2007-08-012024-05-18https://scholars.lib.ntu.edu.tw/handle/123456789/707223摘要：本計畫以光合細菌Rhodopseudomonas palustris為對象，進行系統與計算生物學研究。Rhodopseudomonas palustris是一種紫色非硫光合細菌，為水中底泥及土壤中常見的光合細菌，其不僅能轉換二氧化碳成為體內所需能量，還能將之轉換成生物質量。此類生物體可以應用於生物催化劑，並具有處理有毒工業廢物(例如：氯和苯)及生產能源的潛力(例如：生產氫氣以作為燃料)。另外由於它具有移除二氧化碳的能力，所以在應用上對於全球溫室效應也具有減緩的作用。R. palustris 獲選為DOE Carbon Management Program中定序的目標生物，並於2004年完成其基因體序列定序的工作，也因此使其成為一個模式生物。R. palustris 非常地特別，有四種代謝的方式能支持其生長，包括(1)光合自營生長：其能量來自於太陽光，碳源來自於二氧化碳；(2)光合異營生長：其能量來自於太陽光，碳源來自於有機化合物；(3)化學自營生長：其能量來自於無機化合物，碳源來自於二氧化碳；(4)化學異營生長：其能量及碳源皆來自於有機化合物。R. palustris 可以生長在有氧或無氧的環境中，當無氧時，它會藉由行光合作用而產生能量，藉由吸收二氧化碳或分解有毒化合物而成長；若是在有氧環境，則分解含碳化合物如糖、木質素單體和甲醇，並使用呼吸作用來獲得能量。美國能源部設定了在2030年之前30%的汽油需求將由生物能源取代的長遠目標。為了克服這個問題並達成目標，美國能源部基因體GTL系統生物學計畫開創了一個新的研究領域，GTL將提供系統的方法來了解並操控植物和微生物以產生生物能源。其中所謂的生物能源是指由新的生物原料產生的液體、固體和氣體，而系統的方法指的是以高通量基因體的技術去了解植物和微生物，還有了解蛋白質體到代謝體甚至調節基因網路的系統。 此跨領域計畫包括兩個子計畫：子計畫一應用主持人在癌症蛋白質體學的研究平台，以探討R. palustris的功能性基因體；子計畫二<br> Abstract: Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that belongs to the alpha-proteobacteria. It is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting to biomass. This microbe can also degrade and recycle components of the woody tissues of plants. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program for genome sequencing. R. palustris has extraordinary metabolism versatility and grows by any one of the four modes of metabolism that support life: photoautotrophic or photosynthetic, photoheterotrophic, chemoheterotrophic and chemoautotrophic. Thus it is a model organism to probe how the web of metabolic reactions that operates within the confines of a single cell adjusts and reweaves itself in response to changes in light, carbon, nitrogen and electron sources that are easily manipulates experimentally. The U.S. Department of Energy (DOE) has set a goal of displacing 30% of 2004 gasoline demand with biofuels by 2030. To address critical scientific barriers that must be overcome to advance the biofuels industry, the U.S. DOE's Genomics:GTL systems biology program is creating a new generation of biological research enabled by the genome revolution. GTL will provide a systems-level approach to understanding and manipulating plants and microorganisms central to producing biofuels. Biofuels are liquid, solid, or gaseous fuels derived from renewable biological sources. A systems-level approach is to develop high-throughput, genome-scale technologies needed to understand the workings of biological, primarily microbial, systems from proteomics to metabolomics to gene regulatory networks. This interdisciplinary project includes two sub-projects: 1). Prof. Juan will investigate functional genomics of R. palustris based on her experience in cancer systems biology and the established proteomics platform; 2). Prof. Huang will focus on metabolic and gene network regulation and model construction based on his expertise in computational systems biology. The major objective of this project is to elucidate proteome, metabolome and gene networks of R. palustris using systems and computational biology approach and furthermore to apply the results for bioenergy production.光合細菌基因網路系統生物學計算生物學生物能源Rhodopseudomonas palustrisgene networksystems biologycomputational biologybioenergy