Millar Group - Plant microRNA biology and disease resistance
The principal interest of the lab is gene silencing mediated by microRNAs (miRNAs), with a focus on miRNAs that control plant disease resistance.
MiRNAs are small regulatory RNAs that bind to high complementary mRNA targets to repress their expression. In plants, many of these miRNA-target interactions are ancient, implying they have been indispensable for the emergence of terrestrial plants. As many target genes encode transcription factors, many plant miRNAs correspond to genetic regulatory switches, controlling fundamental plant processes including important agricultural traits.
Recently, we have discovered that the ancient miR159-GAMYB controlled pathway can trigger broad defence-related genetic networks that potentially confers broad-spectrum disease resistance in tobacco (Zheng et al., 2020).
Our major questions are;
- Does the miR159-controlled defence response confer broad-spectrum pathogen resistance? We have shown manipulation of miR159 can confer immunity to the oomycete pathogen Phytophthora (Reviewed in Skelly, 2020). However, based on the broad genetic pathways under control of the miR159-GAMYB pathway, we predict activation of this pathway could confer resistance to bacterial, fungal, viral and potentially nematode pathogens.
- Is this miR159-controlled defence response broadly conserved? Multiple aspects of the miR159-GAMYB system are highly conserved in terrestrial plants (Millar et al., 2019). Despite this conservation, currently only in tobacco is miR159 known to control pathogen defence programs. Therefore, we aim to investigate whether miR159 controls defence systems in other plant species, starting with the Solanaceae and then investigating more divergent plants.
- Signalling: is the constitutively transcribed GAMYB mRNA a pathogen sensor? Although GAMYB is constitutively transcribed in vegetative tissues, GAMYB mRNA is totally silenced by miR159. This full silencing is under strong selective pressure, as ancient RNA 2o structures associated with the miR159-binding site have evolved to ensure full GAMYB silencing (Zheng et al., 2017). Therefore, what is the selective pressure to constitutively transcribe GAMYB, especially given that failure to silence GAMYB results in strong detrimental outcomes (Alonso-Peral et al., 2010; Allen et al., 2007). Therefore, we hypothesis that the ever-present GAMYB mRNA is a primed sensor, enabling rapid response to pathogens. We aim to investigate whether the GAMYB mRNA is a rapid detector of pathogens, potentially acting via the ancient RNA 2o structures that modulate silencing, and may be acting as a riboswitch.
- Proof-of-concept gene technology applications: manipulate miR159 for enhanced disease resistance. Can we manipulate the miR159 genetic switch so to engineer broad-spectrum disease-resistance? Using miRNA Target MIMICRY technology (Reichel et. al., 2015) we are investigating the design of synthetic transgene to manipulate miR159 function upon pathogen infection in order to generate plants with enhance disease resistance.
Wong G, Millar AA. (2022) TRUEE; a bioinformatic pipeline to define the functional miRNA targetome of Arabidopsis. The Plant Journal. 110, 1476-1492. doi: 10.1111/tpj.15751.
Wang N, Millar AA (2021) Use of mRNA-Interactome Capture for Generating Novel Insights into Plant RNA Biology. In G Tang et al., (eds), RNA-based Technologies For Functional Genomics in Plants pp 63-76, doi 10.1007/978-3-030-64994-4_5
Luo J, Butardo VM Jr, Yang Q, Konik-Rose C, Colgrave ML, Millar A, Jobling SA, Li Z. (2020) The impact of the indica rice SSIIa allele on the apparent high amylose starch from rice grain with downregulated japonica SBEIIb. Theoretical and Applied Genetics. doi: 10.1007/s00122-020-03649-2.
Zheng Z, Wang N, Jalajakumari MB, Blackman L, Shen E, Verma S, Wang MB, Millar AA (2020) miR159 represses a constitutive pathogen defense response in tobacco. Plant Physiology 182, 2182-2198. doi: 10.1104/pp.19.00786
Millar AA (2020) The Function of miRNAs in Plants. Plants (Basel) 9, E198. doi:10.3390/plants9020198 (editorial).
