Abdellah Barakate
Abdellah joined The James Hutton Institute in November 2015 and he is a member of the Cell and Molecular Sciences department. Prior to this he worked at the University of Dundee for 18 years after his first Postdoc at Imperial College, London. He was born and educated in Morocco and gained his master’s degree and PhD from the University of Joseph Fourier, Grenoble, France.
Abdellah has 3 decades of experience in Plant Molecular Biology and worked mainly in the areas of cell wall and plant DNA repair and recombination. Over years, he has accumulated huge knowledge of gene manipulation tools including CRISPR-based gene editing. Abdellah loves sharing his knowledge through teaching, collaborations and public outreach.
Current research interests
I joined JHI in November 2015 to work on “meiosis and recombination in large genome crop plants”, funded by a 5-year ERC advanced grant awarded to Prof Robbie Waugh. This project extends my previous work in Prof Claire Halpin’s laboratory on “Meiosis in barley: manipulating crossover frequency and distribution” funded by a BBSRC sLoLa grant.
During meiosis, homologous chromosomes undergo complex and dynamic structural changes resulting in their pairing, synapsis, recombination and segregation. The mechanism that regulates the frequency and distribution of meiotic crossovers (CO) is poorly understood. In grasses, meiotic COs are preferentially formed at sub-telomeric regions resulting in stable linkage blocks in centromic region containing ~30% of genes. This skewed pattern of recombination hampers the breeders’ effort to exploit this important gene pool.
Our aim is to understand the mechanism that governs the formation of meiotic COs in barley and use the gained knowledge to improve crop breeding efficiency. In the current SHUFFLE project, we are using several omics platforms ranging from genomics, transcriptomics to proteomics to study the dynamics of RNA and protein changes during meiosis.
I use molecular biology techniques to study and validate the function of selected genes and Figure 1 summarises my gene manipulation toolbox ranging from RNAi to CRISPR/Cas9.
I am also interested in studying chromatin epigenetics, non-coding RNAs and post-translational modifications during meiosis. However, these targeted analyses necessitate isolation of large numbers of meiocytes that are embedded in complex structures like anthers. In order to solve this problem, I adapted the INTACT technology (isolation of nuclei tagged in specific cell types) that will allow us to quickly harvest large numbers of meiotic nuclei directly from barley inflorescences.
Collaborations
Currently collaborating with:
- Dr Stefan Heckmann, IPK on barley meiotic mutants.
- Dr Jennifer Stephens for improving barley and potato transformations.
- with nine local JHI and University of Dundee groups and ten other international teams on CRISPR/Cas9. I developed user friendly CRISPR/Cas9 vectors for both monocotyledon and dicotyledon plants.
- with Dr Stefania Giacomello and Prof Joakim Lundeberg, SciLifeLab, Stockholm to study spatial transcriptome of barley anthers and spikes.
Measures of esteem
- I have reviewed several international and UK research grant proposals.
- I review papers and reviews for several journals.
- I have been invited to give talks on lignin biosynthesis, TILLING and CRISPR at local, national and international conferences and workshops.
- I also gave invited lectures to 3rd year students at the University of Dundee on plant transformations and CRISPR.
Employment history
- Nov 2015 – Present: Plant Molecular Geneticist, JHI
- Apr 2015 – Oct 2015: Casual Researcher, University of Dundee.
- Jun 2014 – Mar 2015: Temporary Researcher, JHI.
- Aug 1996 – May 2014: Senior Postdoctoral Researcher, University of Dundee.
- Apr 1993 – Jul 1996: Postdoctoral Researcher, Imperial College, London.
Education and professional qualifications
- October 1989 – December 1992: PhD on pollen development, University Joseph Fourier, Grenoble, France.
- Sep 1988 – Jun 1989: Msc in Molecular and Cell Biology, University of Joseph Fourier, Grenoble, France.
- Summer 1988: Intensive course in Molecular Biology, Rabat, Morocco.
- Sep 1984 – Jun 1988: Bsc in plant biology, biochemistry, microbiology, and genetics.
- Oct 1977 – Jun 1984: Secondary school, Baccalaureate, Beni Mellal, Morocco.
Past research
After my PhD I have worked in two main areas of research:
- Lignin biosynthesis with Prof Claire Halpin
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Plant DNA repair and recombination:
- My first Postdoc on using tomato golden mosaic virus-based vectors for gene targeting in plants was with Prof Conrad Lichtenstein, Imperial College, London.
-
I then continued this area by applying for funding with Prof Claire Halpin to study intrachromosomal recombination in somatic and meiotic recombination leading to our work on meiosis in barley.
