Molecular Plant and Microbial Biosciences Research Unit (MPMB-RU)

In MPMB-RU, we carry out both fundamental and translational research in the field of plant and microbial biosciences.

About the Research Unit

We are interested in answering the following fundamental questions; how do obligate pathogens such as downy mildews (Hyaloperonospora arabidopsidis, Hpa and Peronospora vicia f.sp. pisi, Pvp) coordinate their attack to overcome the plants’ defence? What is the basis of their host specificity? Do they synchronize their physiological and metabolic activity with their hosts? Can we carry out reverse genetics to reveal the role of pathogenicity and developmental genes?

Previously, we demonstrated that effectors could play a significant role in suppressing the plant’s immune system. In addition, we showed that light influences spore germination, mycelium development, sporulation and oospore formation of Hpa, along with defence responses in the host. We took this further and identified clock regulated genes in the pathogen. Recently, we showed that short synthesised small interfering RNAs (SS-siRNAs) could be used to inhibit Hpa spore germination and infection of Arabidopsis. Currently, we are using this approach to decipher the function of developmental and pathogenicity genes in this downy mildew pathogen in a high throughput manner. We aim to take the information gained from this work further to develop into a potential disease control strategy against downy mildews on crop plants. In another collaborative research project, we are developing tools for the accurate detection and diagnostics of Pvp isolates using genomics and exploring the use of biological control agents to suppress downy mildew pathogens. Our further translational research includes genomic assisted plant breeding and genome editing for crop improvements.

Professor Mahmut Tör introducing the MPMB-RU

Molecular Plant and Microbial Research Group figure

MYCOsiRNA software

Professor Mahmut Tör, in conjunction with an external bioinformatician and data analyst partner, Weibo Jin, has developed a web-based tool, known as MYCOsiRNA. This software is used to design target-specific small RNAs for fungal and oomycete plant pathogens, which can then be used to study gene function. You can use the MYCOsiRNA tool here: https://mycosirna.wp.worc.ac.uk/.

Members

Staff

Prof Mahmut Tör - Full-time (Chair of Molecular Plant and Microbial Biology)

Dr Deniz Göl - Full-time (Postdoctoral Research Fellow)

Heather Fell - Full-time (Research Technician)

Current Projects

Professor Mahmut Tör (PI), Co-Is, Prof John McDowell (Virginia Tech, USA) Assoc. Prof Sherif Sherif (Virginia Tech, USA), 2023-2027, siRNA for Disease control. BBSRC partnering Award.

Professor Mahmut Tör (PI),Co-Is, Assoc Prof Birsen Cevher Keskin (TUBITAK-MAM, Türkiye), Prof Burhan Arıkan (Çukurova University, Türkiye), Dr Aslı Polat (TAGEM-Tekirdağ Bağcılık, Türkiye), 2023-2027,Microbial biological control agents for downy mildew diseases. BBSRC Partnering Award.

Professor Mahmut Tör(Co-I), PI & Co-I, Prof John McDowell (Virginia Tech, USA), Assoc. Prof Sherif Sherif (Virginia Tech, USA), 2023-2024, EDGE FGT: RNAi-based tools to unlock functional genomics of obligate oomycete plant pathogens. Funding: NSF.

Professor Mahmut Tör (PI), Co-Is, Dr David Studholme (Exeter), Collaborators, Prof Yiguo Hong (Hangzhou, China), Prof John McDowell (Virginia Tech, USA), 2021-2024, Deciphering pathogenicity and development in obligate downy mildew pathogen using small RNA approach. Funding: BBSRC.

Professor Mahmut Tör (PI), Co-Is, Jane Thomas and Tom Wood (NIAB), Claire Domoney (JIC), 2020-2023, Pulse-Downy Mildew Pathosystem: deploying disease resistance, pathogenomics and microbial biocontrol. Funding: BBSRC.

Professor Mahmut Tör (PI), 2023-2026, NGS-assisted resistance breeding. Funding: Manier Seeds.

Recently Completed Projects

Professor Mahmut Tör (Co-I) Development of Non-Transgenic Cucumber Lines Resistant to Powdery Mildew (Sphaerotheca fuliginea) Using CRISPR/Cas9 System, TÜBITAK, 2022-2023

Professor Mahmut Tör (Co-I) Establishing CRISPR/Cas9 Genome Editing Technique to Develop Resistant Lines to Rice Blast Disease. TÜBITAK, 2022-2023.

Professor Mahmut Tör: 2020. Generating molecular markers linked to CVYV resistance in cucumber. Funding: M.Y. Genetik.

Professor Mahmut Tör: 2018. Identifying molecular markers suitable for Frl selection in tomato breeding. Funding: M.Y. Genetik.

