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KaiC CII Ring Flexibility Governs the Rhythm of the Circadian Clock of CyanobacteriaKuo, Nai-Wei 2011 May 1900 (has links)
The circadian clock orchestrates metabolism and cell division and imposes important consequences to health and diseases, such as obesity, diabetes, and cancer. It is well established that phosphorylation-dependent circadian rhythms are the result of circadian clock protein interactions, which regulate many intercellular processes according to time of day. The phosphorylation-dependent circadian rhythm undergoes a succession of phases: Phosphorylation Phase → Transition Phase → Dephosphorylation Phase. Each phase induces the next phase. However, the mechanism of each phase and how the phosphorylation and dephosphorylation phases are prevented from interfering with each other remain elusive. In this research, we used a newly developed isotopic labeling strategy in combination with a new type of nuclear magnetic resornance (NMR) experiment to obtain the structural and dynamic information of the cyanobacterial KaiABC oscillator system. This system is uniquely suited for the mechanistic studies: mixing KaiA, KaiB KaiC, and ATP generates a self-sustained ~24 h rhythm of KaiC phosphorylation in vitro. Our data strongly suggest that the dynamic states of KaiC underpin the timing mechanism of cyanobacterial oscillator.
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Cellular Function and Localization of Circadian Clock Proteins in CyanobacteriaDong, Guogang 2008 December 1900 (has links)
The cyanobacterium Synechococcus elongatus builds a circadian clock on an
oscillator comprised of three proteins, KaiA, KaiB, and KaiC, which can
recapitulate a circadian rhythm of KaiC phosphorylation in vitro. The molecular
structures of all three proteins are known, and the phosphorylation steps of
KaiC, the interaction dynamics among the three Kai proteins, and a weak
ATPase activity of KaiC have all been characterized. A mutant of a clock gene in
the input pathway, cikA, has a cell division defect, and the circadian clock
inhibits the cell cycle for a short period of time during each cycle. However, the
interaction between the circadian cycle and the cell cycle and the molecular
mechanisms underlying it have been poorly understood. In addition, the
subcellular localization of clock proteins and possible localization dynamics,
which are critical in the timing circuit of eukaryotic clock systems and might also
shed light on the interaction between circadian cycle and cell cycle, have remained largely unknown. A combination of genetics, cell biology, and
microscopy techniques has been employed to investigate both questions.
This work showed that the cell division defect of a cikA mutant is a function of
the circadian clock. High ATPase activity of KaiC coincides with the inhibition of
cytokinesis by the circadian clock. CikA likely represses KaiC's ATPase activity
through an unknown protein, which in cikA's absence stimulates both the
ATPase and autokinase activities independently of KaiA or KaiB. SasA-RpaA
acts as an output in the control of cell division, and the localization of FtsZ is the
target, although it still remains to be seen how RpaA, directly or indirectly,
inhibits FtsZ localization.
The project also showed that clock proteins are localized to the cell poles.
KaiC is targeted to the cell pole in a phosphorylation-dependent manner. KaiB
and CikA are also found at the poles independently of KaiC. KaiA likely only
localizes to the cell pole during the dephosphorylation phase, which is
dependent on both KaiB and KaiC, specifically on the phosphorylation of KaiC at
S431.
Overall, significant progress was made in both areas and this project sheds
light on how the circadian oscillator operates in cyanobacterial cells and
interacts with another fundamental cellular function.
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Structure and function of circadian clock proteins and deuterium isotope effects in nucleic acid hydrogen bondsVakonakis, Ioannis 29 August 2005 (has links)
Circadian oscillators or clocks are a widespread, endogenous class of oscillatory mechanisms that control the ~24h temporal pattern of diverse organism functions. In cyanobacteria this mechanism is formed by three proteins, KaiA, KaiB and KaiC. KaiA is shown here to be a two domain protein that directly interacts with KaiC and enhances the KaiC autokinase activity. The amino-terminal domain of KaiA can be structurally categorized as a pseudo-receiver, a class of proteins used in signaling cascades and activated by direct protein??protein interactions. The carboxy-terminal domain interacts directly with KaiC, is sufficient to enhance the KaiC autokinase activity in a manner similar to full-length KaiA, and adopts a unique, all α-helical dimeric fold. The structure of this domain raises interesting probabilities regarding the mode of KaiA??KaiC interaction. The two KaiA domains are shown to directly interact with each other, which suggests a possible mechanism of signal transfer from the amino to carboxy-terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can possibly be correlated to structural properties, such as length. Deuterium/protium fractionation factors, which are sensitive to the vibrational potential well width, were measured for the imino sites of thymidine residues involved in A:T base pairs or free in solution, and a correlation was established between decreasing fractionation factors and increasing imino proton chemical shift, δH3. Similarly, a correlation was observed between δH3and deuterium isotope effects (DIE) on chemical shift of thymidine carbon atoms. Combined these results indicate that as hydrogen-bond strength increases the vibrational potential wells of imino protons widen with a corresponding increase in anharmonicity. However, trans-hydrogen bond DIE on carbon chemical shifts of A:T base-paired adenosine residues do not correlate with those measured on thymidine residues. We propose that this lack of correlation is due to DIE dependence on base-pair geometry, which is not easily measured by traditional NMR experiments.
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Structure and function of circadian clock proteins and deuterium isotope effects in nucleic acid hydrogen bondsVakonakis, Ioannis 29 August 2005 (has links)
Circadian oscillators or clocks are a widespread, endogenous class of oscillatory mechanisms that control the ~24h temporal pattern of diverse organism functions. In cyanobacteria this mechanism is formed by three proteins, KaiA, KaiB and KaiC. KaiA is shown here to be a two domain protein that directly interacts with KaiC and enhances the KaiC autokinase activity. The amino-terminal domain of KaiA can be structurally categorized as a pseudo-receiver, a class of proteins used in signaling cascades and activated by direct protein??protein interactions. The carboxy-terminal domain interacts directly with KaiC, is sufficient to enhance the KaiC autokinase activity in a manner similar to full-length KaiA, and adopts a unique, all α-helical dimeric fold. The structure of this domain raises interesting probabilities regarding the mode of KaiA??KaiC interaction. The two KaiA domains are shown to directly interact with each other, which suggests a possible mechanism of signal transfer from the amino to carboxy-terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can possibly be correlated to structural properties, such as length. Deuterium/protium fractionation factors, which are sensitive to the vibrational potential well width, were measured for the imino sites of thymidine residues involved in A:T base pairs or free in solution, and a correlation was established between decreasing fractionation factors and increasing imino proton chemical shift, δH3. Similarly, a correlation was observed between δH3and deuterium isotope effects (DIE) on chemical shift of thymidine carbon atoms. Combined these results indicate that as hydrogen-bond strength increases the vibrational potential wells of imino protons widen with a corresponding increase in anharmonicity. However, trans-hydrogen bond DIE on carbon chemical shifts of A:T base-paired adenosine residues do not correlate with those measured on thymidine residues. We propose that this lack of correlation is due to DIE dependence on base-pair geometry, which is not easily measured by traditional NMR experiments.
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葉面メタノール資化性細菌の栄養要求性および競合的増殖特性と環境適応の分子機構𠮷田, 裕介 25 March 2019 (has links)
本文PDFには「吉田 裕介」と記載 / 京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21828号 / 農博第2341号 / 新制||農||1067(附属図書館) / 学位論文||H31||N5200(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 阪井 康能, 教授 小川 順, 教授 矢﨑 一史 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM
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