Identification of a Novel Biosynthetic Gene Cluster in Aspergillus niger Using Comparative Genomics.

Gregory Evdokias,Thi Truc Minh Nguyen,Adrian Tsang,Marcos Di Falco,Alexei Savchenko,Cameron Semper,Isabelle Benoit-Gelber,Montserrat Mora-Ochomogo

doi:10.3390/jof7050374

Gregory Evdokias, Thi Truc Minh Nguyen + Show 6 more

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https://doi.org/10.3390/jof7050374

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Abstract

Previously, DNA microarrays analysis showed that, in co-culture with Bacillus subtilis, a biosynthetic gene cluster anchored with a nonribosomal peptides synthetase of Aspergillus niger is downregulated. Based on phylogenetic and synteny analyses, we show here that this gene cluster, NRRL3_00036-NRRL3_00042, comprises genes predicted to encode a nonribosomal peptides synthetase, a FAD-binding domain-containing protein, an uncharacterized protein, a transporter, a cytochrome P450 protein, a NAD(P)-binding domain-containing protein and a transcription factor. We overexpressed the in-cluster transcription factor gene NRRL3_00042. The overexpression strain, NRRL3_00042OE, displays reduced growth rate and production of a yellow pigment, which by mass spectrometric analysis corresponds to two compounds with masses of 409.1384 and 425.1331. We deleted the gene encoding the NRRL3_00036 nonribosomal peptides synthetase in the NRRL3_00042OE strain. The resulting strain reverted to the wild-type phenotype. These results suggest that the biosynthetic gene cluster anchored by the NRRL3_00036 nonribosomal peptides synthetase gene is regulated by the in-cluster transcriptional regulator gene NRRL3_00042, and that it is involved in the production of two previously uncharacterized compounds.

Highlights

The filamentous fungus Aspergillus niger has long been established as an industrial microorganism for the production of enzymes and organic acids
The ability of A. niger to thrive in diverse environments is correlated with its capacity to produce a wide repertoire of secondary metabolites [5]
Using the functional annotation of A. niger NRRL3, the predicted biosynthetic gene cluster structure was identified as the following, a nonribosomal peptide synthetase (NRPS) (NRRL3_00036), a transporter (NRRL3_00039), a cytochrome P450 (NRRL3_00040), a FAD-binding domain-containing protein (NRRL3_00037) and a NAD(P)-binding domain-containing protein (NRRL3_00041)

Summary

Introduction

The filamentous fungus Aspergillus niger has long been established as an industrial microorganism for the production of enzymes and organic acids. Aspergillus niger is capable of high secretion of proteins such as glucoamylase [1] and organic acids such as citric, gluconic and oxalic acids [2]. Aspergillus niger has a versatile lifestyle and can be isolated from many ecological niches, including soil and decaying plant materials, where it encounters other microorganisms. It can be found as a food contaminant [3], a plant parasite and endophyte [4]. It was previously reported that A. niger and Bacillus subtilis altered their metabolism when cultivated together. The whole transcriptome of A. niger during its interaction with

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