Abstract Replicative DNA polymerases (pols) synthesize chromosomal DNA with high accuracy and speed during cell division. In eukaryotes the process involves three family B pols (α, δ, ε), whereas in Archaea, two types of pols, families B and D, are involved. In this study the B-subunits of replicative pols were analysed at the DNA, RNA and protein levels. By cloning the cDNAs for the B-subunits of human and mouse pol ε we were able to show that the encoded proteins are not only homologous to budding yeast pol ε, but also to the second largest subunit of pol α. Later studies have revealed that the B-subunits are conserved from Archaea to human, and also that they belong to the large calcineurin-like phosphoesterase superfamily consisting of a wide variety of hydrolases. At the mRNA level, the expression of the human pol ε B-subunit was strongly dependent on cell proliferation as has been observed for the A-subunit of pol ε and also for other eukaryotic replicative pols. By analysing the promoter of the POLE2 gene encoding the human pol ε B-subunit we show that the gene is regulated by two E2F-pocket protein complexes associated with the Sp1 and NF-1 transcription factors. Comparison of the promoters of the human pol ε and the pol α B-subunit indicates that the genes for the B-subunits may be generally regulated through E2F-complexes whereas adjustment of the basal activity may be achieved by distinct transcription factors. To clarify the function of the B-subunits, we screened through the expression of 13 different recombinant B-subunits. Although they were mainly expressed as insoluble proteins in E. coli, we were able to optimize the expression and purification for the B-subunit (DP1) of Methanococcus jannaschii pol D (MjaDP1). We show that MjaDP1 alone was a manganese dependent 3'-5' exonuclease with a preference for mispaired nucleotides and single-stranded DNA, suggesting that MjaDP1 functions as the proofreader of archaeal pol D. So far, pol D is the only pol family utilising an enzyme of the calcineurin-like phosphoesterase superfamily as a proofreader.

Abstract Overlapping genomic clones coding for the α1 chain of mouse type XV collagen (Col15a1) were isolated. The gene was found to be 110 kb in length and to contain 40 exons. Analysis of the proximal 5'-flanking region showed properties characteristic of a housekeeping gene promoter, and functional analysis identified cis-acting elements for both positive and negative regulation of Col15a1 gene expression. The general exon-intron pattern of the mouse Col15a1 gene was found to be highly similar to that of its human homologue, and comparison of 5'-flanking sequences indicated four conserved domains. The genomic area encoding the end of the N-terminal non-collagenous domain nevertheless showed marked divergence from the human form. Due to the lack of two exons coding for the N-terminal collagenous domain and a codon divergence in one exon, the mouse β1(XV) chain contains seven collagenous domains whereas the human equivalent contains nine. In order to understand the biological role of this protein, a null mutation in the Col15a1 gene was introduced into the germ line of mice. Despite the wide tissue distribution of type XV collagen, the null mice developed and reproduced normally and were indistinguishable from their wild-type littermates. After three months of age, however, microscopic analysis revealed progressive histological changes characteristic of myopathic disorder, and treadmill exercise resulted in greater skeletal muscle injury than in the wild-type mice. Irrespective of potential anti-angiogenic properties of type XV collagen-derived endostatin, the number of vessels appeared normal. Nevertheless, ultrastructural analyses revealed markedly abnormal capillaries and endothelial cell degeneration in the heart and skeletal muscle. Perfused hearts showed a diminished inotropic response, and exercise resulted in cardiac injury, changes that mimic early or mild heart disease. Thus type XV collagen appears to function as a necessary structural component for stabilizing cells with surrounding connective tissue in skeletal muscle cells and microvessels. Mice lacking the type XV collagen homologue, type XVIII collagen, showed delayed regression of blood vessels in the vitreous body of the eye and abnormal outgrowth of the retinal vessels. This suggests that collagen XVIII plays a role in regulating vascular development in the eye. Moreover, type XVIII collagen was found to be important at the surface between the inner limiting membrane and the collagen fibrils of the vitreous body. Col18a1 deficient mice serve as an animal model for the recessively inherited Knobloch syndrome, characterized by various eye abnormalities and occipital encephalocele. The results presented in this thesis indicate diverse biological roles for the closely related collagen types XV and XVIII.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第12763号 / 論農博第2786号 / 新制||農||1016(附属図書館) / 学位論文||H25||N4786(農学部図書室) / 30615 / (主査)教授 平竹 潤, 教授 植田 充美, 教授 小川 順 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

