建立TurboID鄰近標記方法以鑑定根癌農桿菌TssC40的交互作用蛋白質

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鄭勻媜(Yun-Chen Cheng) 查詢紙本館藏

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生命科學系

論文名稱

建立TurboID鄰近標記方法以鑑定根癌農桿菌TssC40的交互作用蛋白質
(Establishment of TurboID Proximity Labeling to identify TssC40-interacting proteins in Agrobacterium tumefaciens)

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至系統瀏覽論文 (2025-1-1以後開放)

摘要(中)

第六型分泌系統(type VI secretion system, T6SS)存在於約25%的革蘭氏陰性菌中，是一種對抗細菌的武器。第六型分泌系統所分泌的效應子或毒素蛋白質可以從攻擊細胞的細胞質通過細胞膜遞送到所接觸的目標細胞中。第六型分泌系統由至少13個核心蛋白質所組成，稱為TssA-TssM (type VI secretion A-M)，它們的構造分別為膜蛋白複合體、底座蛋白、外鞘和攜帶效應器的注射裝置，組成一個可收縮的分子武器。根癌農桿菌是植物的病原菌，會造成冠癭病，也是基因轉移的工具。第六型分泌系統普遍存在許多根癌農桿菌基因複合種的基因體中，除了包含具高度保守性的Tss核心蛋白質外，根癌農桿菌的第六型分泌系統也擁有一些獨特的核心蛋白質，但現今對其分子功能的了解有限。在這項研究中，我的目標是使用一種稱為TurboID的鄰近標記方法，利用其生物素化酶來標記鄰近蛋白質，以鑑定三個第六型分泌系統核心蛋白質，分別為底座蛋白質TssA和TssK以及根癌農桿菌C58的獨特核心蛋白TssC40，與其他第六型分泌系統蛋白質之間的交互作用。我首先將TurboID分別與TssA、TssK和TssC40融合，回補到相對應的突變體中，並以西方墨點法確認其表現第六型分泌系統是否恢復分泌能力。結果表明，TssC40-HA-Turbo可以完全回補突變株的第六型分泌能力，而TurboID融合的TssA和TssK則不能回補。因此，針對TssC40-HA-Turbo進行Streptavidin下拉生物素化蛋白質，再以質譜法鑑定蛋白質身份。我發現，與僅表達TurboID或TssC40的突變體菌株相比，表達TssC40-HA-Turbo的突變體菌株其TssA、TssB、TssC41在Streptavidin下拉的樣品中有較高的量，顯示TssC40-HA-Turbo與TssA、TssB、TssC41蛋白質可能有交互作用。最後，再以免疫共沉澱和蛋白質下拉實驗驗證TssC40分別與TssA、TssB和TssC41有交互作用。

摘要(英)

Type Ⅵ secretion system (T6SS) is an antibacterial weapon found in ~25% of Gram-negative bacteria. T6SS effectors or toxin proteins can be delivered from the cytoplasm of the attacker cell through the cellular envelope into the target cell in a contact-dependent manner. T6SS is composed of at least 13 conserved core proteins, named as TssA-TssM (type VI secretion A-M), which are assembled into a contractile molecular weapon consisting of a membrane complex, baseplate, sheath and puncturing device carrying effectors. T6SS is highly conserved in the Agrobacterium tumefaciens genomospecies complex, a causal agent of crown gall disease and gene transfer tool. While most Tss core proteins encoded in A. tumefaciens are highly conserved among T6SS-containing bacteria, A. tumefaciens harbors some unique core proteins with limited knowledge about their molecular functions. In this study, I aim to use a proximity labeling method termed TurboID, a promiscuous biotinylating enzyme, to identify the interaction proteins of three T6SS core proteins, TssA and TssK baseplate components, and a unique core protein TssC40 of A. tumefaciens C58. I first generated TurboID fusion to TssA, TssK, and TssC40 and determine their expression and functionality by western blotting of cellular and extracellular fractions in each of the respective mutants. The results showed that TssC40-HA-Turbo could fully rescue the T6SS secretion in the mutant while TssA and TssK fused with TurboID could not. Thus, TssC40-HA-Turbo expressing strain was subjected for protein extraction followed by biotinylating and Streptavidin pulldown to identify biotinylated proteins by mass spectrometry. I found that TssA, TssB, TssC41 were identified as enriched proteins in the TssC40-HA-Turbo expression strain as compared to strains expression TurboID only or TssC without fusion to TurboID. The interactions of TssC40 with TssA, TssB, and TssC41 were validated by co-immunoprecipitation and co-purification experiments.

