Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
OMICS. 2010 Apr;14(2):165-75. doi: 10.1089/omi.2009.0118.
Analysis of coexpressed genes in response to different perturbations at the genome-level can provide new insight into global regulatory structures. Here we performed integrated data analysis for a crossspecies comparative investigation by exploring genomes and transcriptional coexpression profiles in Aspergillus oryzae and Aspergillus niger. Based on our analysis of conserved coexpressed genes, fatty acid catabolism via beta-oxidation, fatty acid transport, the glyoxylate bypass, and peroxisomal biogenesis were identified as core coevolved pathways between the two species. The occurrence of coexpression patterns, allowed for identification of DNA regulatory motifs and putative corresponding transcription factors, and we hereby show that comparative transcriptome analysis between two closely related fungi allows for identification of how genes involved in the utilization of fatty acids, peroxisomal biogenesis, and the glyoxylate bypass are regulated. Interestingly, "CCTCGG" was identified as a core binding site for the putative FarA and FarB transcription factors that govern the underlined biological processes. Phylogeny and domain architecture analysis of amino acid sequences of FarA and FarB in eight species of aspergilli, clearly indicate that these proteins are evolutionarily conserved across Aspergillus species as well as they are conserved in other fungi.
对不同基因组扰动的共表达基因进行分析，可以深入了解全局调控结构。在这里，我们通过探索米曲霉和黑曲霉的基因组和转录组共表达谱，进行了跨物种的综合数据分析。基于对保守共表达基因的分析，鉴定出β-氧化途径的脂肪酸分解代谢、脂肪酸运输、乙醛酸循环和过氧化物酶体生物发生是这两个物种共同进化的核心途径。共表达模式的出现，允许鉴定 DNA 调控基序和潜在的相应转录因子，并且我们在此表明，在两个密切相关的真菌之间进行比较转录组分析，可以确定参与脂肪酸利用、过氧化物酶体生物发生和乙醛酸循环的基因是如何被调控的。有趣的是，“CCTCGG”被鉴定为潜在的 FarA 和 FarB 转录因子的核心结合位点，这些转录因子控制着所强调的生物学过程。八种曲霉菌中 FarA 和 FarB 的氨基酸序列的系统发育和结构域分析清楚地表明，这些蛋白质在曲霉菌种中是进化保守的，在其他真菌中也是保守的。
