dr. K. (Kaisa) Kajala
Gegenereerd op 2018-09-24 03:52:47


My main research interest is understanding how different plant cell types have evolved, and how these cell types develop, respond to environmental changes and contribute to plant fitness. Most of my research is carried out in crop species, and my favourite model is tomato.

Plants are the primary source of energy for humankind, and they do an incredible job growing come rain or shine. As they are rooted to the ground and unable to escape the challenges they face, they have evolved a remarkable capacity to modulate their growth and development in response to the environment. This phenotypic plasticity is controlled by tightly regulated changes to gene expression. Understanding the molecular mechanisms of how different plant tissues and plant cell types respond to environmental challenges, such as drought, flooding and light, will allow us to tap into uncharted potential for breeding smarter and more resilient crops.


Plant photobiology
Plants can sense shade and their neighbours through far-red light. For crop species, such as tomato, shade affects resource allocation and very importantly, yield. The overall growth responses to shade, such as stem elongation and suppression of branching, are well known. However, the cellular development responses are not well characterized. I’m intrested in exploring the changes to the cellular morphology and anatomy in stems and roots in response to shade. Then, using cell type-specific tools we can explore the molecular mechanisms that link shade to changes to plant development. 


Exodermis of tomato root has lignified Casparian strip and suberin lamellaExodermis

Exodermis is a root cell type located just under the epidermis, the outermost skin of the root, and it protects the root from drying and drowning. The water- and air-proofing capabilities of exodermis are brought about by two hydrophobic additions to the cell walls: 1) a localized lignin band called Casparian strip that divides the layer to two polarities, inside and outside, and 2) suberin lamellae deposited all around the exodermal cells.

These barriers protect the root in various ways. In drought, the exodermis allows the plants to have higher water retention in drought conditions, making them more drought-tolerant. In flooding, the exodermis prevents oxygen loss from the roots into the soil, leading to more oxygen for root respiration and better flooding tolerance. In saline soils, the exodermis allows increased control of ion and salt uptake from the soil, enhancing salinity tolerance.

Not all plants have exodermis, but all vascular plants have a cell layer called endodermis. Endodermis has both the Casparian strip and the suberin lamella, and the development of endodermis has been elucidated well on the molecular level in the model plant Arabidopsis thaliana that happens to lack the exodermis. The endodermis appears evolutionarily more ancient, but the evolutionary origins of exodermis have yet to be elucidated. Did exodermis evolve by co-opting modules of endodermal development to a new cell layer? What regulates these modules in exodermis? How are the environmental cues integrated with the exodermal development? These are some of the questions that I hope to answer using tomato roots as my model system.





My previous research

Example of cell type-specific TRAP and INTACT lines

I carried out postdoctoral work at the Brady lab at University of California, Davis, where I have been generating an atlas of tomato root gene expression as part of the Integrative Plasticity project. The tomato atlas encompasses combinations of a dozen root cell and tissue types, multiple levels of regulation (chromatin accessibility, nuclear transcriptome, translatome) and different growth conditions (e.g. drought, flooding, plate, soil) for a domesticated tomato Solanum lycopesicum as well as a wild drought-tolerant relative Solanum pennellii.

Combining the functional genomics data with stress-responsive cell development phenotypes sheds light onto molecular mechanisms underlying the plasticity of development on cellular level. For example, we have found changes to the cortex anatomy in response to flooding and changes to exodermal development in response to drought in tomato.


Cross section of C4 leaf

My PhD research was in the Hibberd lab at University of Cambridge. I investigated the transcriptomes of C4 leaves as well as evolution of the elements that directed cell type-specific gene expression in mesophyll cells in the leaves of C4 plant Cleome gynandra.




Masters projects available with me: 

Effects of shade on tomato cellular architecture
This project aims to characterize the responses of tomato shoot and root architecture to different light conditions. Plants sense shade and their neighbours through detecting far-red light, and can respond by changing their development. Typical shade avoidance responses include shoot elongation and suppression of branching. In this project you will characterize the developmental responses of tomato to shade. These include characterization of both shoot and root system architecture responses, but also the underpinning changes to cellular architecture. The aim of this project is to identify the cell types in shoots and roots that play a role in shade responses, and then follow this up with gene expression study from these cell and tissue types.
Regulators of cell type development in tomato roots
Root development responds to changes in the environment, such as drought and flooding. We have identified developmental responses in different cell types of tomato roots. Firstly, we’ve observed increased subrization in exodermis in drought. This cell wall modification seals the root away from the soil environment, protecting it against drying. The second observation we’ve made is changes to the cortex layer number, cell size and intercellular space in response to flooding. These changes help conduct air to the root system. From a cell type-specific gene expression study, we have identified candidate regulators of these developmental changes. In this project, you will clone the candidate transcription factors from tomato and express them under cell type-specific promoters in hairy root cultures. Then, you will observe the developmental phenotypes - e.g. do we see the increased suberin and increased cortex layer number, size and spacing - due to expression of these genes.
Effect of hairy root transformation on tomato root gene expression
This bioinformatics project explores existing tomato root gene expression data to find out how tomato root gene expression is affected by hairy root disease caused by Agrobacterium rhizogenes. Hairy root disease is caused by T-DNA transfer by A. rhizogenes, and this process can be used as a biotechnology tool to rapidly create transgenic root cultures. We are developing the use of hairy root cultures to study cell type development in tomato, and want to understand which aspects of root growth and gene expression are affected by hairy root transformation. In this project, you will use data generated with ATAC-seq (Assay for Transposon Accessible Chromatin) and RNA-seq spanning three diffrent regulatory levels, including nuclear mRNA (currently transcribed), polyA RNA (total mRNA of the cell) and polysomal RNA (currently translated). You will learn how to map sequencing reads against a reference genome/transcriptome and to analyse sequencing information using R. This project is suited for students with strong interest and hopefully some background in bioinformatics. 



