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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Title:	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
Authors:	鄭勻媜;Cheng, Yun-Chen
Contributors:	生命科學系
Keywords:	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;TurboID;Proximity Labeling;Agrobacterium tumefaciens;Type VI secretion system;Biotin;Streptavidin
Date:	2022-09-27
Issue Date:	2022-10-04 11:03:56 (UTC+8)
Publisher:	國立中央大學
Abstract:	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。;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.
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