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
Gatsby Charitable Foundation Sainsbury 4-year PhD Studentships in Plant Science:
Gravity and the shaping of plant form: understanding growth angle control in lateral organs

The overall shape of plants, the space they occupy above and below ground, is determined largely by the number, length, and angle of their lateral branches. 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 of these 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 gravity. We have shown that this capacity to maintain non-vertical GSAs requires the action of an auxin transport-dependent antigravitropic offset mechanism that counteracts graviresponse in lateral roots and shoots. This PhD will give the student the opportunity to study GSA control using natural variation across Arabidopsis ecotypes and by characterising existing novel GSA mutants in the lab. There will also be the possibility to extend this work to look at a wider range of species via an Evo-Devo. The project will provide advanced training in genetics, molecular genetics, and cell biology in the context of a stimulating multidisciplinary environment, allowing the student to uncover the processes underlying the wonderful variation in patterns of growth angle control observed throughout nature.

For further details contact Dr Stefan Kepinski (s.kepinski@leeds.ac.uk).


BBSRC-DTP 4-year PhD studentship:
Multiscale modelling of growth angle control in plants

Gravitropism is a fundamental process in the control of plant architecture and yet despite more than a century of research the mechanisms by which plant organs can be maintained at specific angles with respect to gravity remain poorly understood. Recent work in the Kepinski and Cohen groups at the University of Leeds have combined molecular and genetic methods, novel plant imaging and machine vision, and mathematical modelling to uncover crucial clues as to the nature of the basic mechanism by which plants can detect their orientation in the gravity field and alter their growth accordingly. Together these exciting breakthroughs set the stage for this PhD project, the aim of which is to develop a multiscale model of growth angle control in higher plants. The student will engage directly both in cutting-edge mathematical modelling and lab-based experimentation, with the balance of these activities being dependent on their background and interests. This exciting project therefore offers the opportunity to make important discoveries about one of the fundamental determinants of plant form while at the same time receiving a training that is truly interdisciplinary.

For further details visit its FindaPhD page and/or Contact Dr Stefan Kepinski (s.kepinski@leeds.ac.uk).

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).