Professor Mahmut Tör: 2015. Development of molecular markers tightly linked to Pvr4 gene in pepper using next generation sequencing. Funding: M.Y. Genetik.

Outputs

Peer-Reviewed Journal Papers

Cevher-Keskin, B., Yildizhan, Y., Sekmen-Cetinel, A.H., Sezerman, O.U., Ozer, B., Fayetorbay, R., Onarici, S., Turkan, I. and Tör, M. (2023). Deciphering Drought Response Mechanisms: Transcriptomic Insights from Drought-Tolerant and Drought-Sensitive Wheat (Triticum aestivum L.) Cultivars. bioRxiv. doi: https://doi.org/10.1101/2023.10.26.563210

Devran, Z., Özalp, T., Studholme, D. J. and Tör, M. (2023). Mapping of gene conferring resistance to root-knot nematodes at high soil temperature in tomato. Front. Plant Sci. 14:1267399. doi: 10.3389/fpls.2023.1267399

Kim, D. S., Woods-Tör, A., Cevik, V., Furzer, O. J., Li, Y., Ma, W., Tör, M., Jones, J. D. G. (2023) ATR2^Cala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition. bioRxiv 538220; doi: https://doi.org/10.1101/2023.04.25.538220

Erdoğan, İ., Cevher-Keskin, B., Bilir, Ö., Hong, Y. and Tör, M. (2023) M. Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress

Tör, M, Wood, T., Webb, A., Göl, D., McDowell, J.M. (2023). Recent developments in plant-downy mildew interactions. Seminars in Cell and Developmental Biology. https://doi.org/10.1016/j.semcdb.2023.01.010

Arruebarrena Di Palma A., Perk E. A., Carboni M. E., García-Mata C., Budak H., Tör M., Laxalt A. M. (2022) The isothiocyanate sulforaphane induces respiratory burst oxidase homologue D-dependent reactive oxygen species production and regulates expression of stress response genes. Plant Direct 6: e437. Doi: 10.1002/pld3.437

Bilir, O., Göl, D., Hong, Y., McDowell, J. and Tör, M. (2022) Small RNA-based plant protection. Front. Plant Sci.13:951097. doi: 10.3389/fpls.2022.951097

Jimenez-Quiros C., Okechukwu EC., Hong Y., Baysal Ö., Tör M. (2022) Comparison of Antifungal Activity of Bacillus Strains against Fusarium graminearum In Vitro and In Planta. Plants. 11:1999. Doi: 10.3390/plants11151999

Mohamed, A., Jin, Z., Osman, T., Shi, N., Tör, M., Jackson, S., Hong, H. (2022) Hotspot siRNA Confers Plant Resistance against Viral Infection. Biology. 11: 714. doi: 10.3390/biology11050714.

Yu Z, Wang Y, Mei F, Yan H, Jin Z, Zhang P, Zhang Z, Tör, M., Jackson S, Shi N, Hong Y (2022) Spinach-based RNA mimicking GFP in plant cells. Functional & Integrative Genomics DOI:10.1007/s10142-022-00835-x.

Kahveci, E., Devran, Z., Ozkaynak, E., Hong, Y., Studholme, D. J. and Tör, M. (2021) Genomic-assisted marker development suitable for CsCvy-1 selection in cucumber breeding. Frontiers in Plant Science-Plant Breeding. Front. Plant Sci. 12:691576. doi: 10.3389/fpls.2021.691576.

Zhang, X., Zhang, X., Shi, N., Hu, Y., Jin, Z., Liu, S., Tör, M., Ma, P. and Hong, Y. (2021) Cis and trans effects of a heterologous RNA on virus-induced gene silencing. Planta, under revision.

Jina, Z., Liua, S., Yua, Z., Tan, J., Deng, Z., Zhang, P., Galzi, S., Filloux, D., Shi, N., Tör, M., Wang, W., Liu, Y., Roumagnac, P. and Hong, Y. (2021) On the origin of an endogenous viral element to geminivirus-like extrachromosomal circular DNA in plants. PNAS, under revision.

Zhang, P., Yu, Z., He, C., Zhang, X., Qin, C., Mohamed, A. M., Liu, S., Jin, Z., Zhang, Z., Shi, N., Tör, M., Daròs, J-A., Li, S., Liu, Y.,Hong, Y. (2021) RNA silencing response to a chloroplast-replicating pathogen. Plant Physiology, under revision.

Lai, T., Ye, B., Tan, J., Chen, Y., Li, R., Wang, X., Wang, Y., Zhou, Y., Shi, N., Tör, M., Liu, Y., Jackson, S., Deng, S. and Hong, Y. (2021) A phosphorylated SBP-box transcription factor SPL-CNR involves LIKE HETEROCHROMATIN PROTEIN1 in tomato fruit ripening. In preparation for Plant Journal.

