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Prolyl Endopeptidase (PEP) has the unique ability to hydrolyze the carboxyl terminal peptide bonds of Proline. This enzyme holds great value in various fields including medical research, disease treatment, human diet, and food production. Aspergillus niger is a significant food-grade protein expression system renowned for its high safety. It is considered an ideal system for producing Aspergillus -derived PEP due to its ability to secrete a large amount of endogenous proteins. Our research group successfully constructed the Aspergillus niger PEP engineering strain in the early stages by eliminating the background protein AsaA, thereby increasing secretion protein production. In this article, we explore new solutions to further enhance production. Experimental investigations were conducted to regulate secretory protein production at different levels by modifying the 5′UTR and reconstructing the secretion pathways. The results demonstrate that the strain modified by the 5′UTR and Kozak sequence (glaA5'UTR-GCCACC, glaA::protA) exhibited a 1.88-fold increase in gene transcription and a 105% increase in extracellular PEP activity compared to the non-modified strain. Co-expression of the ERdjs gene AnScj1 further increased extracellular PEP activity by 168%. However, deletion of derA or vps10 , key genes in the Aspergillus niger secretory protein degradation pathway, resulted in reduced levels of gene transcription and secretory expression. This article holds practical significance in enhancing the secretion and expression of PEP, obtaining higher-yield strains, and exploring optimization strategies for highly expressed proteins. [Display omitted] • 5'UTR modification enhances the expression of prolyl endopeptidase. • The ER-located DnaJ family member AnScj1 improves the expression of secretory protein. • Deletion of derA or vps10 does not always favor secretory protein expression. [ABSTRACT FROM AUTHOR]