MicroProtein formation during the shade avoidance response

Access to light is an important parameter for plant growth. Plants use light in their photosynthesis reaction to produce the energy they need to survive. While some plants have evolved to grow in limited light conditions, others are shade-sensitive and induce rapid elongation growth when shaded. Arabidopsis thaliana is a shade-sensitive species and gene expression studies have shown that hundreds of genes are altered in response to shading, including members of the class II homeodomain leucine zipper (HD-ZIPII) transcription factor family. The aim of this thesis is to better understand the molecular and physiological signaling pathways involved in the shadeinduced elongation growth. To understand the transcriptome changes in more detail we performed high-throughput sequencing of transcript isoforms in white light and shade. These studies identified a transcript isoform in HOMEOBOX ARABIDOPSIS THALIANA4 (HAT4), a member of the HDZIPII family. Interestingly, this shorter transcript isoform is predicted to encode a microProtein. MicroProteins are small, single domain proteins that regulate larger protein complexes by forming non-functional complexes. Cis-microProteins are not encoded as unique genes in the genome but are formed for example with an alternative transcription start site. We named this newly identified cis-microProtein, HOMEOBOX ARABIDOPSIS THALIANA4 LEUCINE ZIPPER (HAT4LZ) and found that it governs the shade response by regulating HAT4, demonstrating the importance of microProteins in shade. We also demonstrated that shade affects tissue patterning in the hypocotyl (the embryonic stem) resulting in an increase of the water-conducting xylem elements. On the molecular level, this response involves the interplay of different types of homeodomain transcription factors. In a third study, we further investigated the transcription factor networks and identified the MAX2 ubiquitin ligase interacting with some of the homeodomain transcription factors. Genetic interaction studies revealed a function for these interactors in shade-induced
growth, but also for other developmental pathways such as leaf development, shoot branching and senescence. Finally, the importance of microProteins in plant development is further exemplified by the identification of the LITTLE NINJA (LNJ) microProtein, which acts as a modulator of jasmonic acid (JA) signaling in mono- and dicotyledonous plants. This latter example highlights the potential for microProteins as tools for crop improvement.