Ari Sadanandom is the Principal Investigator of the SUMO code project. Ari Sadanandom’s research group wants to understand how protein modification systems control plant growth and adaptation to their environment. Ari’s laboratory has pioneered the research on SUMO, a new protein modification system that is emerging as a pivotal molecular mechanism in stress biology in plants. AS has demonstrated that SUMOylation coordinates growth control with changing environmental conditions by directly modifying the activity of major transcriptional regulators in plants. Ari Sadanandom is also director of the Durham Centre for Crop Improvement technology, a multi-disciplinary research centre that works with Agriculture industry to develop technology that is effective in field conditions.

The hidden half of plant biology has been an enduring interest throughout Malcolm’s research career. His team has characterised many of the regulatory signals, genes and mechanisms that control root growth, development and adaptations to their soil environment. Highlights include elucidating how roots preferentially branch towards water availability using a SUMO-dependent mechanism termed hydropatterning with colleagues at Durham (Orosa-Puente et al, 2018, Science). His role during the SUMOcode project focuses on co-leading efforts to create a SUMO cell atlas, where every component of the SUMO machinery (and selected targets) are localised within individual root tissues, to reveal their roles during plant responses to environmental stresses.

Andy is Professor of bioinformatics at Liverpool, with particular interest in the development of new approaches and software for interpreting omics data. In the area of proteomics, the group has built several packages for proteomics data analysis, mostly released as open source and one sold commercially. We also have an interest in mechanisms for analysis and integration of multi-omics data (genomics, proteomics and metabolomics) – in particularly the role and function post-translational modifications (PTMs) in cell signalling. In plant sciences, we are developing approaches for integrating and analysing large-scale publicly available data on crops, particularly rice – including the use of proteogenomics, analysis of PTMs, and performing genome annotation. The team increasingly employs data science and machine learning for analysis of data from biological systems including humans/animals, eukaryotic pathogens and plants. The SUMOCode project sits at the intersection of these areas, with Andy taking the lead role for data analysis and multi-omic integration, particularly using time course modelling for predicting causal associations.

Kathryn is fascinated by the subcellular spatial arrangement of the proteome. She and her co-workers have focussed for many years on the development of technologies that allow mapping of proteome to multiple subcellular niches on a systems wide scale; methods that she pioneered in Arabidopsis using proteomics approaches. More recently, her research programme has probed the impact of structure, post translational modifications and interaction of proteins with other biomolecules, e.g. RNA on the location of the proteome. She hopes to understand why proteins reside at multiple locations and context specific moonlighting properties of the proteome. Her role in the SUMOcode project is to apply these techniques to determine the location and interactions of SUMO machinery and its targets, its oxidation status and how these change upon environmental stresses. Her group will also map cell specific SUMO targets using quantitative mass spectrometry approaches.

Professor Salt’s research is strongly interdisciplinary, coupling ecological and evolutionary biology, population and landscape genomics and functional genomics with bioinformatics. He focuses on uncovering the molecular mechanisms controlling the mineral nutrient and trace elements content (ionome) of plants, and understanding how genetic variation in these mechanisms is selected to allow plants to adapt to their local native soil conditions. Role in project: Professor Salt’s role in SUMOcode is the assessment of the impact of SUMOcode Hubs genes on mineral nutrient and trace element homeostasis. As well as the use of the 1001 Arabidopsis thaliana accessions to mine natural variation in SUMOcode Hub genes to better understand their role in evolved adaptive responses to the environment.

Leah Band is a mathematician whose research focuses on modelling plant growth and development. She is an Associate Professor at the University of Nottingham, jointly appointed between the School of Mathematical Sciences and School of Biosciences. Much of Leah’s research focusses on developing models to investigate how the dynamics of networks, both within and between cells, create the developmental patterns that underpin organ phenotypes. In the SUMO grant, she will contribute to the data analysis, using her expertise in modelling and parameterising biological networks to investigate how the interaction networks underlying SUMOlaytion affect the dynamics of stress responses.

I did my PhD studying the crosstalk between environment and hormone signalling in regulating plant growth. Then, moved to UC Davis (CA-USA) to learn about how transcriptional networks and chromatin regulation guide root cellular decisions. The main focus of my lab research is to understand how environmental signals guide cellular decisions by modulating chromatin and protein function. My role in the SUMOcode project is to evaluate the SUMOsystem behaviour at spatial and temporal resolution and its impact in guiding plant adaptation.

Anthony’s research focuses on the regulatory mechanisms controlling root patterning. This work centres around the two hormones auxin and cytokinin. Although his group use interdisciplinary approaches towards investigating the molecular mechanisms underpinning patterning, he has a particular interest in imaging using both confocal and light sheet microscopy. His role within this project is to support the construction of the SUMO cell atlas and is especially excited about imaging changes in gene expression following external stimuli.

Rahul is a BBSRC Discovery Fellow and a member of Future Food Beacon of Excellence at the University of Nottingham. His lab research focuses on deciphering molecular mechanisms underlying root adaptive traits. His group uses bioinformatics and functional genomics approaches for studying genetic diversity in mainstream as well as under-utilised crops. His role in the SUMOcode project is to support the analysis of generated transcriptome datasets and explore the variation of SUMO machinery and downstream pathways in different crop species.

