Development of functional cellomics for comprehensive analysis of the relationship between neural networks and behavior in Caenorhabditis elegans

1.

Alvarez-Castelao, B. et al. Cell-type-specific metabolic labeling of nascent proteomes in vivo.

Nat Biotechnol 35, 1196–1201 (2017).

2.

Li, J. et al. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.

Cell 180, 373-386.e15 (2020).

3.

Yuet, K. P. et al. Cell-specific proteomic analysis in Caenorhabditis elegans. Proc Natl Acad

Sci U S A 112, 2705–2710 (2015).

4.

Ullrich, M. et al. Bio-orthogonal labeling as a tool to visualize and identify newly synthesized

proteins in Caenorhabditis elegans. Nature Protocols vol. 9 2237–2255 Preprint at

https://doi.org/10.1038/nprot.2014.150 (2014).

5.

Stiernagle, T. Maintenance of C. elegans. WormBook : the online review of C. elegans

biology 1–11 Preprint at https://doi.org/10.1895/wormbook.1.101.1 (2006).

6.

Frøkjær-Jensen, C. et al. Single-copy insertion of transgenes in Caenorhabditis elegans. Nat

Genet 40, 1375–1383 (2008).

7.

Wang, H. et al. CGAL, a temperature-robust GAL4-UAS system for Caenorhabditis elegans.

Nat Methods 14, 145–148 (2017).

8.

Aoki, W. et al. Cellomics approach for high-throughput functional annotation of

Caenorhabditis elegans neural network. Sci Rep 8, (2018).

9.

Mitani, S. Genetic regulation of mec‐3 gene expression implicated in the specification of the

mechanosensory neuron cell types in Caenorhabditis elegans. Dev Growth Differ 37, 551–

557 (1995).

10. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image

analysis. Nature Methods vol. 9 671–675 Preprint at https://doi.org/10.1038/nmeth.2089

(2012).

11. Aburaya, S., Aoki, W., Kuroda, K., Minakuchi, H. & Ueda, M. Temporal proteome dynamics

of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. BMC

Microbiol 19, (2019).

12. Angeles-Albores, D., Raymond, R. Y., Chan, J. & Sternberg, P. W. Tissue enrichment

analysis for C. elegans genomics. BMC Bioinformatics 17, (2016).

13. Harris, T. W. et al. WormBase: A modern Model Organism Information Resource. Nucleic

Acids Res 48, D762–D767 (2020).

14. Mahoney, T. R. et al. Regulation of synaptic transmission by RAB-3 and RAB-27 in

Caenorhabditis elegans. Mol Biol Cell 17, 2617–2625 (2006).

15. Coates, J. C. & de Bono, M. Antagonistic pathways in neurons exposed to body fluid regulate

social feeding in Caenorhabditis elegans. Nature 419, 925–929 (2002).

68

16. Inada, H. et al. Identification of guanylyl cyclases that function in thermosensory neurons of

Caenorhabditis elegans. Genetics 172, 2239–2252 (2006).

17. Aoki, I. & Mori, I. Molecular biology of thermosensory transduction in C. elegans. Current

Opinion

in

Neurobiology

vol.

34

117–124

Preprint

at

https://doi.org/10.1016/j.conb.2015.03.011 (2015).

18. Aburaya, S., Aoki, W., Kuroda, K., Minakuchi, H. & Ueda, M. Temporal proteome dynamics

of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. BMC

Microbiol 19, (2019).

19. Komatsu, H., Mori, I. & Rhee, J.-S. Mutations in a Cyclic Nucleotide-Gated Channel Lead

to Abnormal Thermosensation and Chemosensation in C. elegans. Neuron vol. 17 (1996).

20. Hobert, O. et al. Regulation of Interneuron Function in the C. elegans Thermoregulatory

Pathway by the ttx-3 LIM Homeobox Gene. Neuron vol. 19 (1997).

21. Kobayashi, K. et al. Single-Cell Memory Regulates a Neural Circuit for Sensory Behavior.

Cell Rep 14, 11–21 (2016).

22. Kuhara, A., Inada, H., Katsura, I. & Mori, I. Negative regulation and gain control of sensory

neurons by the C. elegans calcineurin TAX-6. Neuron 33, 751–763 (2002).

23. Lockhead, D. et al. The tubulin repertoire of Caenorhabditis elegans sensory neurons and its

context-dependent role in process outgrowth. Mol Biol Cell 27, 3717–3728 (2016).

24. Moore, S. M., Hess, S. M. & Jorgenson, J. W. Extraction, Enrichment, Solubilization, and

Digestion Techniques for Membrane Proteomics. J Proteome Res 15, 1243–1252 (2016).

25. Zhang, Z., Dubiak, K. M., Huber, P. W. & Dovichi, N. J. Miniaturized Filter-Aided Sample

Preparation (MICRO-FASP) Method for High Throughput, Ultrasensitive Proteomics

Sample Preparation Reveals Proteome Asymmetry in Xenopus laevis Embryos. Anal Chem

92, 5554–5560 (2020).

26. Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N. & Mann, M. Minimal, encapsulated

proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat

Methods 11, 319–324 (2014).

27. Hughes, C. S. et al. Ultrasensitive proteome analysis using paramagnetic bead technology.

Mol Syst Biol 10, 757 (2014).

69

Acknowledgements

The author submitted this thesis to Kyoto University for a Ph.D. degree in Agriculture.

The studies presented here have been carried out under the direction of Professor Mitsuyoshi

Ueda, Assistant professor Kouichi Kuroda, and Professor Kenji Sugase in the Laboratory of

Biomacromolecular Chemistry, Division of Applied Life Science, Graduate School of Agriculture,

Kyoto University, during 2017-2023.

I want to express my most significant appreciation to Mitsuyoshi Ueda, Kouichi Kuroda,

Wataru Aoki, and Kenji Sugase, who offered insightful comments, meaningful discussions, and

continuous support throughout the course of my study.

I am also grateful to all my colleagues in the laboratory for wide-ranging discussion,

encouragement, and support. I want to thank the financial support from the research fellowship

of the Japan Society for the Promotion of Science for Young Scientists.

Yuji Yamauchi

Laboratory of Biomacromolecular Chemistry

Division of Applied Life Sciences

Graduate School of Agriculture

Kyoto University

70

Publications

Chapter I

Wataru Aoki, Hidenori Matsukura, Yuji Yamauchi, Haruki Yokoyama, Koichi Hasegawa, Ryoji

Shinya, Mitsuyoshi Ueda

Cellomics approach for high-throughput functional annotation of Caenorhabditis elegans

network

Scientific Reports 8:10380 (2018)

Chapter II

Yuji Yamauchi, Hidenori Matsukura, Keisuke Motone, Mitsuyoshi Ueda, Wataru Aoki

Evaluation of a library of loxP variants with a wide range of recombination efficiencies by Cre

PLOS One 7(10): e0276657 (2022)

Yuji Yamauchi, Hidenori Matsukura, Yusuke Shuto, Keisuke Motone, Tetsuya Kadonosono,

Naoki Honda, Kenji Sugase, Mitsuyoshi Ueda, Wataru Aoki

Development of a novel sparse labeling method by machine learning-guided engineering of Crelox recombination

In preparation

Chapter III

Shunsuke Aburaya, Yuji Yamauchi, Takashi Hashimoto, Hiroyoshi Minakuchi, Wataru Aoki,

Mitsuyoshi Ueda

Neuronal subclass-selective proteomic analysis in Caenorhabditis elegans

Scientific Reports 10:13840 (2020)

71

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