A Synthetic Oxygen Sensor for Plants Based on Animal Hypoxia Signaling

Overview

Journal Plant Physiol

Specialty Physiology

Date 2018 Nov 22

PMID 30459266

Citations 15

Authors

Sergio Iacopino

Sandro Jurinovich

Lorenzo Cupellini

Luca Piccinini

Francesco Cardarelli

Pierdomenico Perata

Benedetta Mennucci

Beatrice Giuntoli

Francesco Licausi

Affiliations

Soon will be listed here.

Abstract

Due to the involvement of oxygen in many essential metabolic reactions, all living organisms have developed molecular systems that allow adaptive physiological and metabolic transitions depending on oxygen availability. In mammals, the expression of hypoxia-response genes is controlled by the heterodimeric Hypoxia-Inducible Factor. The activity of this transcriptional regulator is linked mainly to the oxygen-dependent hydroxylation of conserved proline residues in its α-subunit, carried out by prolyl-hydroxylases, and subsequent ubiquitination via the E3 ligase von Hippel-Lindau tumor suppressor, which targets Hypoxia-Inducible Factor-α to the proteasome. By exploiting bioengineered versions of this mammalian oxygen sensor, we designed and optimized a synthetic device that drives gene expression in an oxygen-dependent fashion in plants. Transient assays in Arabidopsis () mesophyll protoplasts indicated that a combination of the yeast Gal4/upstream activating sequence system and the mammalian oxygen sensor machinery can be used effectively to engineer a modular, oxygen-inducible transcriptional regulator. This synthetic device also was shown to be selectively controlled by oxygen in whole plants when its components were expressed stably in Arabidopsis seedlings. We envision the exploitation of our genetically encoded controllers to generate plants able to switch gene expression selectively depending on oxygen availability, thereby providing a proof of concept for the potential of synthetic biology to assist agricultural practices in environments with variable oxygen provision.

Citing Articles

Recent progress in understanding the cellular and genetic basis of plant responses to low oxygen holds promise for developing flood-resilient crops.

Fagerstedt K, Pucciariello C, Pedersen O, Perata P J Exp Bot. 2023; 75(5):1217-1233.

PMID: 37991267 PMC: 10901210. DOI: 10.1093/jxb/erad457.

Design principles for synthetic control systems to engineer plants.

Bull T, Khakhar A Plant Cell Rep. 2023; 42(12):1875-1889.

PMID: 37789180 DOI: 10.1007/s00299-023-03072-z.

Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurring Environments.

Brazel A, Graciet E Methods Mol Biol. 2023; 2642:23-48.

PMID: 36944871 DOI: 10.1007/978-1-0716-3044-0_2.

The cyclic peptide G4CP2 enables the modulation of galactose metabolism in yeast by interfering with GAL4 transcriptional activity.

Rosa S, Tagliani A, Bertaso C, Tadini L, Visentin C, Gourlay L Front Mol Biosci. 2023; 10:1017757.

PMID: 36936986 PMC: 10014601. DOI: 10.3389/fmolb.2023.1017757.

Target of rapamycin signaling couples energy to oxygen sensing to modulate hypoxic gene expression in .

Kunkowska A, Fontana F, Betti F, Soeur R, Beckers G, Meyer C Proc Natl Acad Sci U S A. 2023; 120(3):e2212474120.

PMID: 36626556 PMC: 9934071. DOI: 10.1073/pnas.2212474120.

References

Gravot A, Richard G, Lime T, Lemarie S, Jubault M, Lariagon C . Hypoxia response in Arabidopsis roots infected by Plasmodiophora brassicae supports the development of clubroot. BMC Plant Biol. 2016; 16(1):251. PMC: 5106811. DOI: 10.1186/s12870-016-0941-y. View

Wang G, Jiang B, Rue E, Semenza G . Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc Natl Acad Sci U S A. 1995; 92(12):5510-4. PMC: 41725. DOI: 10.1073/pnas.92.12.5510. View

Guarente L, Yocum R, Gifford P . A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. Proc Natl Acad Sci U S A. 1982; 79(23):7410-4. PMC: 347349. DOI: 10.1073/pnas.79.23.7410. View