Asadi Khanouki M, Rezanejad F, Millar AA (2019) Sequence and functional analysis of a TERMINAL FLOWER 1 homolog from Brassica juncea: a putative biotechnological tool for flowering time adjustment. GM Crops & Food doi: 10.1080/21645698.2019.1707340
Schumann U, Lee JM, Smith NA, Zhong C, Zhu JK, Dennis ES, Millar AA, Wang MB (2019) DEMETER plays a role in DNA demethylation and disease response in somatic tissues of Arabidopsis. Epigenetics 14, 1074–1087. doi: 10.1080/15592294.2019.1631113.
Millar AA, Lohe A, Wong G (2019) Biology and function of miR159. Plants (Basel) 8, 255. doi:10.3390/plants8080255
Wong G, Millar AA (2019) The use of microRNA decoy technologies to inhibit miRNA function in Arabidopsis. In, S de Folter (ed) Plant microRNAs: Methods and Protocols, Methods of Molecular Biology vol. 1932, Springer Science, New York, pp 227-238.
Wong G, Alonso-Peral M, Li B, Li J, Millar AA (2018) MicroRNA MIMIC binding sites: minor flanking nucleotide alterations can strongly impact MIMIC silencing efficacy in Arabidopsis. Plant Direct 2, e00088.
Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, and Pogson BJ (2018) Pol II read-through promotes expression of neighbouring genes in SAL1-PAP-XRN retrograde signaling. Plant Physiology 178, 1614-1630.
Medina C, da Rocha M, Magliano M, Ratpopoulo A, Revel B, Marteu N, Magnone V, Lebrigand K, Cabrera J, Barcala M, Silva AC, Millar AA, Escobar C, Abad P, Favery B and Jaubert-Possamai S (2017) Characterization of microRNAs from Arabidopsis galls highlights a role for miR159 in the plant response to the root-knot nematode Meloidogyne incognita. New Phytologist 216, 882-896.
Zheng Z, Reichel M, Deveson I, Wong G, Li J and Millar AA (2017) Target RNA secondary structure is a major determinant of miR159 efficacy. Plant Physiology 174, 1764-1778. doi: 10.1104/pp.16.01898.
Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume A-M, Horos R, Hentze MW, Preiss T and Millar AA (2016) In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings. The Plant Cell 28, 2435-2452.
Li Y, Alonso-Peral M, Wong G, Wang M-B and Millar AA (2016) Ubiquitous miR159 repression of MYB33/65 in Arabidopsis rosettes is robust and is not perturbed by a wide range of stresses. BMC Plant Biology 16, 179.
Reichel M and Millar AA (2015) Specificity of plant microRNA target MIMICs: Cross-targeting of miR159 and miR319. Journal of Plant Physiology 180, 45-48.
Reichel M, Li Y, Li J and Millar AA (2015) Inhibiting plant microRNA activity: molecular SPONGEs, target MIMICs and STTMs all display variable efficacies against target microRNAs. Plant Biotechnology Journal 13, 915-926.
Li J, Reichel M, Li Y and Millar AA (2014) The functional scope of plant microRNA-mediated silencing. Trends in Plant Science 19, 750-756.
Li, J, Reichel, M and Millar AA (2014) Determinants beyond both complementarity and cleavage govern miR159 efficacy in Arabidopsis. PLoS Genetics 10, e1004232.
Deveson I, Li J and Millar AA (2013) MicroRNAs with analogous target complementarities perform with highly variable efficacies in Arabidopsis. FEBS Letters 587, 3703-3708.
Allen RS, Nakasugi K, Doran R, Millar AA and Waterhouse PM (2013) Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. Frontiers in Plant Science 4, 362.
Deveson I, Li J and Millar AA (2013) Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis. Frontiers in Plant Science 4, 96.
Li J and Millar AA (2013) Expression of a microRNA-resistant target transgene misrepresents the functional significance of the endogenous microRNA:target gene relationship. Molecular Plant 6, 577-580.
2012 ARC grant success
PS Seminar Series - PhD Exit Seminar - A miRNA mystery: does miR159 play a role in plant defence response
Abstract - miRNAs are a class of small RNAs that negatively regulate gene expression in eukaryotes.