Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes.
Journal
Nature plants
ISSN: 2055-0278
Titre abrégé: Nat Plants
Pays: England
ID NLM: 101651677
Informations de publication
Date de publication:
05 2019
05 2019
Historique:
received:
15
12
2018
accepted:
22
03
2019
pubmed:
1
5
2019
medline:
14
6
2019
entrez:
1
5
2019
Statut:
ppublish
Résumé
The engineering of plant genomes presents exciting opportunities to modify agronomic traits and to produce high-value products in plants. Expression of foreign proteins from transgenes in the chloroplast genome offers advantages that include the capacity for prodigious protein output, the lack of transgene silencing and the ability to express multicomponent pathways from polycistronic mRNA. However, there remains a need for robust methods to regulate plastid transgene expression. We designed orthogonal activators that boost the expression of chloroplast transgenes harbouring cognate cis-elements. Our system exploits the programmable RNA sequence specificity of pentatricopeptide repeat proteins and their native functions as activators of chloroplast gene expression. When expressed from nuclear transgenes, the engineered proteins stimulate the expression of plastid transgenes by up to ~40-fold, with maximal protein abundance approaching that of Rubisco. This strategy provides a means to regulate and optimize the expression of foreign genes in chloroplasts and to avoid deleterious effects of their products on plant growth.
Identifiants
pubmed: 31036912
doi: 10.1038/s41477-019-0412-1
pii: 10.1038/s41477-019-0412-1
doi:
Substances chimiques
Arabidopsis Proteins
0
PPR10 protein, Arabidopsis
0
RNA-Binding Proteins
0
pentatricopeptide repeat protein, Arabidopsis
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
505-511Commentaires et corrections
Type : CommentIn
Références
Boynton, J. E. et al. Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science 240, 1534–1538 (1988).
doi: 10.1126/science.2897716
Svab, Z., Hajdukiewicz, P. & Maliga, P. Stable transformation of plastids in higher plants. Proc. Natl Acad. Sci. USA 87, 8526–8530 (1990).
doi: 10.1073/pnas.87.21.8526
Bock, R. Engineering plastid genomes: methods, tools, and applications in basic research and biotechnology. Annu. Rev. Plant Biol. 66, 211–241 (2015).
doi: 10.1146/annurev-arplant-050213-040212
Ahmad, N., Michoux, F., Lossl, A. G. & Nixon, P. J. Challenges and perspectives in commercializing plastid transformation technology. J. Exp. Bot. 67, 5945–5960 (2016).
doi: 10.1093/jxb/erw360
Waheed, M. T., Ismail, H., Gottschamel, J., Mirza, B. & Lossl, A. G. Plastids: the green frontiers for vaccine production. Front. Plant Sci. 6, 1005 (2015).
doi: 10.3389/fpls.2015.01005
Oey, M., Lohse, M., Kreikemeyer, B. & Bock, R. Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic. Plant J. 57, 436–445 (2009).
doi: 10.1111/j.1365-313X.2008.03702.x
Fuentes, P. et al. A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop. eLife 5, e13664 (2016).
doi: 10.7554/eLife.13664
Gnanasekaran, T. et al. Transfer of the cytochrome P450-dependent dhurrin pathway from Sorghum bicolor into Nicotiana tabacum chloroplasts for light-driven synthesis. J. Exp. Bot. 67, 2495–2506 (2016).
doi: 10.1093/jxb/erw067
Harada, H. et al. Construction of transplastomic lettuce (Lactuca sativa) dominantly producing astaxanthin fatty acid esters and detailed chemical analysis of generated carotenoids. Transgenic Res. 23, 303–315 (2014).
doi: 10.1007/s11248-013-9750-3
Bohmert-Tatarev, K., McAvoy, S., Daughtry, S., Peoples, O. P. & Snell, K. D. High levels of bioplastic are produced in fertile transplastomic tobacco plants engineered with a synthetic operon for the production of polyhydroxybutyrate. Plant Physiol. 155, 1690–1708 (2011).
doi: 10.1104/pp.110.169581
Diretto, G. et al. Metabolic engineering of potato carotenoid content through tuber-specific overexpression of a bacterial mini-pathway. PLoS ONE 2, e350 (2007).
doi: 10.1371/journal.pone.0000350
Hanson, M. R., Lin, M. T., Carmo-Silva, A. E. & Parry, M. A. Towards engineering carboxysomes into C3 plants. Plant J. 87, 38–50 (2016).
doi: 10.1111/tpj.13139
Malhotra, K. et al. Compartmentalized metabolic engineering for artemisinin biosynthesis and effective malaria treatment by oral delivery of plant cells. Mol. Plant 9, 1464–1477 (2016).
