An improved pathway for autonomous bioluminescence imaging in eukaryotes.
Ekaterina S Shakhova, Tatiana A Karataeva, Nadezhda M Markina, Tatiana Mitiouchkina, Kseniia A Palkina, Maxim M Perfilov, Monika G Wood, Trish T Hoang, Mary P Hall, Liliia I Fakhranurova, Anna E Alekberova, Alena K Malyshevskaia, Dmitry A Gorbachev, Evgenia N Bugaeva, Ludmila K Pletneva, Vladislav V Babenko, Daria I Boldyreva, Andrey Y Gorokhovatsky, Anastasia V Balakireva, Feng Gao, Vladimir V Choob, Lance P Encell, Keith V Wood, Ilia V Yampolsky, Karen S Sarkisyan, Alexander S Mishin
Author Information
Ekaterina S Shakhova: Planta LLC, Moscow, Russia. ORCID
Tatiana A Karataeva: Planta LLC, Moscow, Russia.
Nadezhda M Markina: Planta LLC, Moscow, Russia.
Tatiana Mitiouchkina: Planta LLC, Moscow, Russia.
Kseniia A Palkina: Planta LLC, Moscow, Russia.
Maxim M Perfilov: Planta LLC, Moscow, Russia. ORCID
Monika G Wood: Promega Corporation, Madison, WI, USA. ORCID
Trish T Hoang: Promega Corporation, Madison, WI, USA.
Mary P Hall: Promega Corporation, Madison, WI, USA.
Liliia I Fakhranurova: Planta LLC, Moscow, Russia.
Anna E Alekberova: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Alena K Malyshevskaia: Planta LLC, Moscow, Russia.
Dmitry A Gorbachev: Planta LLC, Moscow, Russia.
Evgenia N Bugaeva: Planta LLC, Moscow, Russia.
Ludmila K Pletneva: Planta LLC, Moscow, Russia.
Vladislav V Babenko: Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
Daria I Boldyreva: Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
Andrey Y Gorokhovatsky: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Anastasia V Balakireva: Planta LLC, Moscow, Russia.
Feng Gao: Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK.
Vladimir V Choob: Planta LLC, Moscow, Russia.
Lance P Encell: Promega Corporation, Madison, WI, USA.
Keith V Wood: Light Bio Inc, Ketchum, ID, USA.
Ilia V Yampolsky: Planta LLC, Moscow, Russia. ORCID
Karen S Sarkisyan: Planta LLC, Moscow, Russia. karen@light.bio. ORCID
Alexander S Mishin: Planta LLC, Moscow, Russia. alexander@planta.bio. ORCID
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
References
Meighen, E. A. Molecular biology of bacterial bioluminescence. Microbiol. Rev. 55, 123–142 (1991).
[DOI: 10.1128/mr.55.1.123-142.1991]
Kotlobay, A. A. et al. Genetically encodable bioluminescent system from fungi. Proc. Natl Acad. Sci. USA 115, 12728–12732 (2018).
[DOI: 10.1073/pnas.1803615115]
Gupta, R. K., Patterson, S. S., Ripp, S., Simpson, M. L. & Sayler, G. S. Expression of the Photorhabdus luminescens lux genes (luxA, B, C, D, and E) in Saccharomyces cerevisiae. FEMS Yeast Res. 4, 305–313 (2003).
[DOI: 10.1016/S1567-1356(03)00174-0]
Gregor, C. et al. Autonomous bioluminescence imaging of single mammalian cells with the bacterial bioluminescence system. Proc. Natl Acad. Sci. USA 116, 26491–26496 (2019).
[DOI: 10.1073/pnas.1913616116]
Hollis, R. P. et al. Toxicity of the bacterial luciferase substrate, n-decyl aldehyde, to Saccharomyces cerevisiae and Caenorhabditis elegans. FEBS Lett. 506, 140–142 (2001).
[DOI: 10.1016/S0014-5793(01)02905-2]
Khakhar, A. et al. Correction: Building customizable auto-luminescent luciferase-based reporters in plants. eLife 9, e52786 (2020).
[DOI: 10.7554/eLife.52786]
Mitiouchkina, T. et al. Plants with genetically encoded autoluminescence. Nat. Biotechnol. 38, 944–946 (2020).
