京都大学 / 新制・課程博士 / 博士(医学) / 甲第23462号 / 医博第4769号 / 新制||医||1053(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 長船 健二, 教授 渡邊 直樹, 教授 羽賀 博典 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DGAM

<p>The following work describes the methodology and materials used to study three human protein complexes involved in the etiology and progression of cancer. The first, ubiquitin-specific protease 7 (USP7) is an isopeptidase that employs a unique auto-regulatory mechanism. The second is another ubiquitin-specific protease, USP28, which forms higher order states in solution. Lastly, the third case was a protein complex that utilizes an oxidation-sensitive dimeric protein, Keap1, and two components of an E3 ligase – Cul3-Rbx1. Each of these studies involved overcoming unique challenges for cryo-EM sample optimization. Not all yielded the quality of data that would result in high-resolution (< 6 Å) densities. Despite this, new information was discovered about each system.</p> <p>USP7 has a unique mechanism of intramolecular regulation that stems from a hypothesized tethered-rheostat, whereby the c-terminal distal domains activate the catalytic domain via a hypothetical wide degree of conformational movement. My cryo-EM work, done in collaboration with the Wen Jiang lab, is the first comprehensive structural data that provides structural evidence for the movement of the tethered-rheostat. The particle set showed a great degree of conformational heterogeneity, even after a strategy was employed with a chemically-modified ubiquitin substrate to ameliorate these issues. The data showed that during the ubiquitin-bound state, after the release of a hypothetical substrate, but prior to the release of mono-ubiquitin, the HUBL4-5 domains do not remain engaged with the catalytic domain. This information suggests a change to existing models of catalysis. </p> <p>Additionally, the structural model built from the cryo-EM density has revealed an interfacial region between domains that were previously not thought to interact. This interfacial region between the TRAF domain and HUBL1-3 represents a candidate location of binding for a mixed, non-competitive inhibitor of USP7 previously identified in the lab. Enzyme kinetics, DSF, and Glide molecular docking experiments all yielded data that corroborate this idea.</p> <p>Structural studies on USP28 have been difficult as the multi-domain enzyme adopts oligomers in solution and is generally not amenable to crystallographic analysis. Prior to the work described herein, the only structural data were a solution NMR structure describing a few alpha-helical motifs in the N-terminus. During my graduate studies, two articles were published of the USP28 catalytic domain crystallographic structure. Both corroborated the existence of a dimer. The USP28 catalytic domain migrates during analytical gel filtration assays with the apparent molecular weight of a tetramer. Furthermore, glutaraldehyde crosslinking experiments show the catalytic domain appears to adopt a tetrameric state, like the USP25 tetramer. The USP25 tetramer was published alongside the USP28 catalytic domain dimer, concluding that a USP28 tetrameric state was not observed. Upon cryo-EM data collection and single particle analysis, it was observed that the compositional heterogeneity of the dataset was too great for any meaningful reconstruction. Although, the dataset appeared to how the presence of the <i>E. coli</i> GroEL chaperone complex. Co-expression experiments confirmed that the GroEL chaperone complex migrates with USP28 throughout the purification and may be useful for purifying USPs for structural studies.</p> <p>Currently, our lab has a single-angle X-ray scattering (SAXS) model of the Keap1-Cul3 E3 ligase complex. But, the field does not fully agree on the molecular stoichiometry or the overall structure-function of this oxidation sensor – E3 ligase complex. It is hypothesized that Keap1 forms a dimer through its BTB domain, and a single Cul3 molecule then binds this dimer. The oxidation state of Keap1 cysteines appears to be critical to the interaction, but the field remains uncertain about which residues are responsible for the interaction with the Cul3-Rbx1 E3 ligase. To better understand this interaction and to obtain structural information to corroborate the SAXS model, recombinant Keap1 and Cul3-Rbx1 were purified and their interaction was tested by ITC, gel filtration assay, and a new technique called <i>mass photometry</i>. </p> <p>It was found that the Keap1 Cys151 residue is not the oxidation sensor critical to the interaction, contrary to what some in the field anticipated. Additionally, it was found that under oxidative conditions, WTKeap1 could not form a complex with Cul3-Rbx1. The complex was successfully purified and was measured by SDS-PAGE, gel filtration assay, and mass photometry, and then used for cryo-EM single particle analysis. Full data collection and analysis has not yet been completed. It is anticipated that like the data from mass photometry, analytical SEC, and cryo-EM single particle analysis will show the complex appears to show a 1:1 Keap1-Cul3 stoichiometry, as opposed to the anticipated 2:1 ratio.</p>

