Abstract
The creation of microbial cell factories for sustainable production of natural products is important for medical and industrial applications. This requires stable expression of biosynthetic pathways in a host organism with favorable fermentation properties such as Bacillus subtilis. The aim of this study is to construct B. subtilis strains that produce valuable terpenoid compounds by overexpressing the innate methylerythritol phosphate (MEP) pathway. A synthetic operon allowing the concerted and regulated expression of multiple genes was developed. Up to 8 genes have been combined in this operon and a stably inherited plasmid-based vector was constructed resulting in a high production of C30 carotenoids. For this, two vectors were examined, one with rolling circle replication and another with theta replication. Theta-replication constructs were clearly superior in structural and segregational stability compared to rolling circle constructs. A strain overexpressing all eight genes of the MEP pathway on a theta-replicating plasmid clearly produced the highest level of carotenoids. The level of transcription for each gene in the operon was similar as RT-qPCR analysis indicated. Hence, that corresponding strain can be used as a stable cell factory for production of terpenoids. This is the first report of merging and stably expressing this large-size operon (eight genes) from a plasmid-based system in B. subtilis enabling high C30 carotenoid production.
References
Abdallah II, Quax WJ (2017) A glimpse into the biosynthesis of terpenoids. KnE Life Sci 3:81. https://doi.org/10.18502/kls.v3i5.981
Ajikumar P, Xiao W-H, Tyo KEJ et al (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70–74. https://doi.org/10.1126/science.1191652
Bretzel W, Schurter W, Ludwig B et al (1999) Commercial riboflavin production by recombinant Bacillus subtilis: down-stream processing and comparison of the composition of riboflavin produced by fermentation or chemical synthesis. J Ind Microbiol Biotechnol 22:19–26. https://doi.org/10.1038/sj.jim.2900604
Bron S, Meijer W, Holsappel S et al (1991) Plasmid instability and molecular cloning in Bacillus subtilis. Res Microbiol 142:875–883. https://doi.org/10.1016/0923-2508(91)90068-L
Castillo-Hair S, Fujita M, Igoshin OA et al (2019) An engineered B. subtilis inducible promoter system with over 10,000-fold dynamic range. ACS Synth Biol 8:1673–1678. https://doi.org/10.1021/acssynbio.8b00469
Covello PS (2008) Making artemisinin. Phytochemistry 69:2881–2885. https://doi.org/10.1016/j.phytochem.2008.10.001
Dong H, Zhang D (2014) Current development in genetic engineering strategies of Bacillus species. Microb Cell Fact 13:63. https://doi.org/10.1186/1475-2859-13-63
Guan Z, Xue D, Abdallah II et al (2015) Metabolic engineering of Bacillus subtilis for terpenoid production. Appl Microbiol Biotechnol 99:9395–9406. https://doi.org/10.1007/s00253-015-6950-1
Guiziou S, Sauveplane V, Chang H-J et al (2016) A part toolbox to tune genetic expression in Bacillus subtilis. Nucleic Acids Res 44:7495–7508. https://doi.org/10.1093/nar/gkw624
Hess BM, Xue J, Markillie LM et al (2013) Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics. PLoS One 8:e66104. https://doi.org/10.1371/journal.pone.0066104
Jannière L, Bruand C, Dusko Ehrlich S (1990) Structurally stable Bacillus subtilis cloning vectors. Gene 87:53–61. https://doi.org/10.1016/0378-1119(90)90495-D
Khan SA (1997) Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61:442–455
Kuzma J, Nemecek-Marshall M, Pollock WH et al (1995) Bacteria produce the volatile hydrocarbon isoprene. Curr Microbiol 30:97–103. https://doi.org/10.1007/BF00294190
Li X-RR, Tian G-QQ, Shen H-JJ et al (2015) Metabolic engineering of Escherichia coli to produce zeaxanthin. J Ind Microbiol Biotechnol 42:627–636. https://doi.org/10.1007/s10295-014-1565-6
Lilly J, Camps M (2015) Mechanisms of theta plasmid replication. Microbiol Spectr 3:45–69. https://doi.org/10.1128/microbiolspec.PLAS-0029-2014
Ma T, Zhou Y, Li X et al (2016) Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli. Biotechnol J 11:228–237. https://doi.org/10.1002/biot.201400827
Man Z-W, Rao Z-MI, Cheng Y-P et al (2014) Enhanced riboflavin production by recombinant Bacillus subtilis RF1 through the optimization of agitation speed. World J Microbiol Biotechnol 30:661–667. https://doi.org/10.1007/s11274-013-1492-0
Meijer WJ, Wisman GB, Terpstra P et al (1998) Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria. FEMS Microbiol Rev 21:337–368. https://doi.org/10.1016/S0168-6445(98)00003-5
Nguyen HD, Nguyen QA, Ferreira RC et al (2005) Construction of plasmid-based expression vectors for Bacillus subtilis exhibiting full structural stability. Plasmid 54:241–248. https://doi.org/10.1016/j.plasmid.2005.05.001
Paddon CJ, Westfall PJ, Pitera DJ et al (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496:528–532. https://doi.org/10.1038/nature12051
Quan J, Tian J (2011) Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 6:242–251. https://doi.org/10.1038/nprot.2010.181
