components Msh2, Msh6, and Exo1, but is additionally dependent upon the translesional DNA polymerase eta, a known A:T mutator, and on ubiquitinated PCNA, an initiator of translesion synthesis. The presence of certain types of lesions in the template strand during DNA replication leads to the activation of translesion synthesis. I propose that a similar mechanism operates during somatic hypermutation to activate translesion synthesis and recruit DNA polymerase eta. Our model suggests that mismatch repair-generated single-stranded DNA tracts contain abasic sites produced as a result of uracil excision by uracil-N-glycosylase. Synthesis opposite abasic sites activates translesion synthesis and results in the recruitment of polymerase eta and the subsequent production of A:T mutations. In this thesis, I present data from hypermutating murine B cells and the B cell line Ramos to support this model, demonstrating that the base excision repair and mismatch repair pathways cooperate during somatic hypermutation to generate A:T mutations. In addition, I explore the role of the Mre11-Rad50-Nbs1 complex in its contribution to A:T mutations in Ramos cells. Taken together, these studies demonstrate that conversion of classical DNA repair pathways into mutation-generating processes is driven by the unique environment of the V region in hypermutating B cells.

Monoamine oxidase (MAO) is a mitochondrial deaminating enzyme that exists as two isoforms, MAO-A and -B. The MAO-mediated reaction generates hydrogen peroxide (H2O2) as a normal by-product. Dysregulation of MAO has been implicated in a variety of neuropsychiatric and neurodegenerative disorders, as well as in the aging process. Endogenous regulators of MAO-A function include calcium (Ca2+) and the p38 mitogen-activated protein kinase (MAPK). Although the effect of p38(MAPK) is thought to rely on induction of mao-A gene expression, post-translational modification of the MAO-A protein is also possible. <p>Using standard biochemical approaches in combination with pharmacological interventions and recombinant DNA strategies, specific aspartic acid residues (within putative Ca2+-binding motifs) were demonstrated to contribute to MAO-A activity. Furthermore, MAO-A activity and its sensitivity to Ca2+ was negatively regulated by the p38(MAPK), which is usually activated during cell stress. The effect of p38(MAPK) on MAO-A function relies specifically on Serine209 in MAO-A, which resides in a p38(MAPK) consensus motif. The serine phosphorylation status of MAO-A determines its capacity for generating peroxy radicals and its toxicity in established cell lines (e.g. C6, N2a, HEK293A, HT-22) and in primary cortical neurons. p38(MAPK)-regulated MAO-A activity is also linked to neurotoxicity associated with the Alzheimer disease-related peptide, Ò-amyloid (AÒ). These data suggest a unique neuroprotective role for p38(MAPK) centered on a negative feedback regulation of the Ca2+-sensitive, H2O2-generating enzyme MAO-A.

The development of a proanthocyanidin (PAC) treatment, along with the understanding of its mechanism of action, would provide an alternative method of preventing attachment to and colonization of surfaces by microorganisms, as well as potentially disrupting preexisting biofilms. The purpose of this research is to examine the role a cranberry proanthocyanidin plays in the primary attachment of Bacillus cereus to an abiotic surface. This technology could be employed in food processing plants where a premium is placed on maintaining a sanitized work environment to prevent product contamination. A biofilm assay showed that a surface treated with proanthocyanidins actually promoted rather than prevented the attachment of Bacillus cereus. This was further made evident by the fact that the surface hydrophobicities of B. cereus cells grown in media supplemented with proanthocyanidins were greater than those grown in its absence. In addition, light microscopy analysis showed a greater degree of sporulation of B. cereus cells when grown on TSA plates supplemented with PACs. These results suggest that proanthocyanidins may be inducing endospore formation in Bacillus cereus leading to increased attachment and surface hydrophobicity values.

B cells produce a diverse array of antibody specificities that are of low affinity during the initial phase of a humoral immune response. However, somatic hypermutation of the rearranged V region in the immunoglobulin locus generates new antibody affinities, accompanied by the selection of B cells that produce superior antibody affinities. Somatic hypermutation is initiated by the conversion of G:C base pairs to G:U lesions by the enzyme activation induced cytosine deaminase. Left unrepaired, G:U lesions will give rise to transition mutations at G:C base pairs, but are converted to transition and transversion mutations at G:C and A:T base pairs by the paradoxical participation of the base excision repair and mismatch repair pathways. The mismatch repair pathway, which evolved to correct errors produced during DNA replication, is co-opted by hypermutating B cells to produce A:T mutations via the processing of G:U lesions. This process requires the mismatch repair components Msh2, Msh6, and Exo1, but is additionally dependent upon the translesional DNA polymerase eta, a known A:T mutator, and on ubiquitinated PCNA, an initiator of translesion synthesis. The presence of certain types of lesions in the template strand during DNA replication leads to the activation of translesion synthesis. I propose that a similar mechanism operates during somatic hypermutation to activate translesion synthesis and recruit DNA polymerase eta. Our model suggests that mismatch repair-generated single-stranded DNA tracts contain abasic sites produced as a result of uracil excision by uracil-N-glycosylase. Synthesis opposite abasic sites activates translesion synthesis and results in the recruitment of polymerase eta and the subsequent production of A:T mutations. In this thesis, I present data from hypermutating murine B cells and the B cell line Ramos to support this model, demonstrating that the base excision repair and mismatch repair pathways cooperate during somatic hypermutation to generate A:T mutations. In addition, I explore the role of the Mre11-Rad50-Nbs1 complex in its contribution to A:T mutations in Ramos cells. Taken together, these studies demonstrate that conversion of classical DNA repair pathways into mutation-generating processes is driven by the unique environment of the V region in hypermutating B cells.