Bibliography
- Barakate, A.; Arrieta, M.; Macaulay, M.; Vivera, S.; Davidson, D.; Stephens, J.; Orr, J.; Schreiber, M.; Ramsay, L.; Halpin, C.; Waugh, R. (2021) Downregulation of barley Regulator of Telomere Elongation Helicase 1 alters the distribution of meiotic crossovers., Frontiers in plant science, 12, Article No. 745070
- Shoesmith, J.R; Solomon, C.U; Yang, X.; Wilkinson, L.G.; Sheldrick, S.; van Eijden, E.; Couwenberg, S.; Pugh, L.M.; Eskan, M.; Stephens, J.; Barakate, A.; Drea, S.; Houston, K.; Tucker, M.R.; McKim, S.M. (2021) APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley., Development,148(5), Article No. dev194894.
- Barakate, A.; Orr, J.; Schreiber, M.; Colas, I.; Lewandowska, D.; McCallum, N.; Macaulay, M.; Morris, J.; Arrieta, M.; Hedley, P.E.; Ramsay, L.; Waugh, R. (2021) Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I., Frontiers in Plant Science, 11.
- Garcia-Gimenez, G.; Barakate, A.; Smith, P.; Stephens, J.; Khor, S.F.; Doblin, M.S.; Hao, P.; Bacic, A.; Fincher, G.B.; Burton, R.A.; Waugh, R.; Tucker, M.R.; Houston, K. (2020) Targeted mutation of barley (1,3;1,4)-ß-glucan synthases reveals complex relationships between the storage and cell wall polysaccharide content., The Plant Journal, 104, 1009-1022.
- Schreiber, M.; Barakate, A.; Uzrek, N.; Macaulay, M.; Sourdille, A.; Morris, J.; Hedley, P.E.; Ramsay, L.; Waugh, R. (2019) A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing., Plant Methods, 15, Article No. 99.
- Das Dangol, S.; Barakate, A.; Stephens, J.; Caliskan, M.E.; Bakhsh, A. (2019) Genome editing of potato using CRISPR technologies: current development and future prospective., Plant Cell, Tissue and Organ Culture, 139, 403-416.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Daly, P.; McClellan, C.; Maluk, M.; Oakey, H.; Lapierre, C.; Waugh, R.; Stephens, J.; Marshall, D.; Barakate, A.; Tsuji, Y.; Goeminne, G.; Vanholme, R.; Boerjan, W.; Ralph, J.; Halpin, C. (2019) RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family., Plant Biotechnology Journal, 17, 594-607.
- Colas, I.; Barakate, A.; Macaulay, M.; Schreiber, M.; Stephens, J.; Vivera, S.; Halpin, C.; Waugh, R.; Ramsay, L. (2019) Desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 (DMC1) in barley., Journal of Experimental Botany, 70, 2683-2698.
- Stephens, J.; Barakate, A. (2017) Gene editing technologies - ZFNs, TALENs, and CRISPR/Cas9., In: Thomas, B., Murray, B.G. & Murphy, D.J. (eds.). Encyclopedia of Applied Plant Sciences, Volume 2. Academic Press, Waltham, MA, pp157-161.
- Colas, I.; Macaulay, M.; Higgins, J.D.; Phillips, D.; Barakate, A.; Posch, M.; Armstrong, S.J.; Franklin, F.C.H.; Halpin, C.; Waugh, R.; Ramsay, L. (2016) A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis and crossover resolution in the barley desynaptic mutant des10., New Phytologist, 212, 693-707.
- Barakate, A.; Stephens, J. (2016) An overview of CRISPR-based tools and their improvements: new opportunities in understanding plant-pathogen interactions for better crop protection., Frontiers in Plant Science, 7, Article No. 765.
- Barakate, A.; Higgins, J.D.; Vivera, S.; Stephens, J.; Perry, R.M.; Ramsay, L.; Colas, I.; Oakey, H.; Waugh, R.; Franklin, F.C.H.; Armstrong, S.J.; Halpin, C. (2014) The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley., The Plant Cell, 26, 729-740.
- Phillips, D.; Wnetrzak, J.; Nibau, C.; Barakate, A.; Ramsay, L.; Wright, F.; Higgins, J.D.; Perry, R.M.; Jenkins, G. (2013) Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference., Journal of Experimental Botany, 64, 2139-2154.
- Higgins, J.D.; Perry, R.M.; Barakate, A.; Ramsay, L.; Waugh, R.; Halpin, C.; Armstrong, S.J.; Franklin, F.C.H. (2012) Spatiotemporal asymmetry of the meiotic program underlies the predominantly distal distribution of meiotic crossovers in barley., Plant Cell, 24, 4096-4109.
- Barakate, A.; Stephens, J.; Goldie, A.; Hunter, W.N.; Marshall, D.F.; Hancock, R.D.; Lapierre, C.; Morreele, K.; Boerjane, W.; Halpin, C. (2011) Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco., Plant Cell, 23, 4492-4506.