Telli, O., Jimenez-Guiros, C., McDowell, J and Tör, M (2020) Effect of light and darkness on the growth and development of downy mildew pathogen Hyaloperonospora arabidopsidis. Plant Pathology 2020; 69: 1291-1300 https://doi.org/10.1111/ppa.13207

Yuan, C., Li, H., Chen, Q., Xu, X., Zhang, X., Jin, Z., He, M., Shi, N., Xue, D., Wang, H., Jackson, S., He, Y., Tör, M., Liu, Y., Qin, C. and Hong, Y. (2020) ⁠ A Foxtail Mosaic Virus-induced Flowering (FoMViF) Assay in Monocotyledonous Crops. Journal of Experimental Botany 71: 3012–3023 https://doi.org/10.1093/jxb/eraa080

Lai,T., Wang, X., Ye, B., Jin, M., Chen, W., Wang, Y., Zhou, Y., Blanks, A., Gu, M., Zhang, P., Li, C., Wang, W., Liu, Y., Gallusci,P., Tör, M. and Hong, Y. (2020) Characterization of LeSPL-CNR and its functional relevance to cell death and fruit ripening in tomato. Journal of Experimental Botany. https://doi.org/10.1093/jxb/eraa067

Zhang, X., Kang, L., Zhang, Q., Meng, Q., Pan, Y., Yu, Z., Shi, N., Jackson, S., Zhang, X., Wang, H., Tör, M. and Hong, Y. (2020) An RNAi suppressor activates in planta virus-mediated gene editing. Functional and Integrative Genomics. 20: 471-477 DOI: 10.1007/s10142-019-00730-y.

Bilir, Ö., Telli, O. Norman, C., Budak, H., Hong, Y. and Tör, M. (2019) Small RNA inhibits infection by downy mildew pathogen Hyaloperonospora arabidopsidis. MPP 20:1523-1534. doi: 10.1111/mpp.12863.

Zhang, X., Laia, T., Zhang, P., Zhangb, X., Yuana, C., Jina, Z.,Lia, H., Yua, Z., Qina, C., Tör, M., Mab, P., Cheng, Q., Hong, Y. (2019) Mini review: Revisiting mobile RNA silencing in plants. Plant Science 278: 113-117. 10.1016/j.plantsci.2018.10.025.

Devran, Z., Kahveci, E., Hong, Y., Studholme, D. J. and Tör, M. (2018) Identifying molecular markers suitable for Frl selection in tomato breeding. Theor. Appl Genet. 131: 2099–2105. 10.1007/s00122-018-3136-0

Woods-Tör, A., Studholme, D. J., Cevik, V., Telli, O., Holub, E. B. and Tör, M. (2018) A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Speciﬁcity in Arabidopsis thaliana. Front. Plant Sci. 9:265. doi: 10.3389/fpls.2018.00265

Chen, W., Yu, Z., Wang, H., Wu, C., Kong, J., Wang, Z., Zhen,Q., Shi, N., Zhang, P., Zhong, S., Hunter, P., Manning, K., Tör, M. and Hong, Y. (2018) Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening. Sci. China Life Sci. 61: 244-252. https://doi.org/10.1007/s11427-017-9206-5.

Qin C, Li B, Fan Y, Zhang X, Yu Z, Ryabov E, Zhao M, Wang H, Shi N, Zhang P, Jackson S, Tör M, Cheng Q, Liu Y, Gallusci P, Hong Y (2017) Roles of Dicer-Like proteins 2 and 4 in Intra- and Intercellular Antiviral Silencing. Plant Physiol. 174: 1067–1081. doi: 10.1104/pp.17.00475.

Conference Papers

2023: Invited Speaker:Use of Small Interfering RNAs As a Reverse Genetics Tools in Downy Mildew Pathogen. PAG Australia, International Plant and Animal Genome Conference, online.

2023: Controlling downy mildews using microbial products and ds RNA. BSPP Plant Pathology 2023, 6-8 September, Birmingham, UK.

2023: Invited speaker: Translational research on pulse downy mildews: Deploying resistance genes, pathogenomics and microbial biocontrol. 2^nd Molecular Plant Protection Congress, May 15-18, Bursa, Turkey.

2023: Invited Speaker: Control of downy mildew pathogens using spray induced gene silencing. 2^nd Molecular Plant Protection Congress, May 15-18, Bursa, Turkey.

2022: Invited Speaker: Pathogenomic-assisted plant breeding for disease resistance. 1st International Congress on Biotech Studies, November 9-11, Online.