The pharmacologically important alkaloids morphine and codeine are found in latex of opium poppy (Papaver somniferum). Latex is harbored in laticifers, a specialized vascular cell-type. Isolation and characterization of latex-specific genes may provide a useful tool to metabolically engineer increased alkaloid production. Previous research in the Nessler laboratory identified genes that exhibit latex-specific gene expression. Latex-specific genes were an 2-oxoglutarate-dioxygense (DIOX), involved in hydroxylation, desaturation and epoxidation reactions, and two of the major latex proteins, MLP146 and MLP149. MLP-like proteins function in fruit ripening in various species that do not have the laticifer cell type. The latex-specific promoters (LSPs) for the three genes were sequenced. The 2.5 kb DIOX promoter was fused to the reporter gene Β-glucuronidase (GUS) to characterize its expression pattern. To assess the functional sites within the DIOX promoter, deletions were made 1.5 kb and 0.14 kb upstream of the ATG start codon, fused to GUS, and transformed into opium poppy, Arabidopsis thaliana, and tobacco (Nicotiana tabacum). The 2.5 kb DIOX:GUS and 1.5 kb EcoRIDIOX:GUS reporter gene constructs showed vascular specific expression in opium poppy, Arabidopsis, and tobacco. The 0.14 kb SpeIDIOX promoter deletion construct showed no activity in opium poppy, and limited expression in the shoot apical meristem and root hypocotyl axis in Arabidopsis. These results indicate that the minimum active DIOX promoter is greater than 0.14 kb. Over 1 kb of the LSPs were sequenced and analyzed for regulatory elements using the Plant cis-acting regulatory DNA elements database, PLACE (http://www.dna.affrc.go.jp/PLACE). Knowledge of the cis-elements and regulatory regions of LSPs would serve as a tool for metabolic engineering of poppy alkaloids. Sixty-five elements were conserved among 2 of the 3 LSPs. Among the cis-elements identified, some are associated with basic functions such as: light regulation, carbon metabolism and plant defense. Other elements include: WRKY elements that are binding sites of transcription factors known for signaling plant defense genes, a vascular cis-element, and a fruit specific element. The presence of plant defense and vascular cis-elements in the LSPs, correlate with the concept that latex is a protective defense mechanism found in the vascular system. The latex-specific promoters isolated and cis-elements identified in this research are potential tools for driving increased alkaloid production in opium poppy. / Master of Science

Catharanthus roseus produces a large array of terpenoid indole alkaloids (TIAs) that are an important source of natural or semi-synthetic anticancer drugs. Biosynthesis of TIAs is tissue-specific and induced by certain phytohormones and fungal elicitors, indicating the involvement of a complex transcriptional control network. However, the transcriptional regulation of the TIA pathway is poorly understood. This study reports the isolation and characterization of the G10H promoter and two WRKY transcription factors regulating TIA biosynthesis. Geraniol 10-hydroxylase (G10H) controls the first committed step in the biosynthesis of terpenoid indole alkaloids (TIA). The C. roseus G10H promoter sequence was isolated by a PCR-based genome walking method. Sequence analysis revealed that the G10H promoter contains several potential eukaryotic regulatory elements involved in regulation of gene expression. For functional characterization, fusion constructs of G10H promoter fragments with the GUS reporter gene were generated and expression was analyzed in a tobacco protoplast transient expression assay. Gain-of-function experiments revealed the presence of three potential transcriptional enhancers located in regions between -191 and -147, -266 and -188, and -318 and -266, respectively. The G10H promoter was capable of conferring stable GUS expression in transgenic tobacco plants and C. roseus hairy roots. In transgenic tobacco seedlings, GUS expression was tissue-specific, restricted to the leaf and actively growing cells around the root tip. GUS expression was not detected in the hypocotyls, root cap and older developing areas of the root. The GUS expression in both transgenic C. roseus hairy roots and tobacco seedlings were responsive to fungal elicitors and methyljasmonate. Compared to other known promoters of TIA pathway genes, the G10H promoter contains unique binding sites for several transcription factors, suggesting that the G10H promoter may be regulated by a different transcriptional cascade. The majority of TIA pathway gene promoters contain typical W-box elements, which are frequently found to be the binding sites of WRKY transcription factors. CrWRKY1 and CrWRKY2 transcription factors were isolated using a degenerate PCR method. The C. roseus WRKY transcription factor, CrWRKY1 is preferentially expressed in roots and induced by phytohormones, jasmonate, gibberellic acid and ethylene. Overexpression of CrWRKY1 in C. roseus hairy roots up-regulated several key TIA pathway genes, especially tryptophan decarboxylase (TDC), as well as transcriptional repressors ZCT1, ZCT2 and ZCT3. In contrast, CrWRKY1 overexpression repressed the transcriptional activators ORCA2, ORCA3 and CrMYC2. Overexpression of a dominant-repressive form of CrWRKY1, created by fusing the SRDX-repressor domain to CrWRKY1, resulted in down-regulation of TDC and ZCTs but up-regulation of ORCA3 and CrMYC2. CrWRKY1 bound to the W-box elements of the TDC promoter in electrophoretic mobility shift, yeast one-hybrid and C. roseus protoplast assays. In CrWRKY1 hairy roots, up-regulation of TDC increased TDC activity, tryptamine concentration and resistance to 4-methyl tryptophan inhibition. Compared to control roots, CrWRKY1 hairy roots accumulated up to 3-fold higher levels of serpentine. The preferential expression of CrWRKY1 in roots and its interaction with transcription factors, including ORCA3, CrMYC2 and ZCTs, may play a key role in determining the root-specific accumulation of serpentine in C. roseus plants. CrWRKY2 is induced by methyljasmonate induction. In plant, CrWRKY2 expression is mainly found in young leaves and the stem. The stable transformation of CrWRKY2 in C. roseus hairy roots up-regulated many pathway genes, especially the genes in vindoline biosynthesis. The accumulation of vindoline was observed in CrWRKY2 hairy roots.

