碩士 / 國立陽明大學 / 生物醫學資訊研究所 / 100 / Ganoderma lucidum (GL), which is a basidiomycetous fungus, has been used to a traditional medicine in East Asia for thousands of years. Chemicals extracted from GL fruiting bodies are effective in the treatment of certain cancers in vitro as well as in vivo in model organisms. However, the biological pathways of synthesizing such chemicals remain unclear. Many enzymes can only be annotated with simple functional roles and their ligand specificities are usually unknown. In this study, we re‐annotate the protein domains in the GL genes that are likely to be implicated in such pathways. We retrieved protein families implicated in glycosylation from Pfam. The ligand specificity of each protein family was determined based on the heterogeneity of initial annotations of its seed sequences. For protein families that are less specific than others, each family was further refined to generate more specific domain models. New pHMMs so built were used to re‐annotate the GL genome. The predicted gene 14270_g is the most likely candidate for -1,2-fucosyltransferase. This method can improve the annotation of ligand specificity of glycosylation enzymes in GL. Moreover this method can be easily adapted to investigate the synthesis pathways of other secondary metabolites not only in GL but also in other fungal species. Our method can play a role in annotating the massive amount of genomic sequences being fast accumulated due to the recent advances of the next generation sequencing (NGS) technologies.
| Identifer | oai:union.ndltd.org:TW/100YM005114030 |
| Date | January 2012 |
| Creators | Yu-Chuan Tseng, 曾于銓 |
| Contributors | Ueng-Cheng Yang, 楊永正 |
| Source Sets | National Digital Library of Theses and Dissertations in Taiwan |
| Language | zh-TW |
| Detected Language | English |
| Type | 學位論文 ; thesis |
| Format | 85 |
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