關鍵字(中)

★ 根癌農桿菌
★ 第六型分泌系統
★ 交互作用蛋白質
★ 鄰近標記方法

關鍵字(英)

★ TurboID
★ Proximity Labeling
★ Agrobacterium tumefaciens
★ Type VI secretion system
★ Biotin
★ Streptavidin

論文目次

中文摘要 I
Abstract III
致謝 V
List of figures XII
List of tables XIV
Introduction 1
1. Bacterial secretion systems 1
1.1 Type VI secretion system (T6SS) 1
2. Agrobacterium tumefaciens 3
3. T6SS in A. tumefaciens 4
3.1 TssA and TssK baseplate components, and a unique core protein TssC40 of A. tumefaciens C58 4
4. Proximity labeling 6
4.1 Methods of proximity labeling 6
4.2 Optimization of biotin-based proximity labeling 7
Materials and methods 9
1. Bacterial strains and growth conditions 9
2. Cloning techniques and plasmid construction 9
3. Type VI secretion assay 10
4. Streptavidin pull-down assay 11
5. Identification of biotinylated proteins 13
5.1 Sample preparation 13
5.2 Mass Spectrometry Method 13
5.3 Data analysis 14
6. Co-immunoprecipitation (IP) assay 15
7. Co-purification in E. coli 17
8. GST pull-down assay 18
9. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis 19
10. Sequence analysis 20
Results 22
1. Generation of TurboID vector 22
2. Protein expression analysis of pRL662-HA-Turbo and pRL662-sfGFP-HA-Turbo in A. tumefaciens 22
3. Generation and functional analysis of constructs expressing TurboID fused to TssA, TssK, and TssC40 23
4. Biotin concentration optimized for Turbo-ID experiment 25
5. Specific biotinyltion and streptavidin pull-down of TssC40-HA-Turbo and HA-Turbo 25
6. Mass spectrometry identification of streptavidin pull-down proteins 26
7. TssA, TssB and TssC41 were identified as enriched T6SS proteins in the TssC40-HA-Turbo expression strain 27
8. Sequence analysis and domain prediction of TssC40 27
9. Validation of TurboID results of TssC40 interacting with TssA, TssB and TssC41 28
Discussion 31
References 34
Appendices 27
1. Medium and buffer used in this study 27
1.1 Lysogeny broth (LB) 27
1.2 523 27
1.3 AB-MES 27
1.4 TE buffer 28
1.5 Sample loading buffer (SSB) 28
1.6 RIPA Lysis buffer 28
1.7 Lysis buffer (Co-purification in E. coli) 28
1.8 Washing buffer (Co-purification in E. coli) 29
1.9 Elution buffer 29
1.10 Lysis buffer (purification of GST-tagged proteins) 29
1.11 Washing buffer (GST pull-down) 29
1.12 1X Transfer buffer 30
1.13 TBST 30
Appendix Figure 1. The plasmid maps of pRL662-sfGFP-HA-Turbo and pRL662-HA-Turbo 31
Appendix Figure 2. The plasmid maps of of TssA, TssC40, TssK fused to HA-Turbo or sfGFP-HA-Turbo on pRL662 shown in Appendix Figure 1. Each gene contains its own ribosome binding site. 33
Appendix Figure 3. Repeat data of Co-IP of TssA and TssB withTssC40-HA-Turbo by anti-HA using Wash buffer B with 3 wash times. 34
3. Appendix Tables 1
3.1 All the results of comparison with the protein abundance by proteomic core laboratory……………………………………………………………………………………..1
3.2 All the results of the comparison using PRM with the T6SS of A. tumefaciens C58 protein abundance by proteomic core laboratory. 9
4. Abbreviation in this study 1