Rocky-Salimi K, Hashemi M, Safari M et al (2017) Valorisation of untreated cane molasses for enhanced phytase production by Bacillus subtilis K46b and its potential role in dephytinisation. J Sci Food Agric 97:222–229. https://doi.org/10.1002/jsfa.7716
Saimmai A, Sobhon V, Maneerat S (2011) Molasses as a whole medium for biosurfactants production by Bacillus strains and their application. Appl Biochem Biotechnol 165:315–335. https://doi.org/10.1007/s12010-011-9253-8
Schumann W (2007) Production of recombinant proteins in Bacillus subtilis. Adv Appl Microbiol 62:137–189. https://doi.org/10.1016/S0065-2164(07)62006-1
Shao H, Cao Q, Zhao H et al (2015) Construction of novel shuttle expression vectors for gene expression in Bacillus subtilis and Bacillus pumilus. J Gen Appl Microbiol 61:124–131. https://doi.org/10.2323/jgam.61.124
Sivy TL, Fall R, Rosenstiel TN (2011) Evidence of isoprenoid precursor toxicity in Bacillus subtilis. Biosci Biotechnol Biochem 75:2376–2383. https://doi.org/10.1271/bbb.110572
del Solar G, Giraldo R, Ruiz-Echevarría MJ et al (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62:434–464
Tanaka T, Ishida H, Maehara T (2005) Characterization of the replication region of plasmid pLS32 from the Natto Strain of Bacillus subtilis. J Bacteriol 187:4315–4326. https://doi.org/10.1128/JB.187.13.4315-4326.2005
Tanaka T, Ogura M (1998) A novel Bacillus natto plasmid pLS32 capable of replication in Bacillus subtilis. FEBS Lett 422:243–246. https://doi.org/10.1016/S0014-5793(98)00015-5
Titok M, Chapuis J, Selezneva Y et al (2003) Bacillus subtilis soil isolates: plasmid replicon analysis and construction of a new theta-replicating vector. Plasmid 49:53–62. https://doi.org/10.1016/S0147-619X(02)00109-9
Toymentseva AA, Altenbuchner J (2019) New CRISPR-Cas9 vectors for genetic modifications of Bacillus species. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fny284
Vellanoweth RL, Rabinowitz JC (1992) The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol 6:1105–1114. https://doi.org/10.1111/j.1365-2958.1992.tb01548.x
Wang Y, Weng J, Waseem R et al (2012) Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res 40:e91. https://doi.org/10.1093/nar/gks248
Wang Z, Chen T, Ma X et al (2011) Enhancement of riboflavin production with Bacillus subtilis by expression and site-directed mutagenesis of zwf and gnd gene from Corynebacterium glutamicum. Bioresour Technol 102:3934–3940. https://doi.org/10.1016/j.biortech.2010.11.120
Xie W, Lv X, Ye L et al (2015) Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering. Metab Eng 30:69–78. https://doi.org/10.1016/j.ymben.2015.04.009
Xie W, Ye L, Lv X et al (2015) Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae. Metab Eng 28:8–18. https://doi.org/10.1016/j.ymben.2014.11.007
Xue D, Abdallah II, de Haan IEM et al (2015) Enhanced C30carotenoid production in Bacillus subtilis by systematic overexpression of MEP pathway genes. Appl Microbiol Biotechnol 99:5907–5915. https://doi.org/10.1007/s00253-015-6531-3
Xue J, Ahring BK (2011) Enhancing isoprene production by genetic modification of the 1-deoxy-d-xylulose-5-phosphate pathway in Bacillus subtilis. Appl Environ Microbiol 77:2399–2405. https://doi.org/10.1128/aem.02341-10
Ye J, Coulouris G, Zaretskaya I et al (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinform 13:134. https://doi.org/10.1186/1471-2105-13-134
Zhou K, Zou R, Zhang C et al (2013) Optimization of amorphadiene synthesis in Bacillus subtilis via transcriptional, translational, and media modulation. Biotechnol Bioeng 110:2556–2561. https://doi.org/10.1002/bit.24900
Zhou P, Xie W, Li A et al (2017) Alleviation of metabolic bottleneck by combinatorial engineering enhanced astaxanthin synthesis in Saccharomyces cerevisiae. Enzyme Microb Technol 100:28–36. https://doi.org/10.1016/j.enzmictec.2017.02.006
Zhou Y, Nambou K, Wei L et al (2013) Lycopene production in recombinant strains of Escherichia coli is improved by knockout of the central carbon metabolism gene coding for glucose-6-phosphate dehydrogenase. Biotechnol Lett 35:2137–2145. https://doi.org/10.1007/s10529-013-1317-0
Acknowledgements
We thank I. Maeda for providing the pHYcrtMN plasmid. Funding for this work was obtained through EuroCoRes SYNBIO (SYNMET), NWO-ALW 855.01.161, EU FP-7 grant 289540 (PROMYSE). IIA is a recipient of Erasmus Mundus Action 2, Strand 1, Fatima Al Fihri project ALFI1200161 scholarship and is on study leave from Faculty of Pharmacy, Alexandria University. HP is a recipient of Bernoulli scholarship from University of Groningen.
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Abdallah, I.I., Xue, D., Pramastya, H. et al. A regulated synthetic operon facilitates stable overexpression of multigene terpenoid pathway in Bacillus subtilis. J Ind Microbiol Biotechnol 47, 243–249 (2020). https://doi.org/10.1007/s10295-019-02257-4
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DOI: https://doi.org/10.1007/s10295-019-02257-4