Skip to main content
Log in

Systematic engineering of transport and transcription to boost alkaline α-amylase production in Bacillus subtilis

  • Biotechnologically relevant enzymes and proteins
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

In the present work, we used systematic engineering at transport and transcription levels to significantly enhance alkaline α-amylase production in Bacillus subtilis 168M. Signal peptide YwbN’ proved to be optimal. Alkaline α-amylase production was elevated by deleting a putative peptide segment of YwbN’. Insertion of arginine (R) between residues 5 and 6 of YwbN’∆p further increased the protein yield. Enhancing positive charges at sites 4 and 10 and decreasing the hydrophobicity of the H-region of YwbN’∆p were critical for improving alkaline α-amylase production in B. subtilis 168M. PHpaII was the optimal promoter, and deleting − 27T or − 31A from PHpaII enhanced the transcription of the target gene. Using a single-pulse feeding-based fed-batch system, alkaline α-amylase activity of B. subtilis 168M P∆−27T was increased by 250.6-fold, compared with B. subtilis 168M A1.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Ballschmiter M, Fütterer O, Liebl W (2006) Identification and characterization of a novel intracellular alkaline α-amylase from the hyperthermophilic bacterium Thermotoga maritima MSB8. Appl Environ Microbiol 72:2206–2211

    PubMed  PubMed Central  CAS  Google Scholar 

  • Chen JQ, Zhao LQ, Fu G, Zhou WJ, Sun YX, Zhang DW (2016) A novel strategy for protein production using non-classical secretion pathway in Bacillus subtilis. Microb Cell Factories 15:69

    Google Scholar 

  • Choi J, Lee S (2004) Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol 64:625–635

    PubMed  CAS  Google Scholar 

  • Degering C, Eggert T, Puls M, Bongaerts J, Evers S, Maurer KH, Jaeger KE (2010) Optimization of protease secretion in Bacillus subtilis and Bacillus licheniformis by screening of homologous and heterologous signal peptides. Appl Environ Microbiol 76:6370–6376

    PubMed  PubMed Central  CAS  Google Scholar 

  • Guan C, Cui W, Cheng J, Liu R, Liu Z, Zhou L, Zhou Z (2016a) Construction of a highly active secretory expression system via an engineered dual promoter and a highly efficient signal peptide in Bacillus subtilis. New Biotechnol 33:372–379

    CAS  Google Scholar 

  • Guan C, Cui W, Cheng J, Zhou L, Liu Z, Zhou Z (2016b) Development of an efficient autoinducible expression system by promoter engineering in Bacillus subtilis. Microb Cell Factories 15:66

    Google Scholar 

  • Harwood CR, Cranenburgh R (2008) Bacillus protein secretion: an unfolding story. Trends Microbiol 16:73–79

    PubMed  CAS  Google Scholar 

  • Helmann JD (1995) Compilation and analysis of Bacillus Subtilis σ A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 23:2351–2360

    PubMed  PubMed Central  CAS  Google Scholar 

  • Jiang Z, Niu TF, Lv XQ, Liu YF, Li JH, Lu W, Du GC, Chen J, Liu L (2019) Secretory expression fine-tuning and directed evolution of diacetylchitobiose deacetylase by Bacillus subtilis. Appl Environ Microbiol 85:e01076–e01019

    PubMed  PubMed Central  CAS  Google Scholar 

  • Kwon E-Y, Kim KM, Kim MK, Lee IY, Kim BS (2011) Production of nattokinase by high cell density fed-batch culture of Bacillus subtilis. Bioprocess Biosyst Eng 34:789–793

    PubMed  CAS  Google Scholar 

  • Liu SL, Du K (2012) Enhanced expression of an endoglucanase in Bacillus subtilis by using the sucrose-inducible sacB promoter and improved properties of the recombinant enzyme. Protein Expr Purif 83:164–168

    PubMed  CAS  Google Scholar 

  • Liu L, Yang HQ, Shin HD, Chen RR, Li JH, Du GC, Chen J (2013a) How to achieve high-level expression of microbial enzymes: strategies and perspectives. Bioeng 4:212–223(b)

    Google Scholar 

  • Liu L, Yang HQ, Shin HD, Li JH, Du GC, Chen J (2013b) Recent advances in recombinant protein expression by Corynebacterium, Brevibacterium, and Streptomyces: from transcription and translation regulation to secretion pathway selection. Appl Microbiol Biotechnol 97:9597–9608(a)

    PubMed  CAS  Google Scholar 

  • Liu L, Deng ZM, Yang HQ, Li JH, Shin HD, Chen RR, Du GC, Chen J (2014) In silico rational design and systems engineering of disulfide bridges in the catalytic domain of an alkaline alpha-amylase from Alkalimonas amylolytica to improve thermostability. Appl Environ Microbiol 80:798–807

    PubMed  PubMed Central  Google Scholar 

  • Liu Q, Xun G, Feng Y (2018) The state-of-the-art strategies of protein engineering for enzyme stabilization. Biotechnol Adv 37:530–537