- Gomez, L.D.; Whitehead, C.; Barakate, A.; Halpin, C.; McQueen-Mason, S.J. (2010) Automated saccharification assay for determination of digestibility in plant materials., Biotechnology for Biofuels, 3, 1-12.
- El-Amrani, A.; Barakate, A.; Askari, B.M.; Li, X.; Roberts, A.G.; Ryan, M.D.; Halpin, C. (2004) Coordinate expression and independent subcellular targeting of multiple proteins from a single transgene., Plant Physiology, 135, 16-24.
- Abbott, J.C.; Barakate, A.; Pinþon, G.; Legrand, M.; Lapierre, C.; Mila, I.; Schuch, W.; Halpin, C. (2002) Simultaneous suppression of multiple genes by single transgenes. Downregulation of three unrelated lignin biosynthetic genes in tobacco., Plant Physiology, 128, 844-853.
- Barakate, A.; Arrieta, M.; Macaulay, M.; Vivera, S.; Davidson, D.; Stephens, J.; Orr, J.; Schreiber, M.; Ramsay, L.; Halpin, C.; Waugh, R. (2021) Downregulation of barley Regulator of Telomere Elongation Helicase 1 alters the distribution of meiotic crossovers., Frontiers in plant science, 12, Article No. 745070
- Shoesmith, J.R; Solomon, C.U; Yang, X.; Wilkinson, L.G.; Sheldrick, S.; van Eijden, E.; Couwenberg, S.; Pugh, L.M.; Eskan, M.; Stephens, J.; Barakate, A.; Drea, S.; Houston, K.; Tucker, M.R.; McKim, S.M. (2021) APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley., Development,148(5), Article No. dev194894.
- Barakate, A.; Orr, J.; Schreiber, M.; Colas, I.; Lewandowska, D.; McCallum, N.; Macaulay, M.; Morris, J.; Arrieta, M.; Hedley, P.E.; Ramsay, L.; Waugh, R. (2021) Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I., Frontiers in Plant Science, 11.
- Garcia-Gimenez, G.; Barakate, A.; Smith, P.; Stephens, J.; Khor, S.F.; Doblin, M.S.; Hao, P.; Bacic, A.; Fincher, G.B.; Burton, R.A.; Waugh, R.; Tucker, M.R.; Houston, K. (2020) Targeted mutation of barley (1,3;1,4)-ß-glucan synthases reveals complex relationships between the storage and cell wall polysaccharide content., The Plant Journal, 104, 1009-1022.
- Schreiber, M.; Barakate, A.; Uzrek, N.; Macaulay, M.; Sourdille, A.; Morris, J.; Hedley, P.E.; Ramsay, L.; Waugh, R. (2019) A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing., Plant Methods, 15, Article No. 99.
- Das Dangol, S.; Barakate, A.; Stephens, J.; Caliskan, M.E.; Bakhsh, A. (2019) Genome editing of potato using CRISPR technologies: current development and future prospective., Plant Cell, Tissue and Organ Culture, 139, 403-416.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Daly, P.; McClellan, C.; Maluk, M.; Oakey, H.; Lapierre, C.; Waugh, R.; Stephens, J.; Marshall, D.; Barakate, A.; Tsuji, Y.; Goeminne, G.; Vanholme, R.; Boerjan, W.; Ralph, J.; Halpin, C. (2019) RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family., Plant Biotechnology Journal, 17, 594-607.
- Colas, I.; Barakate, A.; Macaulay, M.; Schreiber, M.; Stephens, J.; Vivera, S.; Halpin, C.; Waugh, R.; Ramsay, L. (2019) Desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 (DMC1) in barley., Journal of Experimental Botany, 70, 2683-2698.
- Colas, I.; Macaulay, M.; Higgins, J.D.; Phillips, D.; Barakate, A.; Posch, M.; Armstrong, S.J.; Franklin, F.C.H.; Halpin, C.; Waugh, R.; Ramsay, L. (2016) A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis and crossover resolution in the barley desynaptic mutant des10., New Phytologist, 212, 693-707.
- Barakate, A.; Stephens, J. (2016) An overview of CRISPR-based tools and their improvements: new opportunities in understanding plant-pathogen interactions for better crop protection., Frontiers in Plant Science, 7, Article No. 765.
- Barakate, A.; Higgins, J.D.; Vivera, S.; Stephens, J.; Perry, R.M.; Ramsay, L.; Colas, I.; Oakey, H.; Waugh, R.; Franklin, F.C.H.; Armstrong, S.J.; Halpin, C. (2014) The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley., The Plant Cell, 26, 729-740.