List of figures
Figure 1. T6SS gene cluster and illustration of T6SS apparatus of A . tumefaciens C58. 1
Figure 2. Construct design for TurboID and its fusion to TssA, TssK, and TssC40 3
Figure 3. The workflow of TurboID for identification of biotinylated proteins 5
Figure 4. The workflow of Co-Immunoprecipitation by anti-HA 6
Figure 5. The workflow of E. coli co-purification 7
Figure 6. GST pull-down 8
Figure 7. Expression of HA-Turbo and sfGFP-HA-Turbo in A. tumefaciens 9
Figure 8. The expression and secretion of TssA fusion proteins in tssA 11
Figure 9. The expression and secretion of TssK fusion proteins in tssK 12
Figure 10. The expression and secretion of TssC40 fusion proteins in tssC40 13
Figure 11. Biotin concentration optimized for Turbo-ID experiment 14
Figure 12. TssC40-HA-Turbo expression strain can be detected by streptavidin pulldown 15
Figure 13. Domain prediction and sequence alignment of TssC40 17
Figure 14. Protein prediction of TssC40 in A. tumefaciens C58 20
Figure 15. Co-IP of TssA and TssB withTssC40-HA-Turbo by anti-HA using Wash buffer A 21
Figure 16. Co-IP of TssA and TssB withTssC40-HA-Turbo by anti-HA using Wash buffer B 22
Figure 17. Co-IP of TssA and TssB withTssC40-HA-Turbo by anti-HA using Wash buffer C 23
Figure 18. GST pull-down for interaction analysis between TssC40 with TssB or TssA. 24
Figure 19. E. coli co-expression of TssC40 and TssB. 26

List of Tables
Table 1. Bacterial strains 38
Table 2. Plasmid information 39
Table 3. Primer information 43
Table 4. The recipe and condition of Gibson assembly DNA polymerase 45
Table 5. The recipe and condition for PCR with Taq DNA polymerase 46
Table 6. The recipe and condition for PCR with KAPA DNA polymerase 47
Table 7. The comparison with the protein abundance by proteomic core laboratory. 1
Table 8. The comparison using PRM with the T6SS of A. tumefaciens C58 protein abundance by proteomic core laboratory. 5

