Identification of Hypoxia-Inducible Target Genes of Aspergillus fumigatus by Transcriptome Analysis Reveals Cellular Respiration as an Important Contributor to Hypoxic Survival

Abstract

Aspergillus fumigatus is an opportunistic, airborne pathogen that causes invasive aspergillosis in immunocompromised patients. During the infection process, A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed a significant increase in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism, and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein-coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts, we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification (fhpA), NAD ؉ regeneration (frdA and osmA), nitrogen metabolism (niaD and niiA), and respiration (rcfB). We show that the nitric oxygen (NO)-detoxifying flavohemoprotein gene fhpA is strongly induced by hypoxia independent of the nitrogen source but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD, the nitrite reductase gene niiA, and the two fumarate reductase genes frdA and osmA, we found that alternative electron acceptors, such as nitrate and fumarate, do not have a significant impact on growth of A. fumigatus during hypoxia, but functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complexes III and IV play a crucial role in the hypoxic growth of A. fumigatus.

Identification and Characterization of a Novel Aspergillus fumigatus Rhomboid Family Putative Protease, RbdA, Involved in Hypoxia Sensing and Virulence

“…4). In contrast, regulation of the flavohemoprotein gene fhpA, whose transcription was found to be commonly responsive to NO and hypoxia (8,30), did not depend on either SrbA or RbdA. These results suggest that RbdA is tightly connected to the transcriptional activator function of SrbA.…”

“…Such levels of hypoxia are normally no threat for many aspergilli, as trace oxygen levels are often sufficient to support their growth. To sustain electron flow during such conditions, A. fumigatus finetunes components of its respiratory machinery (7)(8)(9)(10). Enzymatic steps requiring molecular O 2 in heme or ergosterol biosynthesis are highly sensitive to hypoxia and are under the control of the sterol regulatory element binding proteins (SREBPs) SrbA and SrbB.…”

Insights into the cellular responses to hypoxia in filamentous fungi

“…At present, genome-wide transcriptional profiling data of the hypoxic stress response are available from several filamentous ascomycetes: A. nidulans, A. oryzae, A. fumigatus, and Trichoderma reesei (Barker et al 2012;Bonaccorsi et al 2006;Hillmann et al 2014;Kroll et al 2014;Losada et al 2014;Masuo et al 2010;Terabayashi et al 2012). A somewhat smaller number of studies have been published on proteomic changes of A. nidulans and A. fumigatus during adaptation to low oxygen partial pressures (Barker et al 2012;Shimizu et al 2009;Vödisch et al 2011).…”

“…2). There were drastic differences in study design imposing low O 2 conditions either by shaking in hypoxic atmospheres (Losada et al 2014) or using O 2 -controlled bioreactors (Barker et al 2012;Kroll et al 2014;Hillmann et al 2014). The data sets were generated through either microarray technology or RNA sequencing, but an even larger impact on the set of induced genes could be expected from the duration of the hypoxic period (Fig.…”

“…fumigatus genes (with functional annotation) found to be up-regulated during hypoxic growth conditions in all five transcriptomic studies(Barker et al 2012;Cramer et al 2013;Losada et al 2014;Hillmann et al 2014;Kroll et al 2014) …”