Professor Daniel Gibbs BSc, MSc, PhD

Professor Daniel Gibbs

School of Biosciences
Professorial Fellow

Contact details

Telephone
+44 (0) 121 414 5309
Email
d.gibbs@bham.ac.uk
Twitter
@DJ_Gibbs
View my research portal
Address
S224, School of Biosciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Prof Gibbs' group studies how plants use targeted protein degradation as a mechanism for sensing and transducing signals and regulating cellular processes, with a particular focus on the N-degron pathway of the ubiquitin proteasome system.  The group uses a range of genetic, cell biology and biochemical approaches to uncover new functions for protein degradation in the control of growth, development and stress responsiveness. We are focussed on uncovering the fundamental processes underpinning plant biology, but also aim to identify new targets for improving key traits in important crop species.  Current projects - funded by the ERC and BBSRC - are investigating the connection between protein translation and degradation, and exploring how proteolytic control of chromatin modifying proteins regulates the epigenome in response to the environment.

Qualifications

 

  • 2004 - BSc Biological Sciences (Genetics), University of Birmingham
  • 2005 – MSc Applied Genetics, University of Birmingham
  • 2009 – PhD Plant molecular biology, University of Birmingham

Biography

After completing his undergraduate and master’s studies at the University of Birmingham, Daniel stayed on to complete a PhD with Dr Juliet Coates, where he investigated the proteolytic control of key regulators of root branching in Arabidopsis. In 2009 he moved to the lab of Prof. Michael Holdsworth at the University of Nottingham, where he studied the role of the N-end rule pathway of protein degradation during plant development. This work led to the discovery of the importance of this pathway for the perception of oxygen in plants. In 2012 he was awarded and independent Nottingham Advanced Research Fellowship to develop his research independence, and in October 2013 he returned to the University of Birmingham to establish his own research group.

Teaching

Dr Gibbs teaches and assesses on second year (BIO237, BIO268) and third year (BIO398) courses, and is also an undergraduate tutor. He lectures on plant development and plant-environment interactions, with a particular focus on the molecular mechanisms underpinning plant growth and stress responses, as well as how basic research can be used for crop improvement through traditional breeding and genetic engineering approaches.   

He also supervises final year undergraduate project students as well as MSci, MSc and MRes students in his lab.  

Research

Research in Dr Gibbs' lab utilises molecular, genetic and biochemical approaches to investigate how plants use targeted protein degradation as a mechanism for sensing and responding to diverse developmental and environmental signals.  The general aim of our work is to increase our understanding of how plants develop and respond to the environment, and to identify promising targets that can be manipulated in agriculturally important crops to improve growth, productivity and stress tolerance.

Proteins are major functional components of cells, and the regulation of their turnover is essential for controlling cellular responses and developmental outputs.  In plants, targeted proteolysis has important roles in sensing and coordinating responses to internal developmental cues (e.g. phytohormones, such as auxin) and environmental signals (e.g. oxygen availability).  The "N-end rule pathway" is an ancient and highly evolutionarily conserved proteolytic system that targets proteins for destruction based on the nature of their N-terminus (the beginning of the protein). 

In previous work carried out in the lab of Prof. Michael Holdsworth (University of Nottingham), plant-specific ERFVII transcription factors were identified as the first physiological targets of the N-end rule pathway in plants (Gibbs et al. 2011 Nature). They were shown to mediate plant perception and response to low oxygen stress (hypoxia), a situation that frequently occurs during (Gibbs et al. 2011 Nature). This is the first example of a direct molecular mechanism for oxygen sensing in plants, and represents a major breakthrough for the future development of flood-tolerant crops, a key focus for food security.  The same pathway was also shown to mediate perception and transduction of nitric oxide (NO), an important developmental signaling molecule in plants (Gibbs et al., 2014 Molecular Cell). This highlights the importance of N-end rule-mediated protein degradation in plants, and our ongoing studies suggest that the N-end rule plays a key role in a wide range of other developmental and physiological processes.

Current research is focused on characterizing novel ‘branches’ and protein substrates of the N-end rule pathway in Arabidopsis, with a particular focus on linking the control of protein stability to agriculturally important developmental processes and abiotic stress responses. This includes analysing the relationship between N-terminal protein acetylation and turnover of proteins, as well as characterising a role for the N-end rule in regulating the epigenome through contolling the stability of a key chromatin modifying complex. We are especially keen on linking the control of protein stability via this pathway to agriculturally important developmental processes and abiotic stress responses.