Ritchie M, Phipson B, Wu D, Hu Y, Law C, Shi W . limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(7):e47. PMC: 4402510. DOI: 10.1093/nar/gkv007. View

Weits D, Giuntoli B, Kosmacz M, Parlanti S, Hubberten H, Riegler H . Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat Commun. 2014; 5:3425. PMC: 3959200. DOI: 10.1038/ncomms4425. View

Epstein A, Gleadle J, McNeill L, Hewitson K, ORourke J, Mole D . C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell. 2001; 107(1):43-54. DOI: 10.1016/s0092-8674(01)00507-4. View

Li Q, Shi X, Ye S, Wang S, Chan R, Harkness T . A short motif in Arabidopsis CDK inhibitor ICK1 decreases the protein level, probably through a ubiquitin-independent mechanism. Plant J. 2016; 87(6):617-28. DOI: 10.1111/tpj.13223. View

Mus F, Crook M, Garcia K, Garcia Costas A, Geddes B, Kouri E . Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol. 2016; 82(13):3698-3710. PMC: 4907175. DOI: 10.1128/AEM.01055-16. View

Kosmacz M, Parlanti S, Schwarzlander M, Kragler F, Licausi F, van Dongen J . The stability and nuclear localization of the transcription factor RAP2.12 are dynamically regulated by oxygen concentration. Plant Cell Environ. 2014; 38(6):1094-103. DOI: 10.1111/pce.12493. View

10.

Wu F, Shen S, Lee L, Lee S, Chan M, Lin C . Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method. Plant Methods. 2009; 5:16. PMC: 2794253. DOI: 10.1186/1746-4811-5-16. View

11.

Bailey-Serres J, Voesenek L . Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol. 2008; 59:313-39. DOI: 10.1146/annurev.arplant.59.032607.092752. View

12.

Ceradini D, Kulkarni A, Callaghan M, Tepper O, Bastidas N, Kleinman M . Progenitor cell trafficking is regulated by hypoxic gradients through HIF-1 induction of SDF-1. Nat Med. 2004; 10(8):858-64. DOI: 10.1038/nm1075. View

13.

Mommer L, Visser E . Underwater photosynthesis in flooded terrestrial plants: a matter of leaf plasticity. Ann Bot. 2005; 96(4):581-9. PMC: 4247027. DOI: 10.1093/aob/mci212. View

14.

Knauth K, Bex C, Jemth P, Buchberger A . Renal cell carcinoma risk in type 2 von Hippel-Lindau disease correlates with defects in pVHL stability and HIF-1alpha interactions. Oncogene. 2005; 25(3):370-7. DOI: 10.1038/sj.onc.1209062. View

15.

Maxwell P, Wiesener M, Chang G, Clifford S, Vaux E, Cockman M . The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature. 1999; 399(6733):271-5. DOI: 10.1038/20459. View

16.

Hirt H, Kogl M, Murbacher T, Heberle-Bors E . Evolutionary conservation of transcriptional machinery between yeast and plants as shown by the efficient expression from the CaMV 35S promoter and 35S terminator. Curr Genet. 1990; 17(6):473-9. DOI: 10.1007/BF00313074. View

17.

Walia A, Waadt R, Jones A . Genetically Encoded Biosensors in Plants: Pathways to Discovery. Annu Rev Plant Biol. 2018; 69:497-524. DOI: 10.1146/annurev-arplant-042817-040104. View

18.

Clough S, Bent A . Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1999; 16(6):735-43. DOI: 10.1046/j.1365-313x.1998.00343.x. View

19.

Lohse M, Bolger A, Nagel A, Fernie A, Lunn J, Stitt M . RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012; 40(Web Server issue):W622-7. PMC: 3394330. DOI: 10.1093/nar/gks540. View

20.

Possart A, Fleck C, Hiltbrunner A . Shedding (far-red) light on phytochrome mechanisms and responses in land plants. Plant Sci. 2014; 217-218:36-46. DOI: 10.1016/j.plantsci.2013.11.013. View