Beacon is a 73-amino acid peptide encoded by a novel gene in the hypothalamus of Israeli sand rat Psammomys obesus. Reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemical techniques were used to investigate the presence of beacon mRNA and the distribution of beacon-immunoreactivity (irBC) in the hypothalamus of ICR mice. RT-PCR experiments revealed beacon mRNA in the mouse hypothalamus. Using a rabbit polyclonal antiserum directed against the synthetic C-terminal peptide fragment (47-73), irBC was detected in the mouse hypothalamus and pituitary. In the hypothalamus, irBC was concentrated in perikarya of the supraoptic (SO), paraventricular (PVH) and accessory neurosecretory nuclei and in cell processes of the median eminence and pituitary stalk. In the pituitary, irBC was noted mainly in the posterior lobe. Double-labeling the hypothalamic sections with guinea-pig vasopressin-antiserum or mouse monoclonal oxytocin-antibody and beacon-antiserum revealed that <30% of vasopressin-immunoreactive neurons and nearly all oxytocin-immunoreactive neurons in the PVH and SO were irBC. The result shows the presence of beacon mRNA in the mouse hypothalamus, and the distribution of irBC is distinctively different from that reported in the hypothalamus of Psammomys obesus, but similar to that of the Sprague-Dawley rats described in our earlier study. More interestingly, Blast search uncovered a 73-amino acid peptide, human ubiquitin-like 5, which has the same exact sequence as beacon. Thus, irBC observed in the mouse brain could be that of ubiquitin-like 5.

β-adrenergic receptor (β-AR) stimulation increases extracellular levels of ubiquitin (UB), and exogenous UB plays an important role in β-AR-stimulated myocardial remodeling with effects on heart function, fibrosis and myocyte apoptosis. Cardiac fibroblasts are vital for maintaining the normal function of the heart, and in the structural remodeling of the heart in response to injury. Here we hypothesized that extracellular UB modulates cardiac fibroblast phenotype and function via its interaction with CXC chemokine receptor type 4 (CXCR4). Main methods: Serum starved adult cardiac fibroblasts were used to identify CXCR4 as a receptor for UB. Fluorescent microscopy, co-immunoprecipitation, western blot, proliferation, migration and collagen contraction assays were performed to investigate the role of UB/CXCR4 axis on cell signaling, and modulation of fibroblast phenotype and function. Key findings: Using fluorescent microscopy and co-immunoprecipitation assay, we provide evidence that extracellular UB interacts with CXCR4. CXCR4 antagonist, AMD3100, inhibited interaction of UB with CXCR4. UB activated ERK1/2, not Akt. It enhanced VEGF-A expression, while decreasing β3 integrins expression. Two mutated UB proteins (V70A and F4A; unable to interact with CXCR4) failed to affect the expression of VEGF-A and β3 integrins. UB treatment inhibited migration of cells into the wound and FBS-stimulated cell proliferation. UB enhanced expression of α-smooth muscle actin (marker of myofibroblast differentiation) and contraction of fibroblast-populated collagen gel pads. Most of the effects of UB were negated by AMD3100. Significance: The data presented here suggest that UB interacts with CXCR4, and UB/CXCR4 interaction affects intracellular signaling, and modulates fibroblast phenotype and function.

京都大学 / 0048 / 新制・課程博士 / 博士(生命科学) / 甲第17801号 / 生博第289号 / 新制||生||37(附属図書館) / 30608 / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 松本 智裕, 教授 石川 冬木, 教授 西田 栄介 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19004号 / 工博第4046号 / 新制||工||1623(附属図書館) / 31955 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 白川 昌宏, 教授 渡辺 宏, 教授 跡見 晴幸 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21791号 / 工博第4608号 / 新制||工||1718(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 白川 昌宏, 教授 佐藤 啓文, 教授 跡見 晴幸 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

The ubiquitin-proteasome proteolysis pathway is responsible for the degradation of abnormal and short-lived proteins to regulate many important biochemical activities in eukaryotes. By employing affymetrix microarray analysis, we have identified a novel ubiquitin ligase E3 gene GhRING2 that is expressed differentially between two G. hirsutum lines - Texas Marker-1 and Chromosome Substitution Line CS-B25. The complete GhRING2 gene sequence was obtained by genomic and cDNA walking. The expression of GhRING2 in cotton fiber is developmentally regulated, suggesting that the ubiquitin-proteasome pathway may regulate cotton fiber growth and development. Using a yeast two-hybrid assay GhRING2 was found to interact with a PROTODERMAL FACTOR1 (GhPDF1) protein. GhPDF1 is expressed preferentially in immature ovules and fiber initials and the gene has been suggested to play a role in cell fate determination and fiber development. Pull down and plasmid swap assays were employed to confirm this interaction.