Other activities

  • Recipient of the 2019 Society of Experimental Biology (SEB) Presidet’d Medal (Plant Section)

  • Dan is currently a member of the GARNet advisory committee.  GARNet is the BBSRC-funded network for UK plant science, and interacts with the plant science community through the support of grant applications, organisation of meetings/workshops, responding to calls for evidence as well as keeping the community informed about relevant new developments. For more info see: https://www.garnetcommunity.org.uk/

  • Dan is also the Gatsby mentor at Birmingham, responsible for coordinating undergraduate applications to the annual Gatsby plant science summer school and summer research studentships, as well as acting as a general link between the university and Gatsby. For more info see: http://www.gatsby.org.uk/plant-science/about
  • Member of the International Society of Plant Anaerobiosis (ISPA)
  • Recipient of the 2013 ISPA “Outstanding Scientist” award, presented at the 11th international ISPA conference, held at the International Rice Research Institute (IRRI), Philippines.

Publications

Please see Dr Gibbs’ lab website and Google Scholar profile

Holdsworth MJ and Gibbs DJ (2020) Comparative Biology of Oxygen Sensing in Plants and Animals. Current Biology. doi.org/10.1016/j.cub.2020.03.021

Labandera AM, Tedds H, Bailey M, Sprigg C, Etherington R, Akintewe O, Kalleechurn G, Holdsworth MJ and Gibbs DJ (2020) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. New Phytologist. doi.org/10.1111/nph.16477

Gibbs DJ and Holdsworth MJ (2019) Every Breath You Take: New Insights into Plant and Animal Oxygen Sensing. Cell. doi.org/10.1016/j.cell.2019.10.043

Hartman S, Liu Z. van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van DongenN, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou F, Hebelstrup K, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ (2019) Ethylene-mediated Nitric Oxide depletion pre-adapts plants to hypoxia stress. Nature Communications. 10, Article number: 4020 (2019)

Lin CC, Chao YT, Chen WC, Ho HY, Chou MY, Li YR, Wu YL, Yang HA, Hsieh H, Lin CS, Wu FH, Chou SJ, Jen HC, Huang YH, Irene D, Wu WJ, Wu JL, Gibbs DJ, Ho MC, Shih MC (2019) Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. PNAS (USA). doi: 10.1073/pnas.1818507116

Gibbs DJ*, Tedds HM, Labandera A-M, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ* (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm Polycomb Repressive Complex 2 subunit VERNALIZATION 2. Nature Communications. 9:5438 DOI:10.1038/s41467-018-07875-7 *Corresponding authors

Zhang H, Gannon L, Jones PD, Rundle CA, Hassall KL, Gibbs DJ, Holdsworth MJ, Theodoulou FL (2018) Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedlings establishment.  Scientific Reports. 8(1):15192

 

Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K and Holdsworth MJ (2018) Distinct branches of the N‐end rule pathway modulate the plant immune response. New Phytologist: DOI:10.1111/nph.15387

Meitha K, Agudelo-Romero P, Signorelli S, Gibbs DJ, Considine JA, Foyer CH, Considine MJ (2018) Developmental control of hypoxia during bud burst in grapevine. Plant, Cell and Environment. doi: 10.1111/pce.13141

Dissmeyer N, Graciet E, Holdsworth MJ, Gibbs DJ (2018) N-term 2017: Proteostasis via the N-terminus.  Trends in Biochemical Sciences doi.org/10.1016/j.tibs.2017.11.006

Zhang H, Gannon L, Hassall, KL, Deery M., Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. (2017) N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytologist DOI: 10.1111/nph.14909

Considine MJ, Diaz-Vivancoz P, Kerchev P, Signorelli S, Agudelo-Romero P, Gibbs DJ, Foyer CH (2017) Learning to breathe: Developmental Phase transitions in oxygen status. Trends in Plant science DOI: http://dx.doi.org/10.1016/j.tplants.2016.11.013

Gibbs DJ, Bailey M, Tedds HM, Holdsworth MJ (2016) From start to finish: amino-terminal protein modifications as degradation signals in plants. New Phytologist.DOI: 10.1111/nph.14105

Moody LA, Saidi Y, Gibbs DJ, Choudhary A, Holloway D, Vesty EF, Bansal KK, Bradshaw SJ, Coates JC (2016) An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid. New Phytologist.DOI:10.1111/nph.13938

Gibbs DJ (2015) Emerging functions for N-terminal protein acetylation in plants. Trends in Plant Science.DOI:  http://dx.doi.org/10.1016/j.tplants.2015.08.008

Abbas M, Berckhan S, Rooney DJ, Gibbs DJ, Vicente Conde J, Sousa Correia C, Bassel GW, Marín-de la Rosa N, León J, Alabadí D, Blázquez MA and Holdsworth MJ (2015) Oxygen sensing coordinates photomorphogenesis to facilitate seedling survival. Current Biology. DOI: http://dx.doi.org/10.1016/j.cub.2015.03.060  

