嗜热毛壳菌基因组密码子偏好性研究  

Analysis of codon usage bias in the genome of Chaetomium thermophilum

作　　者：戴明丹 秦丽娜 江贤章[1] DAI Mingdan;QIN Lina;JIANG Xianzhang(National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology,College of Life Sciences,Fujian Normal University,Fuzhou 350000,Fujian,China)

机构地区：[1]福建师范大学生命科学学院、工业微生物发酵技术国家地方联合工程研究中心,福建福州350000

出　　处：《菌物学报》2023年第3期745-758,共14页Mycosystema

基　　金：国家自然科学基金(31800060);福建省自然科学基金(2019I0009,2020J01177)。

摘　　要：嗜热毛壳菌具有强大的木质纤维素降解能力,将其开发为优异的重组蛋白表达宿主有着广阔的应用前景。蛋白表达宿主的密码子偏好性对重组蛋白的表达水平具有重大影响。为确定嗜热毛壳菌中密码子的使用模式及影响因素,本研究以6897条CDS序列为对象,对其进行密码子偏好性分析。结果显示,嗜热毛壳菌中GC3的平均含量为66.2%,高于GC1(59.1%)和GC2(45.6%)的平均含量。Effective number of codon(ENC)分析与中性绘图分析结果显示,自然选择是影响嗜热毛壳菌密码子偏好性的主要因素。相关性分析结果显示,芳香族氨基酸比例与GC1含量及蛋白疏水水平呈极显著相关,说明密码子第一位的碱基组成对氨基酸是否具有芳香性影响较大。此外,在嗜热毛壳菌使用频率较高的密码子中,有24个以G/C末端结尾的密码子,进一步确定了23个高表达优越密码子和1个高表达最优密码子(CGC)。通过与其他模式真菌的密码子偏好性进行比较发现:与嗜热毛壳菌在密码子使用频率上差异较小的为嗜热毁丝菌、粗糙脉孢霉,有显著差异的为酿酒酵母。本研究为在嗜热毛壳菌中异源表达重组蛋白提供了目标基因密码子优化的理论依据,为嗜热毛壳菌在基因组水平上的应用和研究提供了数据支撑,有助于开发高效嗜热丝状真菌表达系统应用于工业酶制剂的生产。Chaetomium thermophilum has strong lignocellulose degradation ability,having broad application prospects to be developed as an excellent host for recombinant protein expression.The codon bias of the protein expression host significantly impact the expression level of recombinant proteins.In this study,the codon usage pattern of C.thermophilum genome was elucidated by analyzing 6897 CDS sequences.The results showed that the average content of GC3 in C.thermophilum was 66.2%,which was higher than the average content of GC1(59.1%)and GC2(45.6%).Effective number of codon(ENC)-plot analysis and neutral analysis demonstrated that natural selection pressure was the main factor affecting codon usage bias of C.thermophilum.Further analysis showed that the rate of aromatic amino acids was significantly correlated with the GC1 content and protein hydrophobicity,indicating that the base composition of the first codon greatly influenced the aromatization of amino acid.Among the frequently used codons in C.thermophilum,there were 24 codons ending in the G/C terminus,of which 23 codons are superior for high expression and 1 is optimal for high expression.In comparison with the codon usage bias of other model fungi,it was found that the codon usage bias of C.thermophilum was close to that of Myceliophthora thermophila and Neurospora crassa,but was significantly different from that of Saccharomyces cerevisiae.This study provided a theoretical basis for the codon optimization of target genes for heterologous expression of recombinant proteins in C.thermophilum,supporting the application and research at the genomic level of C.thermophilum.It is helpful to develop an excellent expression system of thermophilic filamentous fungi in application to the production of industrial enzyme preparations.

关 键 词：嗜热毛壳菌 密码子偏好性 相对同义密码子使用度 最优密码子 

分 类 号：Q933[生物学—微生物学]