光合菌於各種代謝環境下之系統生物學研究

Abstract

Rhodopseudomonas palustris (R. palustris) (沼澤紅假單胞菌)為紫色非硫光合菌的一種，可生活於各種不同的代謝環境；在自然環境中，廣泛分布於土壤與河水中。R. palustris可利用日光或是自然環境中的各種有機與無機物做為能量的來源，並利用大氣中的二氧化碳或是綠色植物衍生物做為碳源。除此之外特別的是，R. palustris尚可在行固氮作用時，產生氫氣做為其副產物。R. palustris也可以藉由調整自身的基因表現，使其能夠在各種不同的光源、碳源、氮源及不同電子來源的環境生存。在本研究中，我們使用了蛋白質二維電泳合併質譜儀研究 R. palustris不同代謝情況的蛋白質體表現；以及利用微陣列晶片研究其基因表現。我們的結果發現，在沼澤紅假單胞菌的四種不同代謝環境：光合自營、光合異營、化學自營、化學異營中，有38 個蛋白質產生變化。在化學自營和光合自營中比較，有 1357 個基因表現差異、光合自營和化學自營有 1629 個基因表現差異、化學異營和化學異營有 2512 個基因表現差異、光合異營和化學異營中有 168 個基因表現差異。有些蛋白質，像是60kDa chaperonin2、ABC transporters 相關蛋白質、PEPCK、catalase和phosphoglycerate dehydrogenase在三種以上的代謝條件均有表現，ABC transporter 並和自營與異營的調控相關。將這些結果利用蛋白質-蛋白質交互作用網路預測，發現60kDa chaperonin 2、transcription terminator rho、acyl-CoA dehydrogenase、S-adenosylmethionine synthetase、alcohol dehydrogenase扮演了重要的角色，甚至60kDa chaperonin 2 被預測和許多 ABC transporter 的蛋白質有交互作用的關係。根據這些變化，我們可以進一步了解光合細菌在不同代謝環境下的調控機制。

Rhodopseudomonas palustris (R. palustris), a purple nonsulfur bacteria, is among the most metabolically versatile bacteria and ubiquitous in soil and water. The microbe could use sunlight, organic or inorganic compound for cellular energy, and use atmosphere carbon dioxide, or green plant-derived compound for cell material. It also could produce hydrogen gas by biological nitrogen fixation. The microbe could adjust and reweave itself in response to changes in light, carbon, nitrogen and electron sources. The ability of R. palustris to use carbon dioxide depends on two metabolic states: photoautotrophic and chemoautotrophic state. In this study, we used microarray for transcriptomic study, and two-dimensional polyacrylamide gel electrophoresis and mass spectrometry for proteomic study, respectively. Our results showed that 1357, 2512, 1629, 168 genes were differentially expressed over two-fold in photoautotrophic verus chemoautotrophic conditions, chemoautotrophic versus chemoheterotrophic conditions, photoautotrophic versus photoheterotrophic conditions, and chemoheterotrophic versus photoheterotrophic conditions, respectively. We identified 38 proteins differentially expressed over two-fold between two of the four major metabolic states. Some proteins, such as 60kDa chaperonin 2, ABC transporter related proteins, phosphoenolpyruvate carboxykinase, catalase, and phosphoglycerate dehydrogenase, could differentially expressed in three of these four major metabolic states. Interestingly, ABC transporter pathway was related to switch of autotroph and heterotroph. With computational prediction of plausible protein-protein interactions among these 38 proteins, we found 60kDa chaperonin 2, transcription terminator rho, acyl-CoA dehydrogenase, S-adenosylmethionine synthetase, alcohol dehydrogenase were the hub proteins in the predicted interaction network. These findings help us understand the regulatory mechanism of R. palustris.