[DOI: 10.1038/s41587-020-0500-9]
Zheng, P. et al. Metabolic engineering and mechanical investigation of enhanced plant autoluminescence. Plant Biotechnol. J. 21, 1671–1681 (2023).
[DOI: 10.1111/pbi.14068]
Moreno-Giménez, E., Selma, S., Calvache, C. & Orzáez, D. GB_SynP: a modular dCas9-regulated synthetic promoter collection for fine-tuned recombinant gene expression in plants. ACS Synth. Biol. 11, 3037–3048 (2022).
[DOI: 10.1021/acssynbio.2c00238]
Calvache, C. A., Vazquez-Vilar, M., Gimenez, E. M. & Orzaez, D. A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology. Plant Biotechnol. J. 22, 37–47 (2023).
[DOI: 10.1111/pbi.14146]
Garcia, A. G. K. & Steinbrenner, A. D. Bringing plant immunity to light: a genetically encoded, bioluminescent reporter of pattern-triggered immunity in Nicotiana benthamiana. Mol. Plant. Microbe. Interact. https://doi.org/10.1094/mpmi-07-22-0160-ta (2023).
Chudakov, D. M., Matz, M. V., Lukyanov, S. & Lukyanov, K. A. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol. Rev. 90, 1103–1163 (2010).
[DOI: 10.1152/physrev.00038.2009]
Dixon, A. S. et al. NanoLuc complementation reporter optimized for accurate measurement of protein interactions in cells. ACS Chem. Biol. 11, 400–408 (2016).
[DOI: 10.1021/acschembio.5b00753]
Schwinn, M. K. et al. CRISPR-mediated tagging of endogenous proteins with a luminescent peptide. ACS Chem. Biol. 13, 467–474 (2018).
[DOI: 10.1021/acschembio.7b00549]
Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6, e16765 (2011).
[DOI: 10.1371/journal.pone.0016765]
Iverson, S. V., Haddock, T. L., Beal, J. & Densmore, D. M. CIDAR MoClo: improved MoClo assembly standard and new E. coli part library enable rapid combinatorial design for synthetic and traditional biology. ACS Synth. Biol. 5, 99–103 (2016).
[DOI: 10.1021/acssynbio.5b00124]
Brady, J. R. et al. Identifying improved sites for heterologous gene integration using ATAC-seq. ACS Synth. Biol. 9, 2515–2524 (2020).
[DOI: 10.1021/acssynbio.0c00299]
Gallie, D. R., Sleat, D. E., Watts, J. W., Turner, P. C. & Wilson, T. M. The 5′-leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo. Nucleic Acids Res. 15, 3257–3273 (1987).
[DOI: 10.1093/nar/15.8.3257]
EasySelect Pichia expression kit: a manual of methods for expression of recombinant proteins using pPICZ and pPICZα in Pichia pastoris. Catalog no. K1740-01. Invitrogen Corporation (2010).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
[DOI: 10.1038/nmeth.2019]
Lazo, G. R., Stein, P. A. & Ludwig, R. A. A DNA transformation-competent Arabidopsis genomic library in Agrobacterium. Biotechnology 9, 963–967 (1991).
[DOI: 10.1038/nbt1091-963]
Nagata, T., Nemoto, Y. & Hasezawa, S. In International Review of Cytology (eds Jeon, K. W. & Friedlander, M.) Vol. 132 1–30 (Academic Press, 1992).
Gengenbach, B. B., Opdensteinen, P. & Buyel, J. F. Robot cookies—plant cell packs as an automated high-throughput screening platform based on transient expression. Front. Bioeng. Biotechnol. 8, 393 (2020).
[DOI: 10.3389/fbioe.2020.00393]
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
[DOI: 10.1046/j.1365-313x.1998.00343.x]
RankFilters Java plugin. National Institutes of Health (accessed 20 February 2022) https://imagej.nih.gov/ij/source/ij/plugin/filter/RankFilters.java
scikit-posthocs 0.8.1. Python Package Index (accessed 20 February 2022) https://pypi.org/project/scikit-posthocs/
Grants
UKRI MC-A658-5QEA0/RCUK | Medical Research Council (MRC)