doi: 10.1016/j.molp.2016.09.013
Lossl, A. et al. Inducible trans-activation of plastid transgenes: expression of the R. eutropha phb operon in transplastomic tobacco. Plant Cell Physiol. 46, 1462–1471 (2005).
doi: 10.1093/pcp/pci157
Lu, Y., Rijzaani, H., Karcher, D., Ruf, S. & Bock, R. Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons. Proc. Natl Acad. Sci. USA 110, E623–E632 (2013).
doi: 10.1073/pnas.1216898110
Scotti, N. & Cardi, T. Transgene-induced pleiotropic effects in transplastomic plants. Biotechnol. Lett. 36, 229–239 (2014).
doi: 10.1007/s10529-013-1356-6
Muhlbauer, S. K. & Koop, H. U. External control of transgene expression in tobacco plastids using the bacterial lac repressor. Plant J. 43, 941–946 (2005).
doi: 10.1111/j.1365-313X.2005.02495.x
Buhot, L., Horvath, E., Medgyesy, P. & Lerbs-Mache, S. Hybrid transcription system for controlled plastid transgene expression. Plant J. 46, 700–707 (2006).
doi: 10.1111/j.1365-313X.2006.02718.x
Emadpour, M., Karcher, D. & Bock, R. Boosting riboswitch efficiency by RNA amplification. Nucleic Acids Res. 43, e66 (2015).
doi: 10.1093/nar/gkv165
Barkan, A. & Small, I. Pentatricopeptide repeat proteins in plants. Annu. Rev. Plant Biol. 65, 415–442 (2014).
doi: 10.1146/annurev-arplant-050213-040159
Small, I. & Peeters, N. The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends Biochem. Sci. 25, 46–47 (2000).
doi: 10.1016/S0968-0004(99)01520-0
Barkan, A. et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet. 8, e1002910 (2012).
doi: 10.1371/journal.pgen.1002910
Shen, C. et al. Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins. Nat. Commun. 7, 11285 (2016).
doi: 10.1038/ncomms11285
Filipovska, A. & Rackham, O. Modular recognition of nucleic acids by PUF, TALE and PPR proteins. Mol. Biosyst. 8, 699–708 (2012).
doi: 10.1039/c2mb05392f
Kindgren, P., Yap, A., Bond, C. S. & Small, I. Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis. Plant Cell 27, 403–416 (2015).
doi: 10.1105/tpc.114.134189
Colas des Francs-Small, C., Vincis Pereira Sanglard, L. & Small, I. Targeted cleavage of nad6 mRNA induced by a modified pentatricopeptide repeat protein in plant mitochondria. Commun. Biol. 1, 166 (2018).
doi: 10.1038/s42003-018-0166-8
Miranda, R. G., McDermott, J. J. & Barkan, A. RNA-binding specificity landscapes of designer pentatricopeptide repeat proteins elucidate principles of PPR–RNA interactions. Nucleic Acids Res. 46, 2613–2623 (2018).
doi: 10.1093/nar/gkx1288
Pfalz, J., Bayraktar, O., Prikryl, J. & Barkan, A. Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts. EMBO J. 28, 2042–2052 (2009).
doi: 10.1038/emboj.2009.121
Prikryl, J., Rojas, M., Schuster, G. & Barkan, A. Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proc. Natl Acad. Sci. USA 108, 415–420 (2011).
doi: 10.1073/pnas.1012076108
Zoschke, R., Watkins, K. & Barkan, A. A rapid microarray-based ribosome profiling method elucidates chloroplast ribosome behavior in vivo. Plant Cell 25, 2265–2275 (2013).
doi: 10.1105/tpc.113.111567
Chotewutmontri, P. & Barkan, A. Dynamics of chloroplast translation during chloroplast differentiation in maize. PLoS Genet. 12, e1006106 (2016).
doi: 10.1371/journal.pgen.1006106
Miranda, R. G., Rojas, M., Montgomery, M. P., Gribbin, K. P. & Barkan, A. RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10. RNA 23, 586–599 (2017).
doi: 10.1261/rna.059568.116
Schoffl, F., Raschke, E. & Nagao, R. T. The DNA sequence analysis of soybean heat-shock genes and identification of possible regulatory promoter elements. EMBO J. 3, 2491–2497 (1984).
doi: 10.1002/j.1460-2075.1984.tb02161.x
Roslan, H. A. et al. Characterization of the ethanol-inducible alc gene-expression system in Arabidopsis thaliana. Plant J. 28, 225–235 (2001).
doi: 10.1046/j.1365-313X.2001.01146.x
Erb, T. J. & Zarzycki, J. A short history of RubisCO: the rise and fall (?) of nature’s predominant CO
doi: 10.1016/j.copbio.2017.07.017
Hui, M. P., Foley, P. L. & Belasco, J. G. Messenger RNA degradation in bacterial cells. Annu. Rev. Genet. 48, 537–559 (2014).