2022: Invited Speaker: Fundamental and translational research on downy mildews: Reverse genetics, pathogenomics and biologics. 21st Annual Meeting of the Oomycete Molecular Genetics Network. August, Brno, Czech Republic.

2021: Keynote speaker: Application of small-RNA technologies in fundamental and translational research for plant protection: advantages, limitations and prospects. III International, Biological & Life Science Conference, Edirne, Turkey, September 1-3.

2021: Invited speaker: Evidence for synchronization of circadian rhythms between a downy mildew pathogen and its plant host. Plant Biology World-Wide Summit, July 19-23.

2019: Keynote Speaker. SIGS and HIGS: investigation into silencing genes in the obligate downy mildew pathogen. International Molecular Plant Protection Congress Adana TURKEY - April 10-13.

Poster Presentations

Göl D, Osborn R, Hong Y, Harrison J, StudholmeD, McDowellJ and Tör M. (2023, July 16-20). siRNA high-throughput screening identifies germination and infection inhibitor and enhancer genes in Arabidopsis downy mildew pathogen (Poster presentation). IS-MPMI Congress in Providence, Rhode Island, USA.

Göl D, Osborn R, Hong Y, Harrison J, StudholmeD, McDowellJ and Tör M. (2023, May 15-18). Gene Knockdown in Arabidopsis downy mildew using small RNA duplexes to assess gene functions (Poster presentation). IMPPC 2^nd International Molecular Plant Protection Congress Bursa, Türkiye.

Göl D, Osborn R, Hong Y, Harrison J, StudholmeD, McDowellJ and Tör M. (2023, September 5). High-throughput screening of pathogenicity and developmental genes by using siRNA in Arabidopsis downy mildew. MBPP Early Career Meeting, Birmingham UK.

Göl D, Osborn R, Hong Y, Harrison J, StudholmeD, McDowellJ and Tör M. (2023, September 6-8). High-throughput screening of pathogenicity and developmental genes by using siRNA in Arabidopsis downy mildew. Plant pathology 2023, Birmingham UK.

Tör, M., Okechukwu, E. C., Göl, D., Osborn, R., Baysal, O., Arikan, B., Arora, S., Domoney, C., Thomas, J., Wood, T. (2022) Integrating R-genes, pathogenomics and biological control for the management of downy mildew disease in pulses. EMBO | EMBL Symposium: Innate immunity in host-pathogen interactions, 17 - 20 July, EMBL Advanced Training Centre.

Göl, D., Osborn, R., Okechukwu, E. O., Hong, Y., Studholme, D., McDowell, J. and Tör, M. (2022) Targeting a tubulin gene in different downy mildews using small RNA inhibits spore germination. 21st Annual Meeting of the Oomycete Molecular Genetics Network. 22-25 August, Brno, Czech Republic.

Okechukwu, E.C., Baysal, O., Kocamaz., S., Arıkan, B., Thomas, J., Wood, T., Domoney, C. and Tör, M. (2021) Exploring Bacillus species to control downy mildew pathogens in pulses. BSPP Presidential Meeting 6-8 December, Birmingham, UK.

Norman, C., Hong, Y., Studholme, D.J., Tör, M. (2021) Elucidating the role of small RNAs in Alternaria alternata-tomato pathosystem.BSPP Presidential Meeting 6-8 December, Birmingham, UK.

Tör, M., Bilir, Ö., Telli, O., John, S., Norman, C., Budak, H. and Hong, Y. and (2019) Silencing genes in Arabidopsis downy mildew using exogenously applied small RNAs. In: XVIII International Congress on Molecular Plant-Microbe Interactions, July, Glasgow, UK.

Tör, M. (2019) Keynote Speaker. SIGS and HIGS: investigation into silencing genes in the obligate downy mildew pathogen. International Molecular Plant Protection Congress Adana TURKEY - April 10-13.

Jimenez-Quiros, C., Baysal, Ö., Nicholson, P. and Tör, M. (2019) Bacillus strains modulate immune response, biomass production and flowering time in Arabidopsis and Brachypodium distachyon. XVIII International Congress on Molecular Plant-Microbe Interactions, July, Glasgow, UK.

Jimenez-Quiros, C., Baysal, Ö., Studholme, D. J.and Tör, M. (2018) Comparative genomic analysis of three species that have an antagonistic effect on Fusarium graminearum. BSPP Presidential Meeting 10-11 December, Warwick, UK.

Jimenez-Quiros, C., Baysal, Ö., Nicholson, P. and Tör, M. (2018) Determining the antifungal activity of Bacillus species against Fusarium graminearum. Phytopathology108: 140-140Supplement: S