- Phillips, D.; Wnetrzak, J.; Nibau, C.; Barakate, A.; Ramsay, L.; Wright, F.; Higgins, J.D.; Perry, R.M.; Jenkins, G. (2013) Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference., Journal of Experimental Botany, 64, 2139-2154.
- Higgins, J.D.; Perry, R.M.; Barakate, A.; Ramsay, L.; Waugh, R.; Halpin, C.; Armstrong, S.J.; Franklin, F.C.H. (2012) Spatiotemporal asymmetry of the meiotic program underlies the predominantly distal distribution of meiotic crossovers in barley., Plant Cell, 24, 4096-4109.
- Barakate, A.; Stephens, J.; Goldie, A.; Hunter, W.N.; Marshall, D.F.; Hancock, R.D.; Lapierre, C.; Morreele, K.; Boerjane, W.; Halpin, C. (2011) Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco., Plant Cell, 23, 4492-4506.
- Gomez, L.D.; Whitehead, C.; Barakate, A.; Halpin, C.; McQueen-Mason, S.J. (2010) Automated saccharification assay for determination of digestibility in plant materials., Biotechnology for Biofuels, 3, 1-12.
- El-Amrani, A.; Barakate, A.; Askari, B.M.; Li, X.; Roberts, A.G.; Ryan, M.D.; Halpin, C. (2004) Coordinate expression and independent subcellular targeting of multiple proteins from a single transgene., Plant Physiology, 135, 16-24.
- Abbott, J.C.; Barakate, A.; Pinþon, G.; Legrand, M.; Lapierre, C.; Mila, I.; Schuch, W.; Halpin, C. (2002) Simultaneous suppression of multiple genes by single transgenes. Downregulation of three unrelated lignin biosynthetic genes in tobacco., Plant Physiology, 128, 844-853.
- Stephens, J.; Barakate, A. (2017) Gene editing technologies - ZFNs, TALENs, and CRISPR/Cas9., In: Thomas, B., Murray, B.G. & Murphy, D.J. (eds.). Encyclopedia of Applied Plant Sciences, Volume 2. Academic Press, Waltham, MA, pp157-161.
- Bonar, N.; Rahamkulov, I.; Dangol, S.D.; Zhang, R.; Dessoly, J.; Stephens, J.; Barakate, A.; Taylor, M.; Hornyik, C. (2019) Post-transcriptional gene regulation and gene editing in potato., 6th Plant Genomics and Gene Editing Congress and Micobiome for Agriculture Congress, Asia, Kuala Lumpur, Malaysia, 29-30 July 2019. (Abstract).
- Schreiber, M.; Barakate, A.; Uzrek, N.; Colas, I.; Lewandowska, D.; Macaulay, M.; Mittmann, S.; Arrieta, M.; Clavijo, B.; Wright, J.; Ramsay, L.; Waugh, R. (2018) Developing bioinformatics resources to study meiosis in the barley cultivar Golden Promise., Plant and Animal Genome, Sa Diego, USA, 13-17 January 2018.
- Barakate, A.; Schreiber, M.; Stephens, J.; Davidson, D.; Uzrek, N.; Macaulay, M.; Colas, I.; Lewandowska, D.; Sourdille, A.; Arrieta, M.; Mittmann, S.; Ramsay, L.; Waugh, R. (2018) Targeted mutagenesis of meiotic genes in barley (Hordeum vulgare): Understanding and manipulating meiotic crossovers., Monogram 2018, Norwich, UK, 24-26 April 2018.
- Escudero-Martinez, C.; Leybourne, D.; Barakate, A.; Morris, J.; Hedley, P.; Stephens, J.; Bos, J. (2018) Understanding the basis of host and non-host defences during barley-aphid interactions., Phytopathology, 108, S1.247. Abstract.
- Barakate, A.; Stephens, J.; Colas, I.; Schreiber, M.; Lewandowska, D.; Uzrek, N.; Macaulay, M.; Arrieta, M.; Mittmann, S.; Ramsay, L.; Waugh, R. (2017) Understanding and manipulating meiotic crossovers in barley (Hordeum vulgare)., British Meiosis Meeting, Dundee, 19-20 April 2017. Poster
- Lewandowska, D.; Uzrek, N.; Ten Have, S.; Hodge, K.; Colas, I.; Barakate, A.; Ramsay, L.; Waugh, R. (2017) Proteomic profile of barley male meiocytes at early stages of meiosis., British Meiosis Meeting, Dundee, 19-20 April 2017. Poster.
- Barakate, A.; Stephens, J.; Higgins, J.; Ramsay, L.; Colas, I.; Halpin, C.; Waugh, R.; Jenkins, G.; Phillips, D.; Armstrong, S.; Franklin, C. (2011) Manipulation of meiotic recombination in barley., 3rd British Meiosis Meeting, Sheffield, April 2011.