Monoamine oxidase (MAO) is a mitochondrial deaminating enzyme that exists as two isoforms, MAO-A and -B. The MAO-mediated reaction generates hydrogen peroxide (H2O2) as a normal by-product. Dysregulation of MAO has been implicated in a variety of neuropsychiatric and neurodegenerative disorders, as well as in the aging process. Endogenous regulators of MAO-A function include calcium (Ca2+) and the p38 mitogen-activated protein kinase (MAPK). Although the effect of p38(MAPK) is thought to rely on induction of mao-A gene expression, post-translational modification of the MAO-A protein is also possible. <p>Using standard biochemical approaches in combination with pharmacological interventions and recombinant DNA strategies, specific aspartic acid residues (within putative Ca2+-binding motifs) were demonstrated to contribute to MAO-A activity. Furthermore, MAO-A activity and its sensitivity to Ca2+ was negatively regulated by the p38(MAPK), which is usually activated during cell stress. The effect of p38(MAPK) on MAO-A function relies specifically on Serine209 in MAO-A, which resides in a p38(MAPK) consensus motif. The serine phosphorylation status of MAO-A determines its capacity for generating peroxy radicals and its toxicity in established cell lines (e.g. C6, N2a, HEK293A, HT-22) and in primary cortical neurons. p38(MAPK)-regulated MAO-A activity is also linked to neurotoxicity associated with the Alzheimer disease-related peptide, Ò-amyloid (AÒ). These data suggest a unique neuroprotective role for p38(MAPK) centered on a negative feedback regulation of the Ca2+-sensitive, H2O2-generating enzyme MAO-A.

Among the available methods of creating selectable variation, induced mutagenesis has been historically under-utilized in cotton improvement. Dick Auld showed that chemical mutagenesis could be used to enhance fiber length of a medium staple cotton cultivar without sacrificing yield. The goal of this project was to determine if mutagenesis could be used to improve the fiber quality of a germplasm line already considered to be at the upper-limits of fiber length. Seed of TAM 94 L-25 were treated with EMS in 2001 and the M2 generation was produced at Lubbock, Texas in 2002. More than 1200 M3 plants were grown at College Station, Texas in 2004, harvested individually, and HVI fiber properties determined. The top and bottom 1 percent for UHML, strength, and elongation were selected and the seeds of these individuals planted as an M4 progeny row nursery in 2005. Approximately ten individual plants per progeny row were harvested for re-evaluation of fiber parameters. From the approximately 1600 individual TAM 94L-25 M4 plants harvested in 2005, 61 were selected and subsequently treated as pure lines. Agronomic performance trials were conducted on 61 of those TAM 94L-25 M lines along with the M0 check and two commercial cultivar checks, Fiber Max 832 and Phytogen 355, in 2008 and 2009 in College Station and Weslaco, Texas. Within-boll yield components were examined for 13 representative mutant lines and the three checks. TAM 94L-25 averaged 751 kg lint ha^-1, 31.1 mm UHML, 303 kN m kg^-1 fiber bundle strength, and 6.0 percent elongation. The 61 mutant lines yielded from 366 to 932 kg lint ha^-1, exhibited UHML from 24.3 to 34.9 mm, fiber bundle strengths of 261 to 333 kN m kg^-1, and elongations from 5.4 to 8.1 percent. Seed surface area of the TAM 94L-25 M-lines was between 99 and 124 mm^2, and fibers per unit seed surface area from 123 to 168 fibers mm^-2. The M0 parent, TAM 94L-25 averaged 125 mm^2 seed-1, and 128 fibers mm^-2. The data presented herein demonstrate that EMS-induced mutagenesis was successful in creating TAM 94L-25 M-lines with superior fiber and yield traits to that of the non-mutated, high fiber quality parent, TAM 94L-25.

Rhodobacter sphaeroides O.U.001 is a purple non-sulphur bacterium producing hydrogen under photoheterotrophic, nitrogen limited conditions. Hydrogen is produced by Mo-nitrogenase but substantial amount of H2 is reoxidized by a membrane bound uptake hydrogenase. In this study, hydrogen production and the expression of structural nitrogenase genes were investigated by varying molybdenum and iron ion concentrations. These two elements are found in the structure of Mo-nitrogenase and they are important for functioning of the enzyme. The results showed that hydrogen production and nifD gene expression increased upon increase in molybdenum concentration. Increasing iron concentration had also positive effect on hydrogen production and nifK gene expression. To improve the hydrogen producing capacity of R. sphaeroides O.U.001, hupSL genes encoding uptake hydrogenase were disrupted in two different methods. In the first method, hup genes were disrupted by gentamicin resistance gene insertion. In the second method, part of the hup gene was deleted without using antibiotic resistance gene. The wild type and the hup- mutant cells showed similar growth patterns but substantially more hydrogen was produced by the mutant cells. The genes coding for hox1 hydrogenase of Thiocapsa roseopersicina was aimed to be expressed in R. sphaeroides O.U.001 to produce H2 under nitrogenase repressed and mixotrophic conditions. The hox1 hydrogenase genes of T. roseopersicina were cloned and transferred to R. sphaeroides. Although the cloning was successful, the expression of hydrogenase was not achieved by using either the native promoter of hox1 hydrogenase or the crtD promoter of T. roseopersicina.