以生物資訊學方法預測不同物種一氧化氮合成酶序列－－以陰道滴蟲為例

Using Smith-Waterman Alignment to Annotate Nitric Oxide Synthase in Trichomonas Vaginalis

一氧化氮（NO）在生物體中扮演重要功能，哺乳類生物的NO與細胞訊息傳遞、免疫反應有關，而在細菌中NO則被發現具有保護免於氧化傷害之作用。另外在其他物種如真菌、藻類及原生動物等都發現可能具有一氧化氮合成酶（NOS）的活性。有學者指出雖然NOS的功能隨著生物演化，但其結構和作用機制並未有太大改變。從2006年Harris的實驗中，發現陰道滴蟲可能具有NOS的功能，但其基因體未被註解出NOS。因此，本研究目的為：（1）使用NCBI protein資料庫提供之所有物種NOS蛋白質序列及陰道滴蟲全部蛋白質序列，以生物資訊學方法比對，預測出陰道滴蟲NOS序列TV1及TV2，並經由實驗驗證其功能。（2）了解生物資訊學方法之比對正確預測性，分別對陰道滴蟲已知蛋白比對進行內部驗證，以及對其他物種NOS比對進行外部驗證，證明本研究方法之可行性。研究方法使用跨物種之蛋白質序列與物種全序列列以Smith-Waterman演算法區域排比，設定選取分數大於100分，以進行後續次數比例判讀。本研究實驗結果發現TV1及TV2具有NOS活性反應，且經由內部驗證及外部驗證的方式可證明本研究分析方法之可行性，預期未來能發展出一套有效註解物種未知蛋白質的方式。 Nitric oxide (NO) plays an important role in the organism. The mammals’ NO is related to signal transduction in cells and immune response, while NO in bacteria is found to protect against oxidative damage. Previous studies have shown that nitric oxide synthase (NOS) may be widely found in many organisms, from bacteria to animals; also, a few in algae, protozoa, fungi and other organisms have found a similar sequence structure of NOS or perform NO activity. Though the biological evolution, its structure and mechanism are only slightly changed. The genome of Trichomonas vaginalis has been published in 2007, although it has not yet been annotated NOS-related genes. However, some research has demonstrated its ability to produce NO. So, we want to annotate the sequences of nitric oxide synthase in Trichomonas vaginalis. Data are downloaded from NCBI protein database. Total 120,757 records of T. vaginalis and 6,631 of NOS protein sequences are aligned by Smith-Waterman algorithm. We also designed two ways of internal and external validation to verify our method. Two sequences (Tv1, Tv2) identified as [Iron only hydrogenase large subunit, C-terminal domain containing protein] are annotated as NOS in T. vaginalis in our study, and it needs experiment validation in further research. In conclusion, we establish an effective way to annotate unknown protein in the organisms, and provide the researchers to find candidate sequences in interest for experiments.

Nitric oxide (NO) plays an important role in the organism. The mammals’ NO is related to signal transduction in cells and immune response, while NO in bacteria is found to protect against oxidative damage. Previous studies have shown that nitric oxide synthase (NOS) may be widely found in many organisms, from bacteria to animals; also, a few in algae, protozoa, fungi and other organisms have found a similar sequence structure of NOS or perform NO activity. Though the biological evolution, its structure and mechanism are only slightly changed. The genome of Trichomonas vaginalis has been published in 2007, although it has not yet been annotated NOS-related genes. However, some research has demonstrated its ability to produce NO. So, we want to annotate the sequences of nitric oxide synthase in Trichomonas vaginalis. Data are downloaded from NCBI protein database. Total 120,757 records of T. vaginalis and 6,631 of NOS protein sequences are aligned by Smith-Waterman algorithm. We also designed two ways of internal and external validation to verify our method. Two sequences (Tv1, Tv2) identified as [Iron only hydrogenase large subunit, C-terminal domain containing protein] are annotated as NOS in T. vaginalis in our study, and it needs experiment validation in further research. In conclusion, we establish an effective way to annotate unknown protein in the organisms, and provide the researchers to find candidate sequences in interest for experiments.