doi: 10.1146/annurev-genet-120213-092340
Germain, A., Hotto, A. M., Barkan, A. & Stern, D. B. RNA processing and decay in plastids. Wiley Interdiscip. Rev. RNA 4, 295–316 (2013).
doi: 10.1002/wrna.1161
Luro, S., Germain, A., Sharwood, R. E. & Stern, D. B. RNase J participates in a pentatricopeptide repeat protein-mediated 5′ end maturation of chloroplast mRNAs. Nucleic Acids Res. 41, 9141–9151 (2013).
doi: 10.1093/nar/gkt640
Beick, S., Schmitz-Linneweber, C., Williams-Carrier, R., Jensen, B. & Barkan, A. The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Mol. Cell. Biol. 28, 5337–5347 (2008).
doi: 10.1128/MCB.00563-08
Hanson, M. R., Gray, B. N. & Ahner, B. A. Chloroplast transformation for engineering of photosynthesis. J. Exp. Bot. 64, 731–742 (2013).
doi: 10.1093/jxb/ers325
Fuentes, P., Armarego-Marriott, T. & Bock, R. Plastid transformation and its application in metabolic engineering. Curr. Opin. Biotechnol. 49, 10–15 (2018).
doi: 10.1016/j.copbio.2017.07.004
Daniell, H., Chan, H. T. & Pasoreck, E. K. Vaccination via chloroplast genetics: affordable protein drugs for the prevention and treatment of inherited or infectious human diseases. Annu. Rev. Genet. 50, 595–618 (2016).
doi: 10.1146/annurev-genet-120215-035349
Zhou, F., Karcher, D. & Bock, R. Identification of a plastid intercistronic expression element (IEE) facilitating the expression of stable translatable monocistronic mRNAs from operons. Plant J. 52, 961–972 (2007).
doi: 10.1111/j.1365-313X.2007.03261.x
Hammani, K., Cook, W. & Barkan, A. RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Proc. Natl Acad. Sci. USA 109, 5651–5656 (2012).
doi: 10.1073/pnas.1200318109
Legen, J. et al. Stabilization and translation of synthetic operon-derived mRNAs in chloroplasts by sequences representing PPR protein-binding sites. Plant J. 94, 8–21 (2018).
doi: 10.1111/tpj.13863
Ramundo, S. & Rochaix, J. D. Controlling expression of genes in the unicellular alga Chlamydomonas reinhardtii with a vitamin-repressible riboswitch. Methods Enzymol. 550, 267–281 (2015).
doi: 10.1016/bs.mie.2014.10.035
Boudreau, E., Nickelsen, J., Lemaire, S. D., Ossenbuhl, F. & Rochaix, J. D. The Nac2 gene of Chlamydomonas encodes a chloroplast TPR-like protein involved in psbD mRNA stability. EMBO J. 19, 3366–3376 (2000).
doi: 10.1093/emboj/19.13.3366
Kuchka, M. R., Goldschmidt-Clermont, M., van Dillewijn, J. & Rochaix, J. D. Mutation at the Chlamydomonas nuclear NAC2 locus specifically affects stability of the chloroplast psbD transcript encoding polypeptide D2 of PS II. Cell 58, 869–876 (1989).
doi: 10.1016/0092-8674(89)90939-2
Yu, Q., Barkan, A. & Maliga, P. Engineered RNA-binding protein for transgene activation in non-green plastids. Nat. Plants https://doi.org/10.1038/s41477-019-0413-0 (2019).
Kuroda, H. & Maliga, P. Sequences downstream of the translation initiation codon are important determinants of translation efficiency in chloroplasts. Plant Physiol. 125, 430–436 (2001).
doi: 10.1104/pp.125.1.430
Shinozaki, K. & Sugiura, M. Sequence of the intercistronic region between the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and coupling factor beta subunit gene. Nucleic Acids Res. 10, 4923–4934 (1982).
doi: 10.1093/nar/10.16.4923
Lutz, K. A., Svab, Z. & Maliga, P. Construction of marker-free transplastomic tobacco using the Cre-loxP site-specific recombination system. Nat. Protoc. 1, 900–910 (2006).
doi: 10.1038/nprot.2006.118
Earley, K. W. et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629 (2006).
doi: 10.1111/j.1365-313X.2005.02617.x
Werner, S., Breus, O., Symonenko, Y., Marillonnet, S. & Gleba, Y. High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector. Proc. Natl Acad. Sci. USA 108, 14061–14066 (2011).
doi: 10.1073/pnas.1102928108