John Brown

Professor John Brown

Position: Chair of Molecular Plant Sciences and Head of the Division of Plant Sciences
Division: Plant Sciences
Address: University of Dundee at JHI, Errol Road, Invergowrie, Dundee
Telephone: +44 1382 568777, int ext.
Email: j.w.s.brown@dundee.ac.uk

Research

RNA processing and expression


Plant growth and development, and how plants respond to pathogens and the environment in which they grow, reflect complex gene expression patterns. Genes are turned on and off (transcription) to produce messenger RNAs (mRNAs) from which proteins are made (translation). We are interested in how gene expression in plants is modulated by post-transcriptional processes such as alternative splicing and small non-coding RNAs.


Alternative splicing:


Alternative splicing of pre-mRNA gives rise to different mRNAs and proteins The importance of alternative splicing is well recognised in animals through diseases caused by mis-regulation of alternative splicing. In plants, around 35% of Arabidopsis/rice genes are estimated to undergo alternative splicing. Key questions are 1) which plant factors determine splice site selection, 2) how do particular combinations of factors in different cells and tissues determine tissue-specific alternative splicing, and 3) how are alternative splicing patterns and levels of splicing factors affected by environmental and developmental cues? We have established an accurate and reproducible RT-PCR system to examine 400 alternative splicing events and are studying trans-acting factors such as PTB, a negative regulator of alternative splicing. We are active members of the European Alternative Splicing Network (EURASNET).


Functions of the nucleolus:


Nucleolar localisation of Arabidopsis proteins The nucleolus is a multifunctional compartment of the nucleus whose main role is in ribosomal RNA processing and ribosomal subunit assembly. It has a growing repertoire of functions in other RNA processing and RNP assembly activities. In plants, the nucleolus and Cajal bodies are involved in the production of heterochromatic siRNAs for transcriptional silencing and in the life cycle of a plant virus (GRV). Examination of mRNAs in the nucleolus suggests further potential roles in mRNA export, mRNA surveillance and/or nonsense-mediated decay. The accumulation of aberrant mRNAs in the nucleolus which are substrates for NMD, and the localisation of NMD factors to the nucleolus further highlights this potential role for the plant nucleolus. This research is a collaboration with Prof. Peter Shaw at the John Innes Centre, Norwich.


Small nucleolar RNAs:


mall nucleolar RNAs exist as ribonucleoprotein particles (snoRNPs) snoRNAs are one of the best studied non-coding RNA groups. The majority of plant sonRNA genes are organized in gene clusters and expressed as polycistronic precursor snoRNAs (pre-snoRNAs). The pre-snoRNAs are processed to generate mature snoRNAs which function in rRNA processing and modification. We are studying the organization and expression of snoRNA gene clusters and their potential use as a bar-coding system for studying plant taxonomy and evolution.

Teaching


Publications


  1. Raczynska, K. D., Simpson, C. G., Ciesiolka, A., Szewc, L. Lewandowska, D., Szweykowska-Kulinska, Z., Brown, J. W. S. and Jarmolowski, A. (2009) Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana. Nucleic Acids Research (doi:10.1093/nar/gkp869).

  2. Cole, C., Sobala, A., Lu, C., Thatcher, S. R., Bowman, A., Brown, J. W. S., Green, P. J., Barton, G. J. and Hutvagner, G. (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer dependent small RNAs derived from tRNAs. RNA (doi:10.1261/rna.1738409 ).

  3. Koroleva, O. A., Brown, J. W. S. and Shaw, P. J. (2009) Localisation of eIF4A-III in the nucleolus and splicing speckles is an indicator of plant stress. Plant Signaling and Behaviour 4:1-4.

  4. Kim, S. H., Koroleva, O. A., Lewandowska, D., Pendle, A. F., Clark, G. P., Simpson, C. G., Shaw, P. J. and Brown, J. W. S. (2009) Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell 21: 2045-2057

  5. Koroleva, O. A., Calder, G., Pendle, A. F., Kim, S. H., Lewandowska, D., Simpson, C. G., Ian M. Jones, Brown, J. W. S. and Shaw, P. J. (2009) Dynamic behaviour of the eIF4A-III putative core protein of the exon junction complex: fast relocation to nucleolus and speckles under hypoxia. Plant Cell 21:1592-606.

