1 Dept of Biology, Concordia University, 7141 Sherbrooke St. W., Montreal, Quebec H4B 1R6.
2 Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montreal, Quebec H4B 1R6.
3 Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.

Many microorganisms are able to use plant-derived aromatic and cyclic compounds like the common plant secondary metabolite quinic acid as carbon and energy sources. In fungi, three enzymatic steps convert quinic acid into the common intermediate protocatechuic acid, which is then further converted into TCA cycle intermediates. The genes encoding these three enzymes are known to be part of a gene cluster in Neurospora crassa along with a permease, a gene of unknown function, and an activator-repressor module controlling expression of the cluster. This gene cluster is conserved in fungi and has also been studied in Aspergillus nidulans, where an additional gene of unknown function is included. Here, we studied these genes in the filamentous fungus Aspergillus niger, where the availability of high-quality, well-annotated genomes and efficient tools for genome-editing and global gene expression analysis could provide new insights into quinic acid utilization in fungi. Using homology and whole transcriptome sequencing, we identified the genes involved in quinic acid utilization. Knockout mutants of these genes were then created to observe the growth phenotype on quinic acid media. We showed that not all the genes involved in quinic acid utilization in A. niger are linked. In addition to the in-cluster permease gene, we identified a second, previously unknown off-cluster permease gene which was upregulated in the presence of quinic acid. These two permeases were determined to function optimally at different pH levels, with the in-cluster permease being more effective at pH 6.5 and the off-cluster permease more effective at pH 3.5.