    PubMed  Google Scholar 

  • Ma YF, Yang HQ, Chen XZ, Sun B, Du GC, Zhou ZM, Song JN, Fan Y, Shen W (2015) Significantly improving the yield of recombinant proteins in Bacillus subtilis by a novel powerful mutagenesis tool (ARTP): alkaline alpha-amylase as a case study. Protein Expr Purif 114:82–88

    PubMed  CAS  Google Scholar 

  • Ma YF, Shen W, Chen XZ, Liu L, Zhou ZM, Xu F, Yang HQ (2016) Significantly enhancing recombinant alkaline amylase production in Bacillus subtilis by integration of a novel mutagenesis-screening strategy with systems-level fermentation optimization. J Biol Eng 10:13

    PubMed  PubMed Central  Google Scholar 

  • Nijland R, Kuipers OP (2008) Optimization of protein secretion by Bacillus subtilis. Recent Patents Biotechnol 2:79–87

    CAS  Google Scholar 

  • Nithya K, Muthukumar C, Dhansasekaran D, Kadaikunnan S, Alharbi NS, Khaled JM, Thajuddin N (2016) Production, optimization and partial characterization of thermostable and alkaline amylase from Bacillus licheniformis KSU-6. Int J Agric Biol 18:1188–1194

    CAS  Google Scholar 

  • Niu C, Liu C, Li Y, Zheng F, Wang J, Li Q (2018) Production of a thermostable 1, 3-1, 4-β-glucanase mutant in Bacillus subtilis WB600 at a high fermentation capacity and its potential application in the brewing industry. Int J Biol Macromol 107:28–34

    PubMed  CAS  Google Scholar 

  • Öztürk S, Calik P, Ozdamar TH (2016) Fed-batch biomolecule production by Bacillus subtilis: a state of the art review. Trends Biotechnol 34:329–345

    Google Scholar 

  • Öztürk S, Ergün BG, Çalık P (2017) Double promoter expression systems for recombinant protein production by industrial microorganisms. Appl Microbiol Biotechnol 101:7459–7475

    PubMed  Google Scholar 

  • Phan TTP, Nguyen HD, Schumann W (2012) Development of a strong intracellular expression system for Bacillus subtilis by optimizing promoter elements. J Biotechnol 157:167–172

    PubMed  CAS  Google Scholar 

  • Phanaksri T, Luxananil P, Panyim S, Tirasophon W (2015) Synergism of regulatory elements in σB-and σA-dependent promoters enhances recombinant protein expression in Bacillus subtilis. J Biosci Bioeng 120:470–475

    PubMed  CAS  Google Scholar 

  • Ploss TN, Reilman E, Monteferrante CG, Denham EL, Piersma S, Lingner A, Vehmaanperä J, Lorenz P, van Dijl JM (2016) Homogeneity and heterogeneity in amylase production by Bacillus subtilis under different growth conditions. Microb Cell Factories 15:57

    Google Scholar 

  • Prakash B, Vidyasagar M, Madhukumar MS, Muralikrishna G, Sreeramulua K (2009) Production, purification, and characterization of two extremely halotolerant, thermostable, and alkali-stable α-amylases from Chromohalobacter sp. TVSP 101. Process Biochem 44:210–215

    CAS  Google Scholar 

  • Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946–950

    PubMed  PubMed Central  CAS  Google Scholar 

  • Sauer C, Ver Loren van Themaat E, LGM B, Groothuis D, Cruz R, Hamoen LW, Harwood CR, van Rij T (2018) Exploring the nonconserved sequence space of synthetic expression modules in Bacillus subtilis. ACS Synth Biol 7:1773–1784

    PubMed  CAS  Google Scholar 

  • Saxena RK, Dutt K, Agarwal L, Nayyar P (2007) A highly thermostable and alkaline amylase from a Bacillus sp. PN5. Bioresour Technol 98:260–265

    PubMed  CAS  Google Scholar 

  • Shen HB, Chou KC (2007) Signal-3L: a 3-layer approach for predicting signal peptides. Biochem Biophys Res Commun 363:297–303

    PubMed  CAS  Google Scholar 

  • Song Y, Nikoloff JM, Zhang D (2015) Improving protein production on the level of regulation of both expression and secretion pathways in Bacillus subtilis. J Microbiol Biotechnol 25:963–977

    PubMed  CAS  Google Scholar 

  • Song Y, Fu G, Dong H, Li J, Du Y, Zhang D (2017) High-efficiency secretion of β-mannanase in Bacillus subtilis through protein synthesis and secretion optimization. J Agric Food Chem 65:2540–2548

    PubMed  CAS  Google Scholar 

  • Spizizen J (1958) Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci U S A 44:1072–1078

    PubMed  PubMed Central  CAS  Google Scholar 

  • Tian RZ, Liu YL, Chen JR, Li JH, Liu L, Du GC, Chen J (2019) Synthetic N-terminal coding sequences for fine-tuning gene expression and metabolic engineering in Bacillus subtilis. Metab Eng 55:131–141

    PubMed  CAS  Google Scholar 

  • Trang Thi Phuong P, Hoang Duc N, Schumann W (2012) Development of a strong intracellular expression system for Bacillus subtilis by optimizing promoter elements. J Biotechnol 157:167–172