Alistair is Professor of Genomics and Director of the Centre of Genomics Research (CGR) at University of Liverpool. Alistair’s group have publications include two Nature, two Science, four PNAS, Nucleic Acids Research, Genome Research and Genome Biology papers. He is the lead in single cell genomics for the CGR, funded by BBSRC ALERT and active in EU MC training network to promote single cell genomics. His group has published papers using single cell genomics to study termite symbiosis (PNAS), bringing valuable experience to SUMOcode in the experimental design and computational analysis for scRNA-Seq.

Diarmuid is a recently appointed Tenure-Track Fellow at University of Liverpool, and will start a BBSRC David Phillips Fellow in 2020 to investigate the molecular mechanisms underlying floral organ photosynthesis in Arabidopsis and several other plant species using, among other techniques, single-cell sequencing. DOM has published 16 articles in journals such as PNAS, Development, Genome Biology, and The Plant Cell. He has expertise in functional genomics, CRISPR-Cas9 gene editing, plant development, confocal microscopy and molecular genetics derived from his experiences at Trinity College Dublin and as a Humboldt Postdoctoral Fellow at The Max Planck Institute for Plant Breeding Research. Diarmuid will thus be involved with experimental design and optimisation, as well as gaining exposure in methods for PTM analysis and signalling, with potential for cross-fertilisation of ideas into his fellowship.

Jason is a post-doctoral researcher in the SUMOcode team based at the University of Nottingham. During his PhD he worked on the deSUMOylating protease OTS1 and its role in root branching. In this work he showed how crucial deSUMOylation of ARF7 is for initiation of branching towards available water termed lateral root hydropatterning. Furthermore, he demonstrated how this adaptive root response is regulated on a tissue and cellular level using Light Sheet Fluorescence Microscopy. He is very keen to delve more into the regulation of the OTS class of proteases and other components of the SUMO machinery using Light Sheet and other imaging approaches. This in order to gain further understanding of how SUMOylation controls the stress response in plants and which players are most important. In the future this knowledge can be used to identify key hubs in gene networks to improve crop resilience to a variety of stresses.

Sumesh’s research is aimed at understanding stress response mechanism in plants. Initially, he focussed on biotic stress resistance, wherein he worked on RNAi mediated resistance against Tomato yellow leaf curl virus (TYLCV) in tomato and cry protein mediated resistance against Helicoverpa armigera. Later, through his PhD study, he identified cassava proteins that interacts with Cassava brown streak virus (CBSV), leading to a better understanding of the overall disease development process. He identified a major role of ubiquitylation in plant viral disease. Currently, in this project, he plans to unravel the mystery of another class of post translational modification system ‘the SUMO system’ determining their role in plant development and plant stress response processes.

Nicola is a BBSRC postdoctoral Research Fellow working in the lab of Malcolm Bennett. The main focus of her research is to address how SUMO-mediated environmental responses create plasticity within root systems. It is known that roots have the ability to distinguish between wet and dry micro environments in the soil and adapt the positioning of lateral roots accordingly. This novel adaptive response is referred to as hydropatterning and was the basis behind her PhD thesis – ‘dissecting the molecular mechanism regulating lateral root hydropatterning’. The work of the team uncovered that this mechanism, for controlling root branching, involves the posttranslational modification of the auxin response factor ARF7 (Orosa-Puente et al., 2018). Her goal and role in the SUMOcode project is to go beyond ARF7 and unravel the SUMO mediated signal transduction pathway that will help to understand a major regulator of plant-environmental responses.

Poonam is an EMBO Long-term/ MSCA post-doctoral fellow with Prof. Malcolm Bennett at University of Nottingham. Her project focusses on studying root branching adaptations in response to heterogenous distribution of soil moisture. She is specifically interested in uncovering molecular mechanisms behind a novel root adaptive response termed ‘Xero-branching’ (Orman-Ligeza et al., 2018, Current Biology). Xero-branching is characterized by complete suppression of root branching in an area of low water availability in soil (e.g. air-filled gap). Her goal is to discover the possible roles of SUMOylation driven ABA and auxin signalling in regulating Xero-branching. Her role in the SUMOcode project is to characterize functions of different component of SUMO machinery during transient moisture stress.

Dipan is a post-doctoral researcher in the SUMOcode team based at the university of Durham. During his PhD from Bose Institute, India, he worked on the characterization of the dynamic changes in the chromatin structure of a stress responsive transcription factor, OsDREB1b implicated in maintenance of phenotypic plasticity in plants during the onslaught of abiotic stresses. Furthermore, he demonstrated that the dynamics of the mutually antagonistic Polycomb and Trithorax group of proteins play a crucial in maintaining the epigenetic state of OsDREB1b locus, where modulations of the DNA binding properties of the Trithorax group protein ULTRAPETALA1 due to changes in the redox status of the of the environment govern the expression state of OsDREB1b. He is interested to understand how SUMO can alter the functions of transcription factors and chromatin landscapes of target genes to modulate the phenotypic plasticity of plants in response to stress. In the future this knowledge can be employed in building an epigenomic atlas of SUMO which in turn can be manipulated to improve crop resilience towards both abiotic and biotic stresses.