Screening for the Suitable Signal Peptide for Secreted Nattokinase Expression in E. coli using an In Silico Approach: Precursor vs. Mature Forms

Authors

• Dewi Purwani Caya Ningsih, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Udayana University, Badung 80361, Indonesia
• Kartika Sari Dewi, Research Centre for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Bogor 16911, IndonesiaFollow
• I Wayan Martadi Santika, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Udayana University, Badung 80361, Indonesia
• Ade Andriani, Research Centre for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Bogor 16911, Indonesia
• Joko Pebrianto Trinugroho, Research Centre for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Bogor 16911, Indonesia
• Muhammad Yusuf, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia

Abstract

Nattokinase (NK), an enzyme with thrombolytic activity, has been widely used in treating cardiovascular disease. The expression of NK in the E. coli cell host is favored due to its several benefits, though it often results in inclusion bodies. Appropriate signal peptides can be attached to the N-terminus of a protein to initiate a secretory expression system, thus preventing the nascent protein from aggregating in the cytoplasm. This study aimed to identify suitable signal peptides for the secretory expression of active NK in E. coli and to investigate the impact of pre-protein in NK secretion using an in silico approach. The target proteins used were mature NK and propeptide-NK. Fifty prokaryotic signal peptides were analyzed using several bioinformatics tools, including SignalP, SoluProt, ProtParam, ProtCompB, I-TASSER, and RNAfold. The computational analysis identified pelB, flgI, Bla1, and ompC as the most suitable signal peptides for secreting NK in the E. coli system. We also found that a propeptide is essential for maintaining the alpha-helical conformation of signal peptides, which is necessary for promoting efficient secretion. Our analysis provides valuable insights for resear-chers seeking to develop secreted recombinant NK. This method can also be applied to optimize the secretion of other proteins in E. coli

Recommended Citation

Ningsih, Dewi Purwani Caya; Dewi, Kartika Sari; Santika, I Wayan Martadi; Andriani, Ade; Trinugroho, Joko Pebrianto; and Yusuf, Muhammad (2026) "Screening for the Suitable Signal Peptide for Secreted Nattokinase Expression in E. coli using an In Silico Approach: Precursor vs. Mature Forms," Makara Journal of Science: Vol. 30: Iss. 2, Article 15.
DOI: 10.7454/mss.v30i2.3000
Available at: https://scholarhub.ui.ac.id/science/vol30/iss2/15