    Google Scholar 

  • van Dijl J, Hecker M (2013) Bacillus subtilis: from soil bacterium to super-secreting cell factory. Microb Cell Factories 12:3

    Google Scholar 

  • Veening JW, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, Kuipers OP (2008) Transient heterogeneity in extracellular protease production by Bacillus subtilis. Mol Syst Biol 4:184

    PubMed  PubMed Central  Google Scholar 

  • Voskuil MI, Chambliss GH (1998) The −16 region of Bacillus subtilis and other gram-positive bacterial promoters. Nucleic Acids Res 26:3584–3590

    PubMed  PubMed Central  CAS  Google Scholar 

  • Wu S-M, Feng C, Zhong J, Huan L-D (2011) Enhanced production of recombinant nattokinase in Bacillus subtilis by promoter optimization. World J Microbiol Biotechnol 27:99–106

    CAS  Google Scholar 

  • Yang HQ, Liu L, Li JH, Du GC, Chen J (2011) Heterologous expression, biochemical characterization, and overproduction of alkaline alpha-amylase from Bacillus alcalophilus in Bacillus subtilis. Microb Cell Factories 10:77

    CAS  Google Scholar 

  • Yang HQ, Liu L, Li JH, Du GC, Chen J (2012a) Advances of alkaline amylase production and applications. Chin J Biotechnol 28:432–439(a)

    CAS  Google Scholar 

  • Yang HQ, Liu L, Li JH, Du GC, Chen J (2012b) Cloning, heterologous expression, and comparative characterization of a mesophilic alpha-amylase gene from Bacillus subtilis JN16 in Escherichia coli. Ann Microbiol 62:1219–1226(b)

    CAS  Google Scholar 

  • Yang HQ, Liu L, Shin HD, Chen RR, Li JH, Du GC, Chen J (2013a) Integrating terminal truncation and oligopeptide fusion for a novel protein engineering strategy to improve specific activity and catalytic efficiency: alkaline alpha-amylase as a case study. Appl Environ Microbiol 79:6429–6438(a)

    PubMed  PubMed Central  CAS  Google Scholar 

  • Yang HQ, Lu XY, Liu L, Li JH, Shin HD, Chen RR, Du GC, Chen J (2013b) Fusion of an oligopeptide to the N terminus of an alkaline alpha-amylase from Alkalimonas amylolytica simultaneously improves the enzyme’s catalytic efficiency, thermal stability, and resistance to oxidation. Appl Environ Microbiol 79:3049–3058(b)

    PubMed  PubMed Central  CAS  Google Scholar 

  • Yang M, Zhang W, Ji S, Cao P, Chen Y, Zhao X (2013c) Generation of an artificial double promoter for protein expression in Bacillus subtilis through a promoter trap system. PLoS One 8:e56321(c)

    Google Scholar 

  • Yang HQ, Hu JY, Lu X, Wang FX, Shen W, Hu W, Wang LL, Chen XZ, Liu L (2019) Improving extracellular protein production in Escherichia coli by overexpressing D, D-carboxypeptidase to perturb peptidoglycan network synthesis and structure. Appl Microbiol Biotechnol 103:793–806

    PubMed  CAS  Google Scholar 

  • Zanen G, Houben EN, Meima R, Tjalsma H, Jongbloed JD, Westers H, Oudega B, Luirink J, van Dijl JM, Quax WJ (2005) Signal peptide hydrophobicity is critical for early stages in protein export by Bacillus subtilis. FEBS J 272:4617–4630

    PubMed  CAS  Google Scholar 

  • Zhang YZ, Shen HB (2017) Signal-3L 2.0: a hierarchical mixture model for enhancing protein signal peptide prediction by incorporating residue-domain cross-level features. J Chem Inf Model 57:988–999

    PubMed  CAS  Google Scholar 

  • Zou M, Guo F, Li X, Zhao J, Qu Y (2014) Enhancing production of alkaline polygalacturonate lyase from Bacillus subtilis by fed-batch fermentation. PLoS One 9:e90392

    PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was funded by National Natural Science Foundation of China (21406089), Natural Science Foundation of Jiangsu Province (BK20140152, BK20191185), and the Open Project Program of the Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, China (KLCCB-KF201802), 111 Project (111-2-06).

Author information

Authors and Affiliations

Authors

Contributions

H.Y. and X.C. designed the research; H.Y. and Y.M. performed the research; W.S., Y.Z., and X.C. analysed the data; H.Y., Y.M., and X.C. wrote this paper.

Corresponding authors

Correspondence to Haiquan Yang or Xianzhong Chen.

Ethics declarations

This work follows ethical standards. It contains no experiments with animals performed or human participants.

Conflict of interest

The authors declare that they have no competing interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(PDF 710 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, H., Ma, Y., Zhao, Y. et al. Systematic engineering of transport and transcription to boost alkaline α-amylase production in Bacillus subtilis. Appl Microbiol Biotechnol 104, 2973–2985 (2020). https://doi.org/10.1007/s00253-020-10435-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-020-10435-z

Keywords

Navigation