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Effect of Target Gene Silencing on Calcite Single Crystal Formation by Thermophilic Bacterium Geobacillus thermoglucosidasius NY05

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Abstract

Geobacillus thermoglucosidasius NY05 catalyzes calcite single crystal formation at 60 °C by using acetate and calcium. Endospores are embedded at the central part of the calcite single crystal and carbon atoms in the calcite lattice are derived from acetate carbon. Here, we synthesized 21-mer antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs and evaluated the effect of these oligonucleotides on calcite formation in G. thermoglucosidasius NY05. G. thermoglucosidasius NY05 cells containing antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs had reduced calcite single crystal formation by 18.7, 50.6, 55.7, and 82.3%, respectively, compared with cells without antisense DNA oligonucleotides. These results support that calcite formation needs endospores as the nucleus to grow, and carbon dioxide generated from acetate, which is metabolized via the glyoxylate pathway and glucogenesis, is supplied to the crystal lattice.

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References

  1. Baldock MI, Denger K, Smits TH, Cook AM (2007) Roseovarius sp. strain 217: aerobic taurine dissimilation via acetate kinase and acetate-CoA ligase. FEMS Microbiol lett 271:202–206

    Article  CAS  PubMed  Google Scholar 

  2. Brumm PJ, Land ML, Mead DA (2015) Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 10:73

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ensign SA (2006) Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Mol Microbiol 61:274–276

    Article  CAS  PubMed  Google Scholar 

  4. Errington J (2003) Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol 1:117–126

    Article  CAS  PubMed  Google Scholar 

  5. Lorenz MC, Fink GR (2001) The glyoxylate cycle is required for fungal virulence. Nature 412:83–86

    Article  CAS  PubMed  Google Scholar 

  6. Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B (2018) Genome-guided analysis of Clostridium ultunense and comparative genomics reveal different strategies for acetate oxidation and energy conservation in syntrophic acetate-oxidising bacteria. Genes 9:225

    Article  CAS  PubMed Central  Google Scholar 

  7. McKinney JD, Zu Bentrup KH, Muñoz-Elías EJ, Miczak A, Chen B, Chan WT, Russell DG (2000) Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406:735–738

    Article  CAS  PubMed  Google Scholar 

  8. Mitsudome Y, Takahama M, Hirose J, Yoshida N (2014) The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes. AMB Express 4:70

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Murai R, Yoshida N (2013) Geobacillus thermoglucosidasius endospores function as nuclei for formation of single calcite crystals. Appl Environ Microbiol 79:3085–3090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Nakashima N, Tamura T (2009) Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli. Nucleic Acids Res 37:e103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Nakashima N, Tamura T, Good L (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli. Nucleic Acids Res 34:e138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rodríguez-Beltrán J, Elabed H, Gaddour K, Blázquez J, Rodríguez-Rojas A (2012) Simple DNA transformation in Pseudomonas based on the Yoshida effect. J Microbiol Methods 89:95–98

    Article  CAS  PubMed  Google Scholar 

  13. Schauder R, Eikmanns B, Thauer RK, Widdel F, Fuchs G (1986) Acetate oxidation to CO2 in anaerobic bacteria via a novel pathway not involving reactions of the citric acid cycle. Arch Microbiol 145:162–172

    Article  CAS  Google Scholar 

  14. Sonenshein AL (2000) Control of sporulation initiation in Bacillus subtilis. Curr Opin Microbiol 3:561–566

    Article  CAS  PubMed  Google Scholar 

  15. Tan H, Fu L, Seno M (2010) Optimization of bacterial plasmid transformation using nanomaterials based on the Yoshida effect. Int J Mol Sci 11:4962–4972

    Article  CAS  Google Scholar 

  16. Yoshida N (2007) Discovery and application of the Yoshida effect: nano-sized acicular materials enable penetration of bacterial cells by sliding friction force. Rec Pat Biotechnol 1:194–201

    Article  CAS  Google Scholar 

  17. Yoshida N, Higashimura E, Saeki Y (2010) Catalytic biomineralization of fluorescent calcite by the thermophilic bacterium Geobacillus thermoglucosidasius. Appl Environ Microbiol 76:7322–7327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry and Applied Biosciences, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki, 889-2192, Japan

    Rie Murai, Keiji Kiyoshi & Naoto Yoshida

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  1. Rie Murai
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  2. Keiji Kiyoshi
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  3. Naoto Yoshida
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Correspondence to Naoto Yoshida.

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Murai, R., Kiyoshi, K. & Yoshida, N. Effect of Target Gene Silencing on Calcite Single Crystal Formation by Thermophilic Bacterium Geobacillus thermoglucosidasius NY05. Curr Microbiol 76, 1298–1305 (2019). https://doi.org/10.1007/s00284-019-01756-y

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  • DOI: https://doi.org/10.1007/s00284-019-01756-y

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