Gibbons John G, Beauvais Anne, Beau Remi, McGary Kriston L, Latgé Jean-Paul, Rokas Antonis
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
Eukaryot Cell. 2012 Jan;11(1):68-78. doi: 10.1128/EC.05102-11. Epub 2011 Jul 1.
Aspergillus fumigatus is the most common and deadly pulmonary fungal infection worldwide. In the lung, the fungus usually forms a dense colony of filaments embedded in a polymeric extracellular matrix. To identify candidate genes involved in this biofilm (BF) growth, we used RNA-Seq to compare the transcriptomes of BF and liquid plankton (PL) growth. Sequencing and mapping of tens of millions sequence reads against the A. fumigatus transcriptome identified 3,728 differentially regulated genes in the two conditions. Although many of these genes, including the ones coding for transcription factors, stress response, the ribosome, and the translation machinery, likely reflect the different growth demands in the two conditions, our experiment also identified hundreds of candidate genes for the observed differences in morphology and pathobiology between BF and PL. We found an overrepresentation of upregulated genes in transport, secondary metabolism, and cell wall and surface functions. Furthermore, upregulated genes showed significant spatial structure across the A. fumigatus genome; they were more likely to occur in subtelomeric regions and colocalized in 27 genomic neighborhoods, many of which overlapped with known or candidate secondary metabolism gene clusters. We also identified 1,164 genes that were downregulated. This gene set was not spatially structured across the genome and was overrepresented in genes participating in primary metabolic functions, including carbon and amino acid metabolism. These results add valuable insight into the genetics of biofilm formation in A. fumigatus and other filamentous fungi and identify many relevant, in the context of biofilm biology, candidate genes for downstream functional experiments.
烟曲霉是全球最常见且致命的肺部真菌感染病原体。在肺部，这种真菌通常会形成一个密集的丝状菌落，嵌入到聚合物细胞外基质中。为了鉴定参与这种生物膜（BF）生长的候选基因，我们使用RNA测序技术比较了BF生长和液体浮游（PL）生长条件下的转录组。将数千万条序列读数与烟曲霉转录组进行测序和比对，确定了两种条件下3728个差异调节基因。尽管其中许多基因，包括编码转录因子、应激反应、核糖体和翻译机制的基因，可能反映了两种条件下不同的生长需求，但我们的实验也鉴定出了数百个导致BF和PL在形态和病理生物学上出现差异的候选基因。我们发现，在转运、次级代谢以及细胞壁和表面功能方面，上调基因出现的频率过高。此外，上调基因在烟曲霉基因组中呈现出显著的空间结构；它们更有可能出现在亚端粒区域，并在27个基因组邻域中共定位，其中许多与已知或候选的次级代谢基因簇重叠。我们还鉴定出1164个下调基因。这个基因集在基因组中没有空间结构，并且在参与初级代谢功能（包括碳代谢和氨基酸代谢）的基因中出现的频率过高。这些结果为烟曲霉和其他丝状真菌生物膜形成的遗传学提供了有价值的见解，并确定了许多在生物膜生物学背景下与下游功能实验相关的候选基因。