Eukaryotic gene expression to proteins is a complex process that begins with transcription which is regulated by numerous regulatory factors and signals. Alterations in these regulatory factors that modulate gene expression are linked with a multitude of cellular pathologies including cancers. Thus, it is important to delineate these transcriptional regulatory mechanisms of gene expression. Therefore, a large number of studies have been aimed at understanding the mechanism of transcription at the level of initiation, elongation, and termination. In line with this, my dissertation work is focused towards elucidating novel regulatory mechanisms of transcription initiation and elongation. Our results illuminate genetically how TOR (target of rapamycin) signaling pathway regulates transcription initiation and hence, transcription, in response to nutrients. The process of transcription initiation at the promoter is followed by RNA polymerase II (Pol II) pausing at the promoter-proximal site for mRNA capping/quality control. Such promoter-proximal pausing of Pol II (paused Pol II) plays an important role in regulating transcription elongation. Our results unveil how paused Pol II is released to engage into productive elongation for mRNA synthesis. We show that the capping enzyme, Cet1, targets a transcription factor known as FACT (facilitates chromatin transcription) which subsequently recruits a transcription elongation factor, Paf1C (RNA polymerase II- associated factor 1 [Paf1] complex), to release the paused Pol II for productive transcription elongation for mRNA synthesis. During such transcription elongation, histones need to be evicted in front of Pol II and reassembled in the wake of Pol II, and this dynamic histone disassembly and reassembly are coordinated by a number of histone chaperones. The aforementioned transcription factor, FACT, is one such histone chaperone that plays a key role in histone reassembly during transcription elongation. Importantly, we find a new regulation of FACT, by the ubiquitin-proteasome system (UPS), and hence, histone dynamics at the coding sequence and transcription. Specifically, the Spt16 component of FACT is ubiquitinated by the E3 ubiquitin ligase San1, and subsequently degraded by the 26S proteasome in yeast. Such proteasomal regulation of Spt16 subunit of FACT regulates transcription, and impairment of this UPS regulation alters transcription, leading to cellular pathologies. Indeed, SPT16 has been found to be associated with a lot of cancers, and our results show that this proteasomal degradation of SPT16 is impaired in cancer cells. Further, upregulation of SPT16 is associated with alterations in transcription of genes linked to cancer. Subsequent to its synthesis, mRNA needs to be exported to cytoplasm for translation to proteins. Importantly, transcription elongation has been found to be coupled to mRNA export, and like elongation, mRNA export is also controlled by UPS. Our findings demonstrate the role of active transcription in the proteasomal degradation of a key mRNA export factor, Sub2, mediated via Mdm30 (an F-box protein), thus, enhancing our understanding of the UPS regulation of mRNA export. Taken together, my dissertation work elucidates novel regulatory mechanisms of gene expression in response to nutrients and UPS, with implications in cellular pathologies including cancers.

Dysregulation of low-voltage-activated calcium channels (CaV3.1-CaV3.3) underlies diseases including chronic pain, autism, and hypertension. As a major determinant of protein half-life, the ubiquitin-proteasome system (UPS) may not only cause abnormal CaV3 expression but also be targeted to control channel levels for therapy. There are >600 E3 ubiquitin ligases that catalyse the final step in ubiquitination. A crucial aspect of harnessing the UPS is knowing which E3 ligases regulate a given substrate, and whether their actions are redundant. We report that CaV3.1 and CaV3.2 are distinctively regulated by two NEDD4 family E3 ligases – NEDD4L and Smurf1. Reconstituted CaV3.1 currents were robustly suppressed by Smurf1 but not NEDD4L, whereas CaV3.2 was inhibited by both NEDD4L and Smurf1, concomitant with diminished channel surface density and expression. FRET experiments revealed NEDD4L and Smurf1 interact with distinct loci in CaV3.1 and CaV3.2. Nanobody-mediated targeting of NEDD4L or Smurf1, but not WWP1, HECT domains to CaV3.1 and CaV3.2 strongly suppressed currents through both channels. shRNA knockdown of either NEDD4L or Smurf1 in dorsal root ganglion (DRG) neurons substantially increased both low-voltage and high-voltage-activated calcium channel currents. The results reveal non-redundant regulation of CaV3 channels by NEDD4L and Smurf1; introduce Smurf1 as a potent determinant of ion channel expression; suggest a new mechanism for CaV3.2 up-regulation in chronic pain; and advance leveraging the UPS to control CaV3 expression for therapy.