Proper development of skeletal muscle occurs through a highly complex process where activation and repression of genes are essential. Control of this process is regulated by timely and spatial expression of specific transcription factors (TFs). Six1 and Six4 are homeodomain TFs known to be essential for skeletal muscle development in mice. Using the C2C12 cell line, a model for skeletal muscle differentiation, I used a functional genomics approach, employing siRNA specific to both these TFs, to characterize their role in skeletal myogenesis. To identify the genes that are regulated by both these TFs, gene expression profiling by microarray of cells treated with siRNA against Six1 and/or Six4 was performed. The knock-down of these TFs caused lower expression of markers of terminal differentiation genes in addition to an impairment of myoblast fusion and differentiation. Interestingly, transcript profiling of cells treated with siRNA against myogenin revealed that several of the Six1 and Six4 target genes are also regulated by myogenin. Through a combination of bioinformatic analyses it was also found that specific knock-down of Six4 causes an up-regulation of genes involved in mitosis and the cell cycle. In summary, these results show that Six1 and Six4 can both independently regulate different genes, but can also cooperate together with other TFs where they play an important role in the proper regulation of skeletal myogenesis.

Proper development of skeletal muscle occurs through a highly complex process where activation and repression of genes are essential. Control of this process is regulated by timely and spatial expression of specific transcription factors (TFs). Six1 and Six4 are homeodomain TFs known to be essential for skeletal muscle development in mice. Using the C2C12 cell line, a model for skeletal muscle differentiation, I used a functional genomics approach, employing siRNA specific to both these TFs, to characterize their role in skeletal myogenesis. To identify the genes that are regulated by both these TFs, gene expression profiling by microarray of cells treated with siRNA against Six1 and/or Six4 was performed. The knock-down of these TFs caused lower expression of markers of terminal differentiation genes in addition to an impairment of myoblast fusion and differentiation. Interestingly, transcript profiling of cells treated with siRNA against myogenin revealed that several of the Six1 and Six4 target genes are also regulated by myogenin. Through a combination of bioinformatic analyses it was also found that specific knock-down of Six4 causes an up-regulation of genes involved in mitosis and the cell cycle. In summary, these results show that Six1 and Six4 can both independently regulate different genes, but can also cooperate together with other TFs where they play an important role in the proper regulation of skeletal myogenesis.

Niemann-Pick disease type C (NPC) is a rare, severe disease with autosomal recessive inheritance. Disease is caused by pathogenic mutations located in genes NPC1/NPC2. These genes encode lysosomal non enzymatic NPC1/NPC2 proteins that are part of lipid transport. As a result of malfunction of these proteins intracellular accumulation of lipids occurs, in particular free cholesterol and glycolipids. Causal therapy is currently still unsatisfactory therefore new therapies are evolved. However these therapies depend on whether the patient cells contain at least residual amount of transcript NPC1 gene. In a group of patiens, for which a fibroblast culture was available, I analyzed the effect of pathogenic mutations on the expression level of the transcript. Results showed that for all pathogenic mutations transcript level is low, but detectable. Moreover, I characterized the structure of the NPC1 gene promoter. By sequence analysis I found polymorphisms rs8099071, rs28403610, rs2981422, rs1652354, rs1788774, rs1788772 in promoter. On the basis of the composition of polymorphisms in individual patiens, I estimate six different haplotypes. I performed mutation analysis in DNA of recently diagnosed patient. I found only one pathogenic mutation p.I1061T (c.3182T> C) in the NPC1 gene. Therefore I tested...

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