Gibbs DJ*, Vicente Conde J, Berckhan S, Mendiondo GM, Prasad G and Holdsworth MJ* (2015) Group VII Ethylene Response Factors coordinate oxygen and nitric oxide signal transduction and stress responses in plants. Plant Physiology. DOI:10.1104/pp.15.00338 *corresponding authors 

Mendiondo G, Gibbs DJ, Szurman-Zubrzycka M, Korn A, Marquez J, Szarejko I, Maluszynski M, King J, Axcell B, Smart K, Corbineau F, Holdsworth MJ (2015) Enhanced waterlogging tolerance in barley by manipulation of expression of the N-end rule pathway E3 ligase PROTEOLYSIS6. Plant Biotechnology Journal. DOI: 10.1111/pbi.12334

Marín-de la Rosa N, Sotillo B, Miskolczi P, Gibbs DJ, Vicente-Condo J, Carbonero P, Oñate-Sánchez  L, Holdsworth MJ, Bhalerao R, Alabadí D, Blázquez MA (2014) Large-scale identification of gibberellin-related transcription factors defines Group VII ERFs as functional DELLA partners. Plant Physiology. DOI:10.1104/pp.114.244723

Gibbs DJ and Coates JC (2014) AtMYB93 is an endodermis-specific transcriptional regulator of lateral root development in Arabidopsis. Plant Signalling and Behaviour. DOI:10.4161/psb.29808 

Gibbs DJ*, Bacardit J, Bachmair A, Holdsworth MJ* (2014) The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions. Trends in Cell Biology. http://dx.doi.org/10.1016/j.tcb.2014.05.001. *co-corresponding author

Gibbs DJ, Isa NM, Movahedi M, Lozano-Juste J, Mendiondo GM, Berckhan S, Marín-de la Rosa N, Vicente Conde J, Sousa Correia C, Pearce, SP, Bassel GW, Hamali B, Talloji P, Tomé DFA, Coego A, Beynon J, Alabadí D, Bachmair A, León J, Gray JE, Theodoulou FL, Holdsworth MJ (2014) Nitric oxide sensing in plants is mediated by proteolytic control of Group VII ERF transcription factors. Molecular Cell, 10.1016/j.molcel.2013.12.020

Gibbs DJ, Voss U, Harding SA, Fannon J, Moody LA, Yamada E, Swarup K, Nibau C, Bassel GW, Choudhary A, Lavenus J, Bradshaw SJ, Stekel DJ, Bennett MJ, Coates JC (2014) AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. New Phytologist. DOI: 10.1111/nph.12879.

Bassel GW, Stamm P, Mosca G, Barbier de Reuille P, Gibbs DJ, Winter RM, Janka A, Holdsworth MJ, Smith RS (2014)Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1404616111

Bailey-Serres J, Fukao T, Gibbs DJ, Holdsworth MJ, Lee SC, Licausi F, Perata P, Voesenek LA, van Dongen JT (2012) Making sense of low oxygen sensing. Trends Plant Sci.17(3):129-38

Gibbs DJ, Lee SC, Isa NM, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, Holdsworth MJ (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature. 479(7373):415-8.

Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ (2011) Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A. 108(23):9709-14

Nibau C, Gibbs DJ, Bunting KA, Moody LA, Smiles EJ, Tubby JA, Bradshaw SJ, Coates JC (2011) ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability. Plant Mol Biol. 75(1-2):77-92.

Nibau C*, Gibbs DJ*, Coates JC (2008) Branching out in new directions: the control of root architecture by lateral root formation. New Phytol. 179(3):595-614. *Joint first author.

Lin CC, Chao YT, Chen WC, Ho HY, Chou MY, Li YR, Wu YL, Yang HA, Hsieh H, Lin CS, Wu FH, Chou SJ, Jen HC, Huang YH, Irene D, Wu WJ, Wu JL, Gibbs DJ, Ho MC, Shih MC (2019) Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. PNAS (USA). doi: 10.1073/pnas.1818507116

 

Gibbs DJ*, Tedds HM, Labandera A-M, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ* (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm Polycomb Repressive Complex 2 subunit VERNALIZATION 2. Nature Communications. 9:5438 DOI:10.1038/s41467-018-07875-7 *Corresponding authors

 

 

Zhang H, Gannon L, Jones PD, Rundle CA, Hassall KL, Gibbs DJ, Holdsworth MJ, Theodoulou FL (2018) Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedlings establishment.  Scientific Reports. 8(1):15192

 

Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K and Holdsworth MJ (2018) Distinct branches of the N‐end rule pathway modulate the plant immune response. New Phytologist: DOI:10.1111/nph.15387

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