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研究生: 彭茜徽
PENG, XIHUI
論文名稱: The time-frequency analysis of FtsZ-Min interactions in bacteria
The time-frequency analysis of FtsZ-Min interactions in bacteria
指導教授: 周家復
Chou, Chia-Fu
張宜仁
Chang, Yi-Ren
口試委員: 吳明佳
Wu, Ming-Chya
周家復
Chou, Chia-Fu
張宜仁
Chang, Yi-Ren
口試日期: 2022/07/27
學位類別: 碩士
Master
系所名稱: 物理學系
Department of Physics
論文出版年: 2022
畢業學年度: 110
語文別: 英文
論文頁數: 64
英文關鍵詞: FtsZ, MinD, Min-oscillation, cell division, E.coli
研究方法: 實驗設計法
DOI URL: http://doi.org/10.6345/NTNU202201822
論文種類: 學術論文
相關次數: 點閱:88下載:3
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  • In Escherichia coli, cell division always plays a vital role in their proliferation when a mother cell is divided, and two identical daughter cells are formed. During the division process, a central component of protein, FtsZ, recruits more than 30 other divisome proteins to the mid-cell and builds a Z-ring structure. To regulate the Z-ring established at the proper site, the Min system: MinC, MinD, and MinE, oscillates from one cell pole to the opposite during the whole cell cycle. It is because that MinC is the inhibitor of preventing FtsZ assembly. In past research, people found that not only the Min-system shows the period oscillation in the cell, but also the FtsZ exhibits treadmilling dynamics to form the Z-ring. However, the majority of researchers focus the dynamics behaviors only on one protein among them, or the analysis methods they utilized only measured the average period/ frequency of one time period.

    In our work, we developed an analysis procedure for investigating the dynamic behavior of FtsZ and MinD, as well as their dynamic relationship in the time-frequency domain over the entire cell cycle. Autocorrelation was utilized to determine the correlations and properties of each signal by itself. In order to gain instantaneous frequency of each protein signal to consult the correlation between two protein systems, we implemented the EEMD technique, which offers denoising signals a powerful tool, to decompose each IMFs of each protein signal and then used dynamic cross-correlation for analysis.

    At last, despite the lack of a lucid result depicting the relationship between FtsZ and MinD proteins, we found that these two proteins may have a potentially in-phase synchronization between them in specific IMFs within their signals on the same-side cell poles during the cell cycle. However, the results cannot exclude the influence of bleeding and still need to be proved confidently by other supplementary control experiments as well.

    Abstract I Acknowledgment III Chapter 1 Introduction 1 1.1 Bacterial cell division and the associated protein systems 2 1.2 The Min-protein system oscillations and the interaction with FtsZ 3 1.3 Motivation and goals 5 Chapter 2 Experimental designs 11 2.1 Experimental designs 13 2.1.1 Sample designs 14 2.1.2 Polydimethylsiloxane (PDMS) device 15 2.2 Total Internal Reflection Fluorescence (TIRF) Microscopy 16 2.3 Auto- and Cross-correlations 18 2.4 Empirical Mode Decomposition (EMD) & Ensemble Empirical Mode Decomposition (EEMD) 19 Chapter 3 Materials and Methods 23 3.1 Sample preparation 23 3.1.1 Bacterial strains 23 3.1.2 Plasmids 25 3.2 Observation method and experimental protocols 25 3.2.1 Optical apparatus 25 3.2.2 Experiment protocols 26 3.3 Data analysis 28 3.3.1 Data pre-process and image process 28 Chapter 4 Results 31 4.1 Time-frequency features of time series for two proteins 31 4.2 Dynamics Cross-Correlations between FtsZ-MinD dynamical interactions 32 4.3 Feature extraction of interacting episodes by EMD 33 4.4 Mode mixing issue and EEMD resolution 35 4.5 Data validation 36 4.5.1 The surrogate test 36 4.5.2 Fluorescent bleeding test 37 Chapter 5 Conclusions and Future works 56 References 60 Appendix 62 Appendix 1. Strain List 62 Appendix 2. Plasmid List 63 Appendix 3. Primer List 64

