Dr. Stefan Kepinski

email: s.kepinski@leeds.ac.uk

Auxin-regulated development and plant geometry

The Kepinski lab is focused on understanding the regulation of plant development by the hormone auxin with projects ranging from the earliest events of auxin receptor complex formation to root hair development and the control of growth angle of plant organs. We are always interested to hear from bright and committed researchers who would like to join the lab.

Current research

Growth angle control in lateral branches and organs

The growth angle of branches and other lateral organs is a fascinating topic in developmental biology and one of tremendous agronomic importance. For the most part root and shoot branches grow at angles that are non-vertical, a crucial adaptation allowing plants to optimise the capture of resources above- and below-ground. Importantly, many lateral branches are maintained at specific angles with respect to gravity rather than to the main or parent axis per se. These growth angles, known as gravitropic setpoint angles or GSAs, are intriguing because their maintenance requires that lateral root and shoot branches are able to effect tropic growth both with and against the gravity vector. We are using using genetics, molecular genetics, cell biology, and computational modelling to understand the mechanisms underlying gravity-dependent and gravity-independent growth angle control.

Context-specificity in auxin signalling

A key question in plant biology is how the hormone auxin controls such a diversity of developmental events. Research in the Kepinski lab is focused on understanding how the specificity which can account for this control arises in the auxin signalling system. Although the current qualitative model of this complex system provides a conceptual framework for understanding how auxin can turn genes on and off, it is unclear how and where specific information is carried in the system and thus how auxin pulses of differing length and amplitude can be translated into quantitatively different genomic outputs both within and between various developmental contexts. To address these questions, we are obtaining quantitative and cell-type-specific genomic and biochemical data to parameterize comparative mathematical models of auxin response in juxtaposed developmental contexts to understand how auxin operates throughout development. Our principal model system is the root epidermis which is made up of hair cells that can produce root hairs and non-hair cells that typically do not. This tissue is of particular interest because these adjacent cell types have dramatically different capacities to transport and respond to auxin. Because of the desire to model, as far as possible, at the level of the single cell and with realistic binding preferences among protein components, we are heavily involved in single-cell-type sampling techniques and in vitro and in vivo quantification of protein interactions and abundance. We work closely with modellers at CPIB in Nottingham and to integrate the experimental and theoretical aspects of the work.

Auxin perception

The formation of the TIR1/AFB-auxin-Aux/IAA auxin receptor complex is one of the most pivotal protein/ligand interaction events in plant biology. In promoting the association between TIR1/AFB receptor F-box proteins and Aux/IAA co-repressors, endogenous auxins regulate almost every aspect of plant development from the earliest events of embryogenesis to the formation of flowers and fruits. The function of this complex is to control gene expression by regulating levels of Aux/IAA transcriptional co-repressor proteins in response to auxin; the auxin-enhanced interaction between TIR1/AFB proteins and Aux/IAAs promotes the polyubiquitnation of the Aux/IAAs, marking them for destruction in the 26S proteasome. Given the central importance of auxin for plant growth it is no surprise that the TIR1/AFB-auxin-Aux/IAA receptor complex is the target for auxinic agrochemicals, particularly herbicides, which include 2,4-D and picloram. Our current research on this topic revolves around understanding the very earliest events of auxin perception using structural, biophysical, and thermodynamic analysis.


Current PhD opportunties

Gosden PhD Studentship:

More crop per drop: re-engineering root system architecture for improved water uptake

The rising world population and increasingly conspicuous effects of climate change are creating a ‘perfect storm’ in which the demand for food and other agricultural commodities is growing dramatically and unsustainably. With limited additional land to be brought into agricultural production and pressure to reduce environmentally-damaging agricultural inputs, increases in food production of ~60% must be achieved through a sustainable intensification of agriculture over the next two-three decades [1]. Key to this will be the development of new crop varieties with improved yields under optimal and sub-optimal soil and climatic conditions. Root systems are central to the acquisition of water and nutrients by plants and have thus become a focus of crop improvement programmes and seed companies. In particular, traits such as root length, branching and growth angle determine the distribution of root surface area within the soil profile where nutrients and water are unevenly distributed[2]. For example, water and nitrogen (in the form of nitrate) are highly mobile within the soil and levels are generally higher within the deeper layers of the soil. For this reason, steep rooting angle has become recognised as a high-value crop improvement target associated with improved performance of crops at lower levels of irrigation and nitrate fertiliser application, both of which are associated with high carbon footprints and financial costs[2].

Our recent work on the mechanisms by which plants set the angle of growth of their lateral organs with respect to gravity has identified multiple exciting new genetic approaches to the manipulation of root growth angle[3,4]. This PhD project will build on these findings by combining functional characterisation of mutations in novel genes regulating root growth angle in Arabidopsis with genome editing of wheat and barley to demonstrate their effects in commercially important crop species. Further, in collaboration with partners at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India, the student will investigate the possibility of translating our fundamental research on root growth angle control to sorghum and maize, crops of high socio-economic significance in the Global South.

