Miao Ji. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (p. 159-165). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Conclusion. Taken together, paternal factors carried in ASG secretion affect genomic imprinting of developing embryos. The outcome of research work described here deepens our understanding of the role of ASG in maximizing reproductive performance mediated by regulating the epigenetic marks of the genome and in particular the imprinted genes. / Introduction. Our previous in vivo studies in golden hamster have shown the accessory sex glands (ASG) secretion facilitate the development of embryos to term but the underlying mechanism is still not clear. Since the deleterious effect caused by the lack of sperm exposure to ASG secretion is heritable to developing fetus and even after birth, we hypothesized that the paternal factor carried in ASG secretion may change the epigenetic regulation and in particular the imprinted genes of embryonic genome. / Materials and methods. Golden hamster and ICR mouse were used in this study. Hamster is a well-established animal model to study the effect of individual ASG but the genetic background of hamster is poorly known. To verify the specificity of our molecular probe and antibodies used in hamster, a mouse model was also established. Five groups of male hamsters and two groups of male mice were established by surgical treatment. In hamster, (SH) sham-operated, (VPX) ventral prostate-removed, (TX) all ASG-removed, (VPVX) castrated with ASG-removed except ventral prostate and (VX) castrated with intact ASG were established. In mouse, SH and VPX were established. In single-mating of hamster, male was copulated with female at estrus for 15 min. In double-mating of hamsters, female mated with each male for 10 min each. In single-mating of mouse, male was caged with female for 1 h. Epididymal sperm, uterine sperm, fertilized oocytes, pre-implantation embryos and fetuses at 13 days gestation (E13) were collected. Global DNA methylation of sperm, fertilized oocytes, early embryos and E13 fetuses were investigated by indirect immunofluorescence and DNA dot-blot using antibody against methylated DNA. Using the same technique, histone acetylation at lysine 5 residue was detected in male pronuclei of fertilized oocytes, protamine 1 and 2 content were detected in sperm, DNA methyltransferase 1, 3a and 3b activities were detected in early embryos. The crown-rump length and weight of fetuses were measured. Morphology was also examined under scanning electron microscope. Two sets of co-ordinately regulated but oppositely expressed imprinted genes Igf2/H19 and Dlk1/Gtl2 were investigated. H19 differentially methylated region (DMR) and Gtl2 promoter were examined by bisulfite sequencing in sperm and E13 fetuses. Expression of Igf2 and Dlk1 were examined by in situ hybridization and real-time PCR in pre-implantation embryos and E13 fetuses. / Results. Uterine sperm in VPX and TX groups showed no change of DNA methylation level and protamine 1 and 2 content. Fertilized oocytes in VPX and TX groups showed similar DNA methylation level as SH group in both hamster and mouse. Histone hypoacetylation was observed in male pronuclei of hamster but not in mouse. Early embryos in VPX and TX groups showed abnormal level of DNA methylation and Dnmt3b during embryo development in hamster. Replenishment of ASG secretion to sperm from VPX and TX group by double-mating restored the DNA methylation level to normal in early embryos. E13 fetuses of VPX and TX groups in hamster and VPX group in mouse showed DNA hypomethylation. E13 fetuses of VPX group in hamster showed increase in average crown-rump length and body weight with larger variations between individuals. One E13 fetus of VPX group in mouse showed polydactyly and malformation in the head. Real-time PCR showed abnormal expression of Igf2 and Dlk1 in both pre-implantation embryos and E13 fetuses of VPX and TX groups. Bisulfite sequencing showed hypermethylation of H19 DMR in VPX and TX groups of hamster and hypomethylation of Gtl2 promoter in VPX group of mouse. / "August 2007." / Adviser: Pak Ham Chow. / Source: Dissertation Abstracts International, Volume: 69-08, Section: B, page: 4739. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (p. 194-224). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

