The Ding Lab focuses on understanding the mechanisms by which plants activate immunity upon recognition of different pathogens, especially via transcriptional regulation. To tackle this, we apply cutting-edge technologies and multi-disciplinary approaches. We welcome both academic and industrial partnerships to contact us for collaborations.

More information about Pingtao Ding

Brief biography

Pingtao Ding completed his PhD in Biochemistry and Molecular Biology in 2014 at the joint program between the Beijing Normal University and the National Institute of Biological Sciences (NIBS), Beijing, China. Between 2011 and 2013, he was awarded with a China Scholar Council (CSC) PhD visiting scholarship to study plant innate immunity at the Michael Smith Laboratory (MSL) and the botany department at the University of British Columbia (UBC), Vancouver, Canada. Thereafter, Dr. Pingtao Ding continued as a postdoctoral research scientist, Marie-Curie Research Fellow and an independent BBSRC Future Leader Fellow working at the Sainsbury Laboratory (TSL), Norwich, United Kingdom, from 2014 to 2021. During his postdoc and independent fellow research period, he led the research on understanding how plants ‘switch’ on their immunity via transcriptional regulation upon activations of both cell-surface and intracellular immune receptors.

Currently, Dr. Pingtao Ding is an Assistant Professor of Molecular Plant Biology and the Head of Systems Biology in Plant Immunity at the Institute Biology Leiden (IBL or the Sylvius Laboratory), Leiden University, the Netherlands. His research continues to understand detailed mechanisms by which plant cells activate effective immune responses via transcriptional regulation, and particularly focused on the earliest activation of intracellular receptor-mediated immunity or commonly known as effector-triggered immunity (ETI). A pioneering research of his group at IBL will decipher the transcriptional regulatory mechanisms at the single-cell level using the systems biology approach.

Research

Plant diseases are everywhere. It is vital to understand how plants defend themselves against pathogen threats from the changing environment (e.g., global warming and pollution, over usage of toxic chemicals during farming, growing population, etc.), which therefore is important for the well-being of humanity. The main goal of my research is to understand how plants turn on their immune systems upon recognition of different pathogens, and find means of controlling crop diseases, improving and advancing agriculture.

The Ding Lab at IBL Leiden is currently leading research on the following projects (selected):

I. Probing mechanisms of defense gene activation to elevate plant disease resistance.
Intracellular immune receptors in plants are main molecular surveillance mediators in disease resistance, and they are also known as Resistance (R) proteins, nucleotide-binding (NB) and leucine-rich-repeat (LRR) domain-containing receptors (NLRs) and they can form inflammasome-like high-order protein complexes or known as “resistosomes”. Recognition of effectors (molecules secreted by pathogens, and some can suppress the host immunity) leads to the activation of NLR proteins or resistosomes and enhanced disease resistance (also known as effector-triggered immunity, or ETI). An early physiological signature of such activation is the rapid upregulation of defense genes. Malfunction of transcriptional reprogramming in ETI compromises the NLR-mediated immunity.

Recently the Ding Lab has generated multiple novel toolkits to uncouple the general regulatory mechanisms by which defense genes are transcriptionally activated.  We aim to identify and characterize the common regulatory components downstream of NLRs. On one hand, we will focus on understanding the functions of known several transcriptional regulators by answering the following questions: how are they recruited and activated? do they have co-regulators? how do they regulate their downstream targets? One the other hand, we will use novel genetic approaches to uncover novel components that are involved in the activation of ETI.

II. Identification of gene-regulatory networks (GRNs) and functional characterization of transcription factors (TFs) involved in the activation of plant innate immunity.
Plant responses to biotic threats under a changing environment demands precise cellular regulations. Due to the high redundancy of the genetic components in plant genome, it is difficult to predict the exact immune outcomes (e.g., resistance or susceptible) of a certain input with many other perturbations. Furthermore, it is challenging to look at one specific process without understanding the whole picture of the system. Thus, identifying gene-regulatory networks (GRNs) becomes robust to understand how plants respond to the environment, because it collects the information of how molecular regulators (such as transcription factors or TFs, and their target genes) interact with each other and other substances (e.g., hormones).

Currently, the Ding Lab aims to identify the dynamics and hierarchies of TFs and their target genes during the activation of intracellular immune receptors (NLRs) with cutting-edge multi-omics approaches. We will also validate and characterize the functions of TFs identified from such GRN studies. Ultimately, we aim at applying the knowledge we obtained in such studies for guiding plant breeding for disease resistance.

III. Decoding plant immune activation at the single-cell resolution and systems-biology level.
Our understanding of plant immunity is mostly built at the level of entire plant, organ or tissue. However, plant-microbe interactions mostly begin at the single-cell or single-cell-type level, and the research on this topic suffers from the cellular complexity of the analyzed sample; for instance, RNA-seq without isolating cells that directly interacting with pathogens from those that are not infected, cannot define transcriptional reprogramming specifically undergoing in those two distinct types of cells during the infection. Recent methodological advances allow us to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of different biological processes in plants, including the activation of plant immunity.

The Ding Lab aims at developing novel approaches and resources for understanding plant immune activation at the single-cell level. We will apply multi-disciplinary approaches including multi-omics, bioinformatics, mathematical modelling and machine learning.

Model plant systems: Thale cress (Arabidopsis thaliana), tomato (Solanum lycopersicum), tobacco plants (Nicotiana benthamiana and Nicotiana tobaccum), barley (Hordeum vulgare), common liverwort (Marchantia polymorpha) and C-fern (Ceratopteris richardii).

Grands

• Marie Skłodowska-Curie Actions (MSCA) Individual Fellowship (IF), Horizon 2020 (2016 - 2018)
• Biotechnology and Biological Sciences Research Council (BBSRC) Future Leader Fellowship (FLF) (2018 - 2021)

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