This exciting project will allow the student to make fundamental discoveries with real-world impact while gaining a broad range of research experience from genomics, genetics and cell biology, through to CRISPR/Cas9-based genome editing and crop transformation. The student will be based in Leeds under the supervision of Dr Stefan Kepinski but will be co-supervised by Prof. Wendy Harwood at the John Innes Centre, Norwich, who will provide guidance and training in genome editing and plant transformation. 

The project will also benefit from collaborations with Dr Cristobal Uauy (JIC, UK), Dr Jana Kholova (ICRISAT, India), Dr Pooja Bhatnagar Mathur (ICRISAT, India), and Prof Rajeev Varshney (ICRISAT, India).

Potential applicants are encouraged to contact Dr Stefan Kepinski (s.kepinski@leeds.ac.uk) if they would like to discuss the project.

1. Food and Agriculture Organization of the United Nations. 2017. “The Future of Food and agriculture – Trends and Challenges.” 

2. Lynch, JP. 2013. Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems. Annals of Botany 112:347–357.

3. Roychoudhry, S., Del Bianco, M., Kieffer, M., Kepinski, S. (2013) Auxin controls gravitropic setpoint angle in higher plant lateral branches. Current Biology 23:1497-504.

4. Roychoudhry, S, Kieffer, M, Del Bianco, M, Liao, C, Weijers, D and Kepinski, S. (2017) The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean. Scientific Reports 7:42664 | DOI: 10.1038/srep42664

BBSRC-DTP 4-year PhD studentship:
Understanding and predicting specificity and selectivity in auxin receptor complex formation

The formation of the TIR1/AFB-auxin-Aux/IAA auxin co-receptor complex is one of the most pivotal protein/ligand interaction events in plant biology. In promoting the association between TIR1/AFB F-box proteins and Aux/IAA co-repressors, endogenous auxins regulate almost every aspect of plant development from the earliest events of embryogenesis to the control of architecture of the entire adult plant. The function of this complex is to control gene expression by regulating levels of Aux/IAA transcriptional co-repressor proteins in response to auxin; the auxin-enhanced interaction between TIR1/AFB proteins and Aux/IAAs promotes the polyubiquitnation of the Aux/IAAs, marking them for destruction in the 26S proteasome.  

Recent thinking about the TIR1 co-receptor complex has been dominated by a crystal structure of the complex that shows the auxin and Aux/IAA components binding to TIR1 in the same pocket. Within this pocket, auxin acts as a kind of ‘molecular glue’ to stabilise binding of the complex. Our recent work has defined a set of early interactions in the formation of the complex that are predicted to determine the specificity of TIR1-Aux/IAA interactions and also the selectivity of endogenous auxin molecules and synthetic auxinic herbicides. In this project, you would build of these exciting discoveries, learning and using techniques including nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and Cryo-electron microscopy (Cryo-EM) to address an intellectually intriguing and economically important question in structural and plant biology.

Potential applicants are encouraged to contact Dr Stefan Kepinski (s.kepinski@leeds.ac.uk) if they would like to discuss the project.

 

Current projects
  • Vertical-stage confocal microscopy for live imaging of growing plants (BBSRC, 2017-2018)

  • Gravitropic setpoint angle control in higher plants (BBSRC, 2016-2019)

  • Next generation auxins and anti-auxins: principles for binding and design (BBSRC, 2014-2017) Collaboration with Prof. Richard Napier, Warwick

  • GCRF-AFRICAP - Agricultural and Food-system Resilience: Increasing Capacity and Advising Policy (BBSRC-RCUK, 2017-2020)

  • The molecular basis of antigravitropism (BBSRC DTP, 2015-2018)

  • The molecular basis of primary root and shoot gravitropism (BBSRC DTP, 2017-2021)

  • Computational modelling of growth angle control across the higher plants (BBSRC DTP, 2013-2017) Collaboration with Prof. Netta Cohen, Leeds

  • Characterisation of novel regulators of auxin signalling (INRA, 2015-2017)

  • Understanding specificity in auxin perception (Syngenta, 2017-2020)

Publications
Lateral roots growing at non-vertical GSAs show no asymmetry in auxin response, visualised using the reporter DR5v2
Expression of the auxin co-receptor protein AFB3 in the Arabidopsis root
The TIR1/AFB-auxin-Aux/IAA auxin receptor complex (based on Tan et al. 2007), looking down into the auxin binding pocket of TIR1 (grey) with the auxin indole-3-acetic acid at the base of the pocket (green) and the Aux/IAA above it (orange).