With the advent of large scale genome sequencing efforts along with more sophisticated methods of genetic mapping, a number of loci have been identified that are associated with human diseases. Intriguingly, many genes identified in these loci remain uncharacterized. Although current annotation can provide a prediction of putative function of some of these proteins at a biochemical level, understanding their cellular roles require analysis at a single gene level. Bioinformatic analysis carried out in the laboratory during studies on cyclic nucleotide metabolism in mycobacteria identified putative Class III cyclic nucleotide phosphodiesterases (Class III cNMP PDEs) from the non-redundant database of proteins. One of the proteins identified was the Rv0805 gene product from Mycobacterium tuberculosis. Detailed biochemical characterization of this protein revealed that Rv0805 is indeed a phosphodiesterase (PDE) and could hydrolyze 3’, 5’-cyclic adenosine monophosphate (cAMP) as well as 3’, 5’-cyclic guanosine monophosphate (cGMP). Structural analysis of Rv0805 revealed a metallophosphoesterase (MPE) like fold and presence of two metal atoms at the binuclear metal centre of the protein. Moreover, overexpression of Rv0805 in E. coli and M. smegmatis reduced intracellular cAMP levels indicating that it possesses cAMP PDE activity in vivo. The majority of proteins identified in this bioinformatic analysis were of bacterial or archaebacterial in origin but it was interesting to find some mammalian proteins, since, till date, no Class III cNMP PDE has been found in higher eukaryotes. Interestingly, two genes were identified in the human genome. These genes, 239FB and 239AB, are expressed in the fetal brain and adult brain, respectively and have been annotated as metallophosphoesterases but there has been no biochemical or functional characterization of these proteins. The 239FB gene is present between the FSHB and PAX6 genes on chromosome 11. This gene locus is present within a deletion interval (11p13-14) that is associated with the mental retardation phenotype of WAGR syndrome (Wilms’ tumor, aniridia, genitourinary anomalies, mental retardation). Inspection of available sequenced mammalian genomes indicated a shared synteny of the genes in the WAGR locus, highlighting it’s evolutionary conservation. Most interestingly, nucleotide sequences within the WAGR locus (which include the 5 genes WT1, PAX6, RCN1, ELP4 and 239FB) are amongst the 481 ultra conserved regions of the human genome. Moreover, 239FB is one of only 24 instances where an ortholog of an ultra-conserved element could be partially traced back by sequence similarity in lower eukaryotes such as Ciona intestinalis, Drosophila melanogaster, or Caenorhabditis elegans. Although the function of the 239FB protein is unknown so far, the distinctive expression of the gene in the fetal brain and the presence of an “ancient conserved region” in this gene suggest that this gene may be vital for the development of the nervous system. The work carried out in this thesis has attempted to understand the physiological functions of the 239FB/AB gene family. Amino acid sequence comparison revealed two amino acids changes between the human and rat proteins indicating the extra-ordinary sequence conservation of these proteins. Therefore, to characterize the biochemical properties of 239FB and 239AB proteins, rat proteins were used as model enzymes. Reverse transcription-PCR analysis of RNA prepared from the fetal and adult rat brains as well as Western blot analysis on cytosolic fractions of rat brains from various developmental stages indicated that 239FB is predominantly expressed in fetal brain. Detailed biochemical analyses of the rat 239FB and 239AB proteins were performed which showed that they possess metallophosphodiesterase activity. 239FB showed activity only in the presence of Mn2+ and Co2+ as the added metal cofactors. Surprisingly, the Km for Mn2+ of 239FB was found to be 1.5 mM, which is nearly 60-fold higher than that of its mycobacterial ortholog, Rv0805. A systematic mutational analysis was performed to characterize the residues that are involved in binding either one or both the metals found in the catalytic site of 239FB. Although 239FB shares some of the residues that have been shown to be essential for metal binding and catalytic activity with other MPEs including Rv0805, there are some differences as well. One histidine residue that has been conserved in other MPEs and has been shown to be important for metal binding is replaced by glycine (Gly-252) in 239FB. To study the consequence of replacing the glycine with a histidine in 239FB, a 239FBGly252His mutant protein was generated and characterized. Interestingly, the single mutation of Gly-252 to a histidine residue not only increased