Updating genome annotation for the microbial cell factoryAspergillus nigerusing gene co-expression networks

Abstract

A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.

Comparative genomic analysis reveals metabolic mechanisms for Kluyveromyces marxianus’ fast growth during evolution

“…Based on the recognition that genes with strong co-expression may be in the same or closely related pathway [17,18], we used the function known gene with the highest Pearson correlation coefficient to infer the function of KMS genes. The predicted function of KMS genes were generally accordant with the findings of homologous genes (Fig.…”

“…3B) and occupied approximately 40% of the total KMS genes. To explore their possible functions, Pearson correlation coefficient (denoted as r) was calculated between KMS gene and gene with known function, based on the hypothesis that strongly co-expressed genes are likely to function in the same or closely related biological pathways [17,18]. Genes with the highest r value (at least r > 0.8) were used to infer the possible function of KMS genes.…”

“…Inspired by the idea of using gene co-expression network to predict the function of hypothetical genes in Aspergillus niger [17], in this study we employed Pearson correlation coefficient (denoted as r) to infer the function of K. marxianus-specific (KMS) genes, which was calculated between a KMS gene and a function known gene along the time points during cultivation. If r > 0.8, the function known gene can be considered as candidate for function prediction, finally the gene with the highest r value was chosen for function inference.…”

Fungal Biotechnology in Space: Why and How?

“…Most importantly, highly sophisticated genetic engineering, systems biology and synthetic biology tools have been established during the last decade to understand and reprogramme the genetic and metabolic landscape of A. niger. These tools include targeted genetic transformation systems ranging from ku70 to CRISPR/Cas9 technologies (Meyer et al 2007;Carvalho et al 2010;Kuivanen et al 2016;Sarkari et al 2017;Zheng et al 2018b, a;Song et al 2018); highly controlled mono-and polycistronic Tet-onbased expression systems ensuring high product titres (Geib and Brock 2017; Schuetze and Meyer 2017); a well-annotated genome sequence (Pel et al 2007); a high-quality transcriptomic database, most recently updated (Schäpe et al 2018); and optimized cultivation protocols for stirred-tank and wave-mixed bioreactor cultivations ensuring reproducible growth, morphology and physiology of A. niger (Kurt et al 2018). Notably, the medium composition and environmental conditions to which A. niger can be subjected and cultivated span a broad spectrum too.…”

Comparative evaluation of Aspergillus niger strains for endogenous pectin-depolymerization capacity and suitability for d-galacturonic acid production

“…From a genomics perspective, genomic sequences are openly available for A. niger strains CBS 513.88 [38], ATCC 1015 [4], and NRRL 3 [2]-the latter with a recent advance in annotation [45]-as well as for three additional isolates [55]. Comparison of intra-species genomic data revealed the cause of some of the observed phenotypic differences between the strains, such as overproduction of glucoamylase in A. niger CBS 513.88, which was due to an additional glucoamylase gene acquired by horizontal gene transfer [4,55].…”