Exploring the genetics underlying the Zn deficiency response in Arabidopsis thaliana

Abstract

Zn is an essential element for life and the second most abundant transition element in all organisms. Zn deficiency is one of most widespread micronutrient deficiencies in soils and plants need to cope with it. Plants are able to sense the shortage of Zn supply and adjust their Zn homeostasis accordingly. In this thesis, I explored the genetic architecture of the Zn deficiency response of Arabidopsis thaliana. I initiated functional analyses on some of the Zn transporter genes long known to be transcriptionally induced by Zn deficiency, but so far not investigated in much detail. Soon after the exposure to Zn deficiency the expression of these transporters is first induced in roots and later in shoots. Each Zn transporter gene is expressed in one, or more, specific root cell layer(s), which location may differ, depending on the root part. These transporters showed partial functional redundancy among them, which makes it difficult, if not impossible, to detect particular Zn deficiency phenotypes in single Zn transporter mutants. Considering that the effect of mutations on Zn transporter genes is difficult to detect, the Zn deficiency response can be studied from the perspective of their regulatory components. In the search of these regulators I found that the disruption of the N-ALPHA-TERMINAL ACETYLTRANSFERASE 25 (NAA25) gene, involved in N-terminal-acetylation of proteins, causes a strong Fe deficiency sensitivity and a slightly, but consistently, higher expression of several Zn deficiency responsive genes upon Zn sufficiency, when compared to wild-type plants. The causes for the unusual expression pattern of these genes still remain unknown. One hypothesis I postulate is that the lack of N-terminal acetylation of the Zn deficiency regulators bZIP19 and bZIP23, which are possible targets N-terminal acetylation, alters their regulatory activity. To identify more unconventional genetic players underlying the Zn deficiency response, that is not the known suspects involved in Zn homeostasis, such as the transporter genes, the bZIP19/23 transcription factors or the genes involved in Zn chelation, I investigated the natural variation for the Arabidopsis ionome of plants grown under Zn deficiency, in a genome wide association approach. The loss of function of seven genes, identified in this approach, each causes an increase in ionome profile changes due to Zn deficiency, some of the element concentrations significantly affected by the loss of function of these genes are those for Fe, Mn and Cu. The identified genes are involved in various, diverse, functions such as microtubule organization during cell division, defence against pathogens, control of the circadian clock, Fe storage and phosphorylation of carbohydrates. Thus, their role in Zn deficiency response can be direct or mediated. The genome wide association study also identified a cluster of five tandemly arrayed genes, encoding for HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEINS (HIPPs). Functional analyses of these HIPPs suggest they function as negative plant-growth regulators induced by Zn and Fe deficiency. Single hipp mutant lines are tolerant to Zn and especially Fe deficiency, while constitutive overexpression of HIPP10 reduces plant size. Yeast 2-hybrid analysis identified several transcription factors to interact with one or more HIPPs, suggesting these HIPPs to be part of a regulatory network controlling plant growth in response to adverse Zn and Fe supply. In conclusion, this thesis contributes to our understanding of the complexity of the Arabidopsis Zn deficiency response, with analysis of obvious and much less obvious genetic factors contributing to the Zn deficiency response. While again a small part of the puzzle is completed, several new leads are uncovered in this thesis, which would be of great interest to follow up on. Such investigations are likely to bring us one step further in improving the Zn content of plant products and the Zn deficiency tolerance of crops.