the affinity of the protein for metals but increased catalytic activity as well with various phosphodiesters. Moreover, 239FBGly252His mutant protein showed significant activity with cAMP and cGMP which were not hydrolysed by wild type 239FB. Interestingly, in the 239AB protein, histidine 284 is present at a position equivalent to Gly-252 in the 239FB protein. Biochemical characterization of 239AB showed 2’, 3’-cAMP hydrolyzing activity similar to 239FBGly252His mutant protein. A rat 239FB protein with a mutation (His67Arg) corresponding to a single nucleotide polymorphism seen in human 239FB, led to complete inactivation of the protein. The occurrence of this SNP at a very low frequency and only as a heterozygous condition suggests that a complete loss-of-function mutation of 239FB in human populations cannot be tolerated. To gain insights into the function of 239FB in its physiological milieu, yeast two-hybrid screening was performed with 239FB using human fetal brain cDNA library. Dipeptidyl peptidase III, a zinc dependent metallopeptidase, was found as an interacting partner of 239FB in this analysis and the functional consequences of this interaction would be an interesting area of study in future. While a number of metallophosphoesterases have been characterized biochemically and structurally, their biological role(s) and in vivo substrate(s) remain elusive. In order to elucidate the physiological role of 239FB/AB family, the ortholog of 239FB/AB in D. melanogaster was characterized. Sequence comparison of Drosophila ortholog with both the mammalian proteins indicated that it may be an ortholog of 239AB and hence, it was named as d239AB. Enhancer-promoter analysis with a putative promoter region of the d239AB indicated the expression of d239AB in the mushroom bodies in brain and in enterocytes in mid gut. Characterization of a Drosophila line, BS#16242, with a piggybac element inserted in the intron of d239AB showed disruption of d239AB expression. This suggested that BS#16242 line can serve as a d239AB knockout line and hence, was selected for further phenotypic characterization to unravel the physiological roles of d239AB. Though, BS#16242 flies did not show any developmental defects, a severe reduction in the fecundity of these files was observed. Further analysis revealed defective ovulation as a probable reason for reduced fecundity of these flies. In addition to compromised fecundity, BS#16242 flies showed a significant reduction in the life span of male as well as female flies. Moreover, these flies showed less resistance to thermal stress and desiccation. Most interestingly, all these phenotypes were rescued upon neuronal expression of the d239AB transgene in BS#16242 flies indicating that neuronal function of d239AB is important for diverse physiological processes. The phenotypes observed in BS#16242 flies mimic the physiological state under increased insulin signaling, such as decrease in life span, and susceptibility to various stress conditions suggesting that d239AB could play a role in the insulin signaling pathway. Interestingly, overexpression of d239AB transgene in neurons reduced cAMP levels in the brains of Drosophila, indicating that the protein may have cAMP phosphodiesterase activity in vivo. This is the first analysis of the presence of a Class III phosphodiesterase in eukaryotes. Thus, d239AB mediated regulation of cAMP levels in a particular subsets of cells, such as neurons, could also be one of the molecular mechanisms responsible for reduced fecundity and longevity of BS#16242 flies. Interacting partners of d239AB were inspected in the Drosophila interactome (built on protein-protein interactions identified using a yeast two-hybrid approach). Strikingly, most of the d239AB interacting proteins were involved either in transcriptional or translational regulation indicating that d239AB could be involved in the regulation of expression of genes involved in diverse physiological processes. This could explain why disruption of d239AB led to various physiological defects such as reduced fecundity, decreased life span and compromised fitness. In summary, studies described in this thesis suggest that 239FB and 239AB proteins are the first Class III cyclic nucleotide phosphodiesterases reported in eukaryotes. Results shown here suggest the critical role of their ortholog in the physiology of Drosophila. Further genetic manipulation in D. melanogaster and other organisms which harbor orthologs of the 239FB/AB gene could throw light on the diverse biological roles of these enzymes in humans.