Scientific expertise
developmental biology
functional genomics
cell type-specificity
plant abiotic stress
evolutionary biology
plant responses to drought
plant responses to flooding and hypoxia
RNA sequencing, transcriptome analysis
Plant development
Confocal Microscopy
Cell type-specific functional genomics
Gegenereerd op 2018-09-24 03:52:47
Curriculum vitae

BA (2006) Biological Natural Sciences. University of Cambridge, United Kingdom.

PhD (2010) Plant Sciences. Julian Hibberd lab, Department of Plant Sciences, University of Cambridge, United Kingdom. Thesis title: An mRNA blueprint for C4 photosynthesis

Post-doctoral Associate (2011) Ian Small lab, Plant Energy Biology, University of Western Australia.

Post-doctoral Researcher (2012-2017) Siobhan Brady lab, Department of Plant Biology and Genome Center, University of California Davis.

Assistant Professor (2017-) Plant Ecophysiology, Utrecht University, The Netherlands.


Gegenereerd op 2018-09-24 03:52:47

Maher KA, Bajic M, Kajala K, Reynoso MA, Pauluzzi G, West DA, Zumstein K, Woodhouse M, Bubb K, Dorrity M, Queitsch C, Bailey-Serres J, Sinha N, Brady SM, Deal R (2018). Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cellhttps://doi.org/10.1105/tpc.17.00581Open access pre-print: http://www.biorxiv.org/content/early/2017/07/24/167932

Reynoso MA, Pauluzzi G, Kajala K, Cabanlit S, Velasco J, Bazin J, Deal R, Sinha N, Brady SM,Bailey-Serres J (2018). Nuclear transcriptomes at high resolution using retooled INTACT. Plant Physiol., 176: 270–281

Turco G, Kajala K, Kunde-Ramamoorthy G, Ngan C-Y, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei C-L, Etchells JP, Brady SM (2017). DNA Methylation and Gene Expression Regulation Associated with Vascularization in Sorghum bicolor. New Phytol., 214: 1213-1229.

Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Federici F, Sinha N, Deal R, Bailey-Serres J, Brady SM (2014). Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol., 166: 455-469.

Kajala K, Coil DA, Brady SM (2014). Draft genome of Rhizobium rhizogenes strain ATCC 15834. Genome Announc. 2: e01108-14.

Kajala K, Ramakrishna P, Fisher A, Bergmann DC, De Smet I, Sozzani R, Weijers D, Brady SM (2014). Omics and modelling approaches for understanding regulation of asymmetric cell divisions in Arabidopsis and other angiosperm plants. Ann. Bot. 113: 1083-1105.

Kajala K, Brown NJ, Williams BP, Borrill P, Taylor LE, Hibberd JM (2012). Multiple Arabidopsis genes primed for recruitment into C4 photosynthesis. Plant J., 69: 47-56.

Bräutigam A*, Kajala K*, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Maß J, Lercher MJ, Westhoff P, Hibberd JM, Weber APM (2011).  An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiol., 155: 142-156.

Kajala K, Covshoff S, Karki S, Woodfield H, Tolley BJ, Dionora MJA, Mogul R, Elmido-Mabilangan A, Danila F, Hibberd JM, Quick WP (2011). Strategies for engineering a two-celled C4 photosynthetic pathway into rice. J. Exp. Bot., 62: 3001-3010.

Brown NJ, Newell CJ, Stanley S, Chen JE, Perrin AJ, Kajala K, Hibberd, JM (2011). Independent and parallel recruitment of preexisting mechanisms underlying C4 photosynthesis. Science, 331: 1436-1439.

Brown NJ, Palmer BG, Stanley S, Hajaji H, Janacek SH, Astley HM, Parsley K, Kajala K, Quick WP, Trenkamp S, Fernie AR, Maurino VG, Hibberd JM (2010). C4 acid decarboxylases required for C4 photosynthesis are active in the mid-vein of the C3 species Arabidopsis thaliana, and are important in sugar and amino acid metabolism. Plant J., 61: 122-133.