參考文獻

1. Christie, P.J., et al., The Rich Tapestry of Bacterial Protein Translocation Systems. Protein J, 2019. 38(4): p. 389-408.
2. Pena, R.T., et al., Relationship Between Quorum Sensing and Secretion Systems. Microbiol, 2019.
3. Palmer, T., et al., A holin/peptidoglycan hydrolase-dependent protein secretion system. Mol Microbiol, 2020.
4. Coulthurst, S., et al., The Type VI secretion system: a versatile bacterial weapon. Microbiology (Reading), 2019. 165(5): p. 503-515.
5. Lin, J.S., et al., Systematic Dissection of the Agrobacterium Type VI Secretion System Reveals Machinery and Secreted Components for Subcomplex Formation. PLoS One, 2013. 8(7): p. e67647.
6. Zoued, A., et al., Architecture and assembly of the Type VI secretion system. Biochim Biophys Acta, 2014. 1843(8): p. 1664-73.
7. Hwang, H.H., et al., Agrobacterium-Mediated Plant Transformation: Biology and Applications. The Arabidopsis Book Vol. 15. 2017: American Society of Plant Biologists.
8. Lacroix B., et al., Pathways of DNA Transfer to Plants from Agrobacterium tumefaciens and Related Bacterial Species. Annu Rev Phytopathol, 2019. 57: p. 231-251.
9. Zechner, E.L., et al.,Assembly and mechanisms of bacterial type IV secretion machines. Philos Trans R Soc Lond B Biol Sci, 2012. 367(1592): p. 1073–1087.
10. Wu, H.Y., et al., Secretome Analysis Uncovers an Hcp-Family Protein Secreted via a Type VI Secretion System in Agrobacterium tumefaciens. J. Bacteriol, 2008. 190(8): p. 2841-2850.
11. Wu, C.F., et al., Plant-Pathogenic Agrobacterium tumefaciens Strains Have Diverse Type VI Effector-Immunity Pairs and Vary in In-Planta Competitiveness. Molecular Plant-Microbe Interactions, 2019. 32(8): p. 961-971.
12. Wu, C.F., et al., Diversification of the Type VI Secretion System in Agrobacteria. mBio, 2021. 12(5): p. e0192721.
13. Chou, L., et al., Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol, 2022. 20(1): p. 16.
14. Ma, L.S., et al., Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe, 2014. 16(1): p. 94-104.
15. Planamente, S., et al., TssA forms a gp6-like ring attached to the type VI secretion sheath. EMBO J, 2016. 35(15): p. 1613-27.
16. Santin, Y.G., et al., In vivo TssA proximity labelling during type VI secretion biogenesis reveals TagA as a protein that stops and holds the sheath. Nat Microbiol, 2018. 3(11): p. 1304-1313.
17. Nazarov, S., et al., Cryo-EM reconstruction of Type VI secretion system baseplate and sheath distal end. EMBO J, 2018. 37(4).
18. Wu, C.F., et al., Effector loading onto the VgrG carrier activates type VI secretion system assembly. Embo Reports, 2020. 21(1).
19. Huang Y., et al., Deciphering molecular interactions by proximity labeling. Nature Methods 2021: p. 133–143.
20. Roux K.J., et al., A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. Journal of Cell Biology, 2012. 196(6): p. 801-10.
21. Kubitz L., et al., Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells. communications biology 2022.
22. Kado C.I., et al., Selective media for isolation of Agrobacterium, Corynebacterium, Erwinia, Pseudomonas, and Xanthomonas. Phytopathology, 1970. 60(6): p. 969-76.
23. TW, K., et al., Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis. bioRxiv, 2019.
24. Kong A.T., et al., MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat Methods, 2017. 14(5): p. 513-520.
25. Teo G.C., et al., Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine. J Proteome Res, 2021. 20(1): p. 498-505.
26. Ali J., et al., N-terminal Domain of Type Six Secretion System Effector Tde1 Governs Secretion and Translocation into Target Cells. 2022, preprint.
27. Studer S., et al., Chaperone Activity and Homo- and Hetero-oligomer Formation of Bacterial Small Heat Shock Proteins. Journal of Biological Chemistry 2000. 275: p. 37212-37218.
28. Schagger H., et al., Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem, 1987. 166(2): p. 368-79.
29. Lai E.M., et al., Processed VirB2 is the major subunit of the promiscuous pilus of Agrobacterium tumefaciens. J Bacteriol, 1998. 180(10): p. 2711-7.
30. Samavarchi-Tehrani P., et al., Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Molecular & Cellular Proteomics, 2020. 19(5): p. 757-773.
31. Salih O., et al., Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa. Structure, 2018. 26(2): p. 329-336.
32. Studier, F.W., et al., Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol, 1990. 185: p. 60-89.
33. Vergunst, A., et al., VirB/D4-dependent protein translocation from Agrobacterium into plant cells. SCIENCE, 2000. 290(5493): p. 979-982.

指導教授

賴爾珉吳少傑(Erh-Min Lai Shaw-Jye Wu)

審核日期

2022-9-27

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