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Background  As a ubiquitous filamentous fungal,  Aspergillus  spp. play a critical role in lignocellulose degradation, which was also defined as considerable cell factories for organic acids and industrially relevant enzymes producer. Nevertheless, the production of various extracellular enzymes can be influenced by different factors including nitrogen source, carbon source, cultivation temperature, and initial pH value. Thus, this study aims to reveal how amino acids affect the decomposition of lignocellulose by  Aspergillus fumigatus  Z5 through transcriptional and proteomics methods.    Results  The activities of several lignocellulosic enzymes secreted by  A. fumigatus  Z5 adding with cysteine, methionine, and ammonium sulfate were determined with the chromatometry method. The peak of endo-glucanase (7.33 ± 0.03 U mL −1 ), exo-glucanase (10.50 ± 0.07 U mL −1 ), β-glucosidase (21.50 ± 0.22 U mL −1 ), and xylanase (76.43 ± 0.71 U mL −1 ) were all obtained in the Cys treatment. The secretomes of  A. fumigatus  Z5 under different treatments were also identified by LC–MS/MS, and 227, 256 and 159 different proteins were identified in the treatments of Cys, Met, and CK (Control, treatment with ammonium sulfate as the sole nitrogen source), respectively. Correlation analysis results of transcriptome and proteome data with fermentation profiles showed that most of the cellulose-degrading enzymes including cellulases, hemicellulases and glycoside hydrolases were highly upregulated when cysteine was added to the growth medium. In particular, the enzymes that convert cellulose into cellobiose appear to be upregulated. This study could increase knowledge of lignocellulose bioconversion pathways and fungal genetics.    Conclusions  Transcriptome and proteome analyses’ results indicated that cysteine could significantly promote the secretion of lignocellulosic enzymes of an efficient lignocellulosic decomposing strain,  A. fumigatus  Z5. The possible reason for these results is that Z5 preferred to use amino acids such as cysteine to adapt to the external environment through upregulating carbon-related metabolism pathways.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1350-2) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles