Unraveling transcriptional and translational control in plant energy homeostasis: a bioinformatic approach

A. Peviani

Research output: ThesisDoctoral thesis 1 (Research UU / Graduation UU)

Abstract

Due to their sessile nature, plants require a tight regulation of energy homeostasis in order to survive and reproduce in changing environmental conditions. Regulation of gene expression is controlled at several levels, from transcription to translation and beyond. Sugars themselves can act directly as signaling molecules, accelerating molecular adaptation processes. Understanding these processes is relevant both for fundamental research in plant biology and for agricultural applications, such as targeted crop improvement programs.
In this thesis, we investigated specific transcriptional and translational regulatory systems in plant energy homeostasis using different bioinformatic approaches. In Chapter 2 and 3, we discuss specific examples of transcriptional regulators whose activity is affected by sugars: ABI4 and the C/S1 bZIP transcription factor network. Both chapters investigate these regulators from an evolutionary and comparative genomics perspective. In Chapter 4, we moved our focus from transcriptional to translational control, also changing our analysis approach from phylogenetics to integrative bioinformatics.
In Chapter 2, we showed that ABI4, well known for its role in seed development and germination, is conserved across land plants predominantly as a single copy gene, which suggests a strictly conserved function. We also discovered a highly conserved ‘ABI4’ motif, which is likely necessary for ABI4 activity.
In Chapter 3, we investigated the evolution and conservation of members of the C and S1 families of bZIP transcription factors. Our results show that the two ortholog groups likely originated from a duplication event in algae, indicating that these genes are much more ancient than previously thought, and could have played a crucial role in the adaptation of plants to new environments. The discovery also provides a plausible scenario for the origin of heterodimerization between C and S1 bZIPs, which we discuss thoroughly. Importantly, the chapter includes experimental work showing the translational repression by sucrose (SIRT) of newly discovered gymnosperm S1 sequences, indicating that this regulatory mechanism emerged early on in the evolution of S1 bZIPs, and is likely conserved in other plant species.
In Chapter 4, we focused exclusively on translational regulation, trying to identify sequence features responsible for the differential translational efficiency of specific subsets of transcripts during sucrose treatment and seed germination. Our results indicate that both general sequence properties and specific mRNA features, such as motifs and structured elements, play a role in translational control; in particular, it appears that a combination of signals rather than a single one is required to achieve condition-dependent changes in translational efficiency.
Overall, our work clarified in detail the evolution of long-known energy-responsive transcriptional regulators which still lacked a phylogenetic description, and revealed precious clues on the much less explored field of translational regulation, providing directions for future studies.
Original languageEnglish
Awarding Institution
  • Utrecht University
Supervisors/Advisors
  • Snel, Berend, Primary supervisor
  • Smeekens, Sjef, Supervisor
  • Hanson, S.J., Co-supervisor
Award date8 Jul 2016
Publisher
Print ISBNs978-90-393-6584-7
Publication statusPublished - 8 Jul 2016

Keywords

  • bZIP
  • SIRT
  • sucrose
  • transcription
  • translation
  • plant
  • phylogenetics
  • evolution
  • bioinformatics

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