All publications
  2017 - Scholarly publications
Kajala, K. (08.09.2017) Invited speaker Annual Botanical Society of Japan Meeting Noda (08.09.2017 - 10.09.2017) Development of tomato root cell types in response to drought and flooding
Kajala, K. (07.09.2017) Invited speaker RIKEN Development of tomato root cell types in response to drought and flooding
Turco, Gina M, Kajala, Kaisa, Kunde-Ramamoorthy, Govindarajan, Ngan, Chew-Yee, Olson, Andrew, Deshphande, Shweta, Tolkunov, Denis, Waring, Barbara, Stelpflug, Scott, Klein, Patricia, Schmutz, Jeremy, Kaeppler, Shawn, Ware, Doreen, Wei, Chia-Lin, Etchells, J Peter & Brady, Siobhan M (2017). DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytologist, 214 (3), (pp. 1213-1229) (17 p.). © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust..
Reynoso, Mauricio, Pauluzzi, Germain, Kajala, Kaisa, Cabanlit, Sean, Velasco, Joel, Bazin, Jérémie, Deal, Roger, Sinha, Neelima, Brady, Siobhan M & Bailey, Julia (27.09.2017). Nuclear transcriptomes at high resolution using retooled INTACT. Plant Physiology {copyright, serif} 2017 American Society of Plant Biologists. All rights reserved..
Maher, Kelsey A, Bajic, Marko, Kajala, Kaisa, Reynoso, Mauricio, Pauluzzi, Germain, West, Donnelly, Zumstein, Kristina, Woodhouse, Margaret, Bubb, Kerry L, Dorrity, Michael W, Queitsch, Christine, Bailey-Serres, Julia, Sinha, Neelima, Brady, Siobhan M & Deal, Roger (11.12.2017). Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell, 29 (12). © 2017 American Society of Plant Biologists. All rights reserved..
Kajala, K. (28.08.2017) Invited speaker EPS Summer School Utrecht (28.08.2017 - 30.08.2017) Root development in drought and flooding
Kajala, K. (21.09.2017) Invited speaker Institute of Environmental Biology Day Utrecht (21.09.2017) Tomato cell type development and gene expression in drought and flooding.
  2014 - Scholarly publications
Kajala, Kaisa, Coil, David A & Brady, Siobhan M (2014). Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834. Genome Announcements, 2 (5). Copyright © 2014 Kajala et al..
Ron, Mily, Kajala, Kaisa, Pauluzzi, Germain, Wang, Dongxue, Reynoso, Mauricio A, Zumstein, Kristina, Garcha, Jasmine, Winte, Sonja, Masson, Helen, Inagaki, Soichi, Federici, Fernán, Sinha, Neelima, Deal, Roger B, Bailey-Serres, Julia & Brady, Siobhan M (2014). Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiology, 166 (2), (pp. 455-69) (15 p.). © 2014 American Society of Plant Biologists. All Rights Reserved..
  2012 - Scholarly publications
Kajala, Kaisa, Brown, Naomi J, Williams, Ben P, Borrill, Philippa, Taylor, Lucy E & Hibberd, Julian M (2012). Multiple Arabidopsis genes primed for recruitment into C₄ photosynthesis. Plant Journal, 69 (1), (pp. 47-56) (10 p.). © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd..
  2011 - Scholarly publications
Bräutigam, Andrea, Kajala, Kaisa, Wullenweber, Julia, Sommer, Manuel, Gagneul, David, Weber, Katrin L, Carr, Kevin M, Gowik, Udo, Mass, Janina, Lercher, Martin J, Westhoff, Peter, Hibberd, Julian M & Weber, Andreas P.M. (2011). An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiology, 155 (1), (pp. 142-56) (15 p.).
Brown, Naomi J, Newell, Christine A, Stanley, Susan, Chen, Jit E, Perrin, Abigail J, Kajala, Kaisa & Hibberd, Julian M (2011). Independent and parallel recruitment of preexisting mechanisms underlying C₄ photosynthesis. Science, 331 (6023), (pp. 1436-9) (4 p.).
  2010 - Scholarly publications
Brown, Naomi J, Palmer, Ben G, Stanley, Susan, Hajaji, Hana, Janacek, Sophie H, Astley, Holly M, Parsley, Kate, Kajala, Kaisa, Quick, W Paul, Trenkamp, Sandra, Fernie, Alisdair R, Maurino, Veronica G & Hibberd, Julian M (2010). C acid decarboxylases required for C photosynthesis are active in the mid-vein of the C species Arabidopsis thaliana, and are important in sugar and amino acid metabolism. Plant Journal, 61 (1), (pp. 122-33) (12 p.).
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Gegenereerd op 2018-09-24 03:52:47

BSc, Level 3: Plant Development & Environment, UU (teacher, B-B3PDE18)

BSc, Level 3:Advanced Molecular Cell Biology, UCU (teacher, UCSCIBIO31)


Gegenereerd op 2018-09-24 03:52:47
Additional functions and activities


Gegenereerd op 2018-09-24 03:52:47
Full name
dr. K. Kajala Contact details
Hugo R. Kruytgebouw

Padualaan 8
Room Z306
The Netherlands

Phone number (direct) +31 30 253 6871
Gegenereerd op 2018-09-24 03:52:47
Last updated 18.09.2018