  6. Brown, J. W. S., Marshall, D. F. and Echeverria, M. (2008) Intronic non-coding RNAs and splicing. Trends in Plant Sciences 13, 335-342.

  7. Simpson, C. G., Lewandowska, D., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Raczynska, D., Jarmolowski, A., Barta, A. and Brown, J. W. S. (2008) Alternative splicing in plants. Biochem. Soc. Trans. 36, 508-510.

  8. Canetta, E., Kim, S. H., Kalinina, N. O., Shaw, J., Adya, A. K., Gillespie, T. Brown, J. W. S. and Taliansky, M. (2008) A plant virus movement protein forms ring-like complexes with the major nucleolar protein, fibrillarin, in vitro. J. Mol. Biol. 376, 932-937

  9. Simpson, C. G. and Brown, J. W. S. (2008) Plant U12-dependent (AT-AC) introns. In: "Nuclear pre-mRNA processing in plants". Curr. Topics in Microbiol. Immunol. 326, 69-82.

  10. Brown, J. W. S. and Shaw, P. J. (2008) The plant nucleolus and mRNA biogenesis. In: "Nuclear pre-mRNA processing in plants". Curr. Topics in Microbiol. Immunol. 326, 291-311.

  11. Simpson, C. G., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Barta, A. and Brown, J. W. S. (2008) Monitoring changes in alternative pre-mRNA splicing in multiple gene transcripts Plant Journal 53, 1035–1048.

  12. Kim, S.H., MacFarlane, S., Kalinina, N.O., Rakitina, D.V., Ryabov, E.V., Gillespie, T., Haupt, S., Brown, J.W.S., and Taliansky M. (2007) Interaction between a plant virus-encoded protein and the major nucleolar protein, fibrillarin, is required for virus systemic infection. Proc. Natl. Acad. Sci. USA 104, 11115-11120

  13. Kim, S.H., Ryabov, E.V., Kalinina, N.O., Rakitina, D.V., MacFarlane, S., Gillespie, T., Haupt, S., Brown, J.W.S., and Taliansky M. (2007) Cajal bodies and the nucleolus are required for systemic infection of a plant virus. EMBO J. 26, 2169-2179.

  14. Brown, J. W. S., Shaw, P. J., Shaw, P. and Marshall, D. F. (2005) The Arabidopsis nucleolar protein database. Nucl. Acids Res. 33. D633-D636.

  15. Pendle, A. F., Clark, G. P., Boon, R., Lewandowska, D., Lam, Y. W., Andersen, J., Mann, M., Lamond, A. I., Brown, J. W. S. and Shaw, P. J. (2005) Proteomic analysis of the Arabidopsis nucleolus suggests a role in mRNA export or surveillance. Mol. Biol. Cell 16, 260-269.

  16. Shaw, P. J. and Brown, J. W. S. (2004) Plant nuclear bodies. Curr. Opin. in Plant Biol. 7, 614-620.

  17. Kim, S.H., Ryabov, E. V., Brown, J.W.S. and Taliansky, M. (2004) Involvement of the nucleolus in plant virus systemic infection. Biochem. Soc Transactions 32, 557-560.

  18. Lewandowska, D., Simpson, C. G., Clark, G. P., Jennings, S. N., Barciszewska-Pacak, M., Lin, C.-F., Makalowski, W, Brown, J. W. S. and Jarmolowski, A. (2004) Determinants of plant U12-dependent intron splicing efficiency. Plant Cell 16, 1340-1352

  19. Simpson, C. G., Jennings, S. N., Clark, G. P., Thow, G. and Brown, J. W. S. (2004) Dual functionality of a plant U-rich intronic sequence element. Plant Journal 37, 82-91.