College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China.
Gene. 2012 Apr 10;497(1):116-24. doi: 10.1016/j.gene.2012.01.016. Epub 2012 Jan 27.
Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry.
丝状真菌因其能够大量分泌酶和代谢物而广泛应用于食品工业。最近获得的真菌基因组序列为探索这些与食品相关的丝状真菌的基因组特征提供了机会。在本文中，我们选择了在食品加工和安全领域具有代表性的 12 种丝状真菌，包括棒曲霉、黄曲霉、烟曲霉、构巢曲霉、黑曲霉、米曲霉、土曲霉、红曲霉、粗糙脉孢菌、产黄青霉、米根霉和里氏木霉，并对它们的 tRNA 基因分布、密码子使用模式和氨基酸组成的基因组特征进行了比较研究。结果表明，同功接受 tRNA 基因的拷贝数差异很大，分布似乎与翻译过程有关。结果还表明，基因组组成的变化可能限制了第三密码子的碱基选择，影响了整体氨基酸组成，但似乎对整体氨基酸的综合理化特性影响不大。进一步的分析表明，摆动配对和碱基修饰是密码子-反密码子相互作用的重要机制。据作者所知，这是第一篇关于与食品相关的丝状真菌基因组特征分析的报告，该报告将有助于分析丝状真菌基因组的进化及其在食品工业中的实际应用。
