免對齊序列比對法分析片段化阿拉伯芥轉錄因子ICE1之本質無序區域

Abstract

ICE1 (Inducer of CBF Expression 1) 為阿拉伯芥轉錄因子中的鹼性螺旋-環-螺旋 (basic helix-loop-helix , bHLH) 家族的一員，參與許多不同植物逆境反應與生長調控機制。AtICE1共有494個胺基酸，除了bHLH (300-365 a.a.) 和ACTL (405-494 a.a.) 具有可摺疊構造， 其餘約 70％ 的序列被預測為本質無序區域 (intrinsically disorder regions, IDRs)，這些區域多由親水性或極性的胺基酸組成，其在分子層次的功能仍不確定。根據IDRs的胺基酸組成特性，許多序列分析方法被開發出來以預測特性區域的存在或其功能。具有摺疊結構的蛋白，其結構可以與其序列密切相關，所以可以以對齊序列比較法 (Alignment-based sequence comparison) 找尋到類似構造或功能的蛋白質，然而，對於保守性低的IDRs，對齊序列分析方法搜尋類似蛋白質的差異性較大。因此，若以胺基酸物化特性作為序列對應的比較方式，便可以去除對齊序列比對中保守性序列的限制，有利於 IDRs 的序列對應與分析。本研究採用一種片段化分析法，利用提取胺基酸特性的免對齊序列比對法 (Alignment-free sequence comparison) 分析不同長度的 AtICE1 片段序列，並與 Disprot 資料庫收集的 IDRs 進行對應搜尋，嘗試以對應到的IDR做為AtICE1參考的功能探索。相對於整個蛋白質胺基酸特性的計算，片段化序列分析法可避免蛋白質序列長度的差異而影響分析。在序列對應上， AtICE1的長片段 IDRs有初步的對應，且在 ICE1的不同物種同源蛋白上也有看到類似的對應，說明此方法的可行性。這些分析結果將有助於 AtICE1 潛在功能的探討。

ICE1 (Inducer of CBF Expression 1) is a member of the basic helix-loop-helix (bHLH) family of transcription factors in Arabidopsis thaliana, involved in various plant stress responses and plant growth development. AtICE1 consists of 494 amino acids, with the bHLH (300-365 a.a.) and ACTL (405-494 a.a.) regions forming foldable structured domains. Approximately 70% of the remaining sequence is predicted to be intrinsically disordered regions (IDRs), which are primarily composed of hydrophilic or polar amino acids. The molecular functions of these IDRs remain uncertain. Based on the unique amino acid composition of IDRs, various sequence analysis methods have been developed to predict the presence of IDR. For proteins with structured domains, their structure is typically determined by their sequence, allowing alignment-based sequence comparison methods to identify proteins with similar structures or functions. However, for IDRs with low sequence conservation, alignment-based methods is limiting its accountability. Therefore, comparing sequences based on the physicochemical properties of amino acids can eliminate the constraints of the necessity of a sequential arrangement in alignment-based sequence comparisons, facilitating finding counterpart of IDRs. This study employs a fragment-based analysis method, utilizing an alignment-free sequence comparison that extracts amino acid properties to analyze AtICE1 IDRs. These IDRs properties are then matched with IDPs/Rs collected in the DisProt database, attempting to find the corresponding IDRs as functional references for AtICE1. Compared to calculating the physicochemical properties of entire protein sequences, the fragment-based analysis method avoids the influence of protein sequence length differences on the analysis. In terms of sequence correspondence, the IDRs of long AtICE1 fragments showed correspondences, and similar matches were observed in homologous proteins of ICE1 across different species, demonstrating the feasibility of this method. These analysis results will contribute to exploring the potential functions of AtICE1.