    Vollmer, A.J.F.E.a.W., The physiology of bacterial cell division. ANNALS OF THE NEW YORK ACADEMY OF SCIENCES, 2013. 1277: p. 8-28.
    Piet de Boer, R.C.L.R., The essential bacterial celldivision protein FtsZ is a GTPase. NATURE, 1992. 359: p. 254-256.
    Lutkenhaus, E.B.J., FtsZ ring structure associated with division in Escherichia coli. LETTERS TO NATURE, 1991. 354(14): p. 161.
    Zonglin Hu, A.M., Sebastien Pichoff, and Joe Lutkenhaus, The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization. PNAS, 1999. 96(26): p. 14819-14824.
    Eva Nogales, K.H.D., Linda A. Amos and Jan L6we, Tubulin and FtsZ form a distinct family of GTPases. nature structural biology 1998. 5(6): p. 451.
    Sue Vaughan, B.W., Keith Gull, Stephen G. Addinall, Molecular Evolution of FtsZ Protein Sequences Encoded Within the Genomes of Archaea, Bacteria, and Eukaryota. JOURNAL OF MOLECULAR EVOLUTION 2004. 58: p. 19-39.
    ADDINALL, S.G., FtsA Is Localized to the Septum in an FtsZ-Dependent Manner. American Society for Microbiology, 1996. 178(24): p. 7167-7172.
    Boer, C.A.H.a.P.A.J.d., Direct Binding of FtsZ to ZipA, an Essential Component of the Septal Ring Structure That Mediates Cell Division in E. coli. Cell 1997. 88: p. 175-185.
    Xinxing Yang, Z.L., Amanda Miguel, Ryan McQuillen, and J.X. Kerwyn Casey Huang, GTPase activity–coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. SCIENCE, 2017. 355: p. 744-747.
    Kevin D. Whitley, C.J., Nicholas Tregidgo, Eleni Karinou, Pedro Almada, Yann Cesbron, and C.D.S.H. Ricardo Henriques, FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division. NATURE COMMUNICATIONS, 2021. 12(2448).
    Errington, L.J.W.a.J., Nucleoid occlusion and bacterial cell division. NATURE REVIEWS | MICROBIOLOGY, 2011. 10: p. 8-12.
    Schwille, B.R.T.H.P., The E. coli MinCDE system in the regulation of protein patterns and gradients. Cellular and Molecular Life Sciences, 2019. 76: p. 4245-4273.
    Martin Loose, E.F.-F., Jonas Ries, Karsten Kruse, Petra Schwille, Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro. SCIENCE, 2008. 320: p. 789-792.
    Lutkenhaus, S.P.a.J., Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA. Molecular Microbiology, 2005. 55(6): p. 1722-1734.
    Paola Bisicchia, S.A., Petra Schwille, David Sherratt, MinC, MinD, and MinE Drive Counter-oscillation of Early-Cell-Division Proteins Prior to Escherichia coli Septum Formation. mBio, 2013. 4(6): p. e00856-13.
    Yang, X., et al., GTPase activity–coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. 2017. 355(6326): p. 744-747.
    Ana Isabel Rico, M.K., and Miguel Vicente, In the Beginning, Escherichia coli Assembled the Proto-ring: An Initial Phase of Division*. JOURNAL OF BIOLOGICAL CHEMISTRY, 2013. 288(29): p. 20830–20836.
    Desmond A. Moore, a.Z.N.W., b* Chandra P. Joshi,c* Masaki Osawa,c and H.P. Erickson, Probing for Binding Regions of the FtsZ Protein Surface through Site-Directed Insertions: Discovery of Fully Functional FtsZ-Fluorescent Proteins. Journal of Bacteriology, 2017. 199(1): p. e00553-16.
    HUANG, Z.W.a.N.E., ENSEMBLE EMPIRICAL MODE DECOMPOSITION: A NOISE-ASSISTED DATA ANALYSIS METHOD. Advances in Adaptive Data Analysis, 2009. 1(1): p. 1-41.

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