Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis

Bin Wang; Yangyong Lv; Xuejie Li; Yiying Lin; Hai Deng; Li Pan

doi:10.1016/j.resmic.2017.10.002

Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis

Res Microbiol. 2018 Feb-Mar;169(2):67-77. doi: 10.1016/j.resmic.2017.10.002. Epub 2017 Oct 18.

Authors

Bin Wang¹, Yangyong Lv², Xuejie Li³, Yiying Lin⁴, Hai Deng⁵, Li Pan⁶

Affiliations

¹ School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China. Electronic address: btbinwang@scut.edu.cn.
² School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China. Electronic address: happy123488@163.com.
³ School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China. Electronic address: 1923206986@qq.com.
⁴ School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China. Electronic address: 419106557@qq.com.
⁵ School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China; Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK. Electronic address: h.deng@abdn.ac.uk.
⁶ School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China. Electronic address: btlipan@scut.edu.cn.

PMID: 29054463
DOI: 10.1016/j.resmic.2017.10.002

Abstract

The global regulator LaeA controls the production of many fungal secondary metabolites, possibly via chromatin remodeling. Here we aimed to survey the secondary metabolite profile regulated by LaeA in Aspergillus niger FGSC A1279 by genome sequencing and comparative transcriptomics between the laeA deletion (ΔlaeA) and overexpressing (OE-laeA) mutants. Genome sequencing revealed four putative polyketide synthase genes specific to FGSC A1279, suggesting that the corresponding polyketide compounds might be unique to FGSC A1279. RNA-seq data revealed 281 putative secondary metabolite genes upregulated in the OE-laeA mutants, including 22 secondary metabolite backbone genes. LC-MS chemical profiling illustrated that many secondary metabolites were produced in OE-laeA mutants compared to wild type and ΔlaeA mutants, providing potential resources for drug discovery. KEGG analysis annotated 16 secondary metabolite clusters putatively linked to metabolic pathways. Furthermore, 34 of 61 Zn₂Cys₆ transcription factors located in secondary metabolite clusters were differentially expressed between ΔlaeA and OE-laeA mutants. Three secondary metabolite clusters (cluster 18, 30 and 33) containing Zn₂Cys₆ transcription factors that were upregulated in OE-laeA mutants were putatively linked to KEGG pathways, suggesting that Zn₂Cys₆ transcription factors might play an important role in synthesizing secondary metabolites regulated by LaeA. Taken together, LaeA dramatically influences the secondary metabolite profile in FGSC A1279.

Keywords: Aspergillus niger; Comparative genomics; LaeA; Secondary metabolites; Transcriptomics; Zn(2)Cys(6) transcription factor.

MeSH terms

Aspergillus niger / genetics*
Aspergillus niger / metabolism*
Fungal Proteins / genetics*
Fungal Proteins / metabolism
Gene Expression Regulation, Fungal
Genome, Fungal
Multigene Family
Polyketides / metabolism
Secondary Metabolism*
Transcription Factors / genetics*
Transcription Factors / metabolism

Substances

Fungal Proteins
Polyketides
Transcription Factors