| 引用本文: | 高贝,李小双,张道远.基于HMM的齿肋赤藓VOZ转录因子的预测与分析[J].生物信息学,2014,12(02):77-83. |
| GAO Bei,LI Xiaoshuang,ZHANG Daoyuan.Identification and characterization of a VOZ transcription factor in Syntrichia caninervisusing profile HMM method[J].Chinese Journal of Bioinformatics,2014,12(02):77-83. |
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| 摘要: |
| VOZ(Vascular plant One Zinc finger protein)作为与植物的进化与发育密切相关的基因,在极端耐旱荒漠苔藓植物齿肋赤藓(Syntrichia caninervis)中对VOZ基因进行挖掘和分析有利于更好的揭示VOZ基因的进化关系,且可作为抗逆基因进行更为深入的分子生物学研究。在VOZ转录因子蛋白中VOZ-domain是一个保守的DNA结合结构功能域,利用VOZ-domain多序列联配构建隐马尔可夫模型序列谱能够很好的进行家族成员的识别和预测。利用拟南芥、小立碗藓和水稻等植物已知的转录因子序列信息构建HMM序列谱模型,对荒漠苔藓齿肋赤藓转录组进行比对搜索。最终得到一条新的齿肋赤藓VOZ转录因子ScVOZ1(NCBI/EBI检索号:HG764415),序列长度为1 495 bp,具有完整的VOZ-domain结构域。生物信息学分析表明其具有转录调控功能和核定位潜能。多序列比对、进化和保守基序分析表明,ScVOZ1蛋白序列与小立碗藓VOZ家族和拟南芥AtVOZ1相似度较高。本研究为进一步研究ScVOZ1基因的功能以及其进化起源奠定了基础。 |
| 关键词: 齿肋赤藓 VOZ转录因子 隐马模型 生物信息学 |
| DOI：10.3969/j.issn.1672-5565.2014-02.20140201 |
| 分类号:Q811.4 |
| 基金项目: |
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| Identification and characterization of a VOZ transcription factor in Syntrichia caninervisusing profile HMM method |
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GAO Bei1,2, LI Xiaoshuang1,2, ZHANG Daoyuan1
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(1.Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Instate of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; 2. University of Chinese Academy of Sciences,Beijing 100049, China)
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| Abstract: |
| As VOZ gene is highly related with evolution and development in plants, the prediction and characterization of a VOZ gene in the stress-tolerant desert moss Syntrichia caninerviswill help reveal its evolutionary history. Furthermore, it may also serve as a stress resistant gene for further molecular analysis. The VOZ-domain is a conserved functional DNA-binding domain in VOZ transcription factors. The HMM profile constructed based on multiple sequence alignment of VOZ-domain could be used for novel VOZ gene prediction and identification. Based on the transcriptome of Syntrichia caninervisand the HMM profile constructed from the VOZ genes in A. thaliana, P. patensand O. sativa, a novel VOZ transcription factor was identified in Syntrichia caninervisand named as ScVOZ1 with NCBI/EBI accession number HG764415, the mRNA sequence length 1 495 bp and containing complete VOZ-domain. Bioinformatics analysis showed that ScVOZ1 is provided with the function of transcription regulation and the potential of nuclear localization. Multiple sequence alignment, phylogenetic and conserved motif analysis showed ScVOZ1 has the highest similarity with PpVOZ1/2 in P. patensand AtVOZ1 in A. thaliana, this study laid foundation for further functional and phylogenetic study of this evolution and development important gene. |
| Key words: Syntrichia caninervis VOZ transcription factor HMM Bioinformatics |
