Regulation of gene expression by SnRK1 kinases and miRNAs during the plant stress response

Dissertation presented to obtain the Ph.D degree in Plant Physiology

SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants

Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

SUMOylation represses SnRK1 signaling in Arabidopsis

The SnRK1 protein kinase balances cellular energy levels in accordance with extracellular conditions and is thereby key for plant stress tolerance. In addition, SnRK1 has been implicated in numerous growth and developmental processes from seed filling and maturation to flowering and senescence. Despite its importance, the mechanisms that regulate SnRK1 activity are poorly understood. Here, we demonstrate that the SnRK1 complex is SUMOylated on multiple subunits and identify SIZ1 as the E3 Small Ubiquitin-like Modifier (SUMO) ligase responsible for this modification. We further show that SnRK1 is ubiquitinated in a SIZ1-dependent manner, causing its degradation through the proteasome. In consequence, SnRK1 degradation is deficient in siz1-2 mutants, leading to its accumulation and hyperactivation of SnRK1 signaling. Finally, SnRK1 degradation is strictly dependent on its activity, as inactive SnRK1 variants are aberrantly stable but recover normal degradation when expressed as SUMO mimetics. Altogether, our data suggest that active SnRK1 triggers its own SUMOylation and degradation, establishing a negative feedback loop that attenuates SnRK1 signaling and prevents detrimental hyperactivation of stress responses.

Proteínas que interagem com SnRK1.1 e o seu envolvimento na via de sinalização do ácido abscísico e na resposta ao défice de energia

As plantas são organismos sésseis, incapazes de se movimentar de modo a procurar melhores condições ambientais ou nutricionais. Desenvolveram, assim mecanismos que lhes permitem adaptar-se e sobreviver em condição de stress. O stress parece ser parcialmente descodificado num sinal de défice de energia que desencadeia uma resposta, que envolve a indução da expressão de genes relacionados com processos catabólicos e a repressão de genes envolvidos em processos anabólicos. As proteínas quinases e fosfatases desempenham um papel fundamental na regulação das vias de sinalização de stress e, em particular as quinases da superfamília das SnRK encontram-se envolvidas em vários processos da resposta a stress, principalmente abióticos. Enquanto as SnRK2 e SnRK3 estão sobretudo envolvidas na resposta a ABA e a stress hídrico e salino, as SnRK1 têm sido descritas como reguladores chave da resposta a défice energético. No entanto, um número crescente de estudos tem evidenciado a interligação entre estas duas vias de sinalização. Apesar da importância de SnRK1 na regulação da resposta ao stress e na regulação do crescimento e desenvolvimento em plantas, os mecanismos moleculares envolvidos são ainda pouco conhecidos. Com o objetivo de identificar proteínas que interagem com SnRK1 e que poderão estar envolvidas na sua via de sinalização, foi efetuado um rastreio, pelo método Y2H, utilizando uma biblioteca comercial normalizada construída a partir de mRNA extraído de onze tecidos de Arabidopsis. Foram identificadas 32 proteínas que potencialmente interagem com SnRK1.1, entre as quais MARD1 e NDF4. O estudo destas interações permitiu verificar que MARD1 medeia a interação entre SnRK1.1 e RAPTOR1B, sugerindo que, de forma semelhante à que ocorre em mamíferos, esta interação pode interligar a resposta ao défice energético envolvendo os complexos SnRK1 e TOR. Curiosamente, verificou-se que MARD1 medeia igualmente a interação entre SnRK1.1 e várias das MAPKs de Arabidopsis, o que poderá indicar que estas duas vias de sinalização estão igualmente interligadas. Foi também verificado que, no sistema de Y2H, SnRK1.1 interage, em alguns casos de forma depende de NDF4, com as proteínas DELLA, componentes essências da via de sinalização de giberelinas, o que pode sugerir uma interligação entre estas duas vias de sinalização e, desta forma, explicar parcialmente o papel de SnRK1 no crescimento e desenvolvimento das plantas. Um novo mecanismo de interligação entre as vias de sinalização de ABA e energia é sugerida pelos resultados obtidos em ensaios de Y2H mostrando que SnRK1.1 interage com SnRK2.3 e, pela observação de que em plantas que não expressam SnRK1.1/2, a expressão de genes de resposta a ABA é fortemente comprometida, sugerindo que SnRK1 poderá ativar as SnRK2 e, deste modo, ativar a resposta a ABA. No seu conjunto, estes dados evidenciam o papel de SnRK1 como regulador central da resposta ao défice energético em plantas e sugerem alguns dos mecanismos moleculares que poderão estar envidos, nomeadamente através da interação com várias outras vias de sinalização como o complexo TOR (interagindo com RAPTOR1B), as MAPKs, a via de sinalização de ABA (através da interação com SnRK2) e a via de sinalização de giberelinas (através da interação com proteínas DELLA).

Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation

Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.

Inhibition of SNF1-related protein kinase1 by trehalose 6-phosphate and other metabolites and the interrelation with plant gorwth

All life forms need to monitor carbon and energy availability to survive and this is especially true for plants which must integrate unavoidable environmental conditions with metabolism for cellular homeostasis maintenance. Sugars, in the heart of metabolism, are now recognized as crucial signaling molecules that translate those conditions. One such signal is trehalose 6- phosphate (T6P), a phosphorylated dimer of glucose molecules which levels correlate well with those of sucrose (Suc). Central integrators of stress and energy regulation include the conserved plant Snf1-related kinase1 (SnRK1) which respond to low cellular energy levels by up-regulating energy conserving and catabolic metabolism and down-regulating energy consuming processes. In 2009 T6P was shown to inhibit SnRK1. The in vitro inhibition of SnRK1 by T6P was confirmed in vivo through the observation that genes normally induced by SnRK1 were repressed by T6P and vice-versa, promoting growth processes. These observations provided a model for the regulation of growth by sugar.(...)

ABI1 and PP2CA Phosphatases Are Negative Regulators of Snf1-Related Protein Kinase1 Signaling in Arabidopsis

Plant survival under environmental stress requires the integration of multiple signaling pathways into a coordinated response, but the molecular mechanisms underlying this integration are poorly understood. Stress-derived energy deprivation activates the Snf1-related protein kinases1 (SnRK1s), triggering a vast transcriptional and metabolic reprogramming that restores homeostasis and promotes tolerance to adverse conditions. Here, we show that two clade A type 2C protein phosphatases (PP2Cs), established repressors of the abscisic acid (ABA) hormonal pathway, interact with the SnRK1 catalytic subunit causing its dephosphorylation and inactivation. Accordingly, SnRK1 repression is abrogated in double and quadruple pp2c knockout mutants, provoking, similarly to SnRK1 overexpression, sugar hypersensitivity during early seedling development. Reporter gene assays and SnRK1 target gene expression analyses further demonstrate that PP2C inhibition by ABA results in SnRK1 activation, promoting SnRK1 signaling during stress and once the energy deficit subsides. Consistent with this, SnRK1 and ABA induce largely overlapping transcriptional responses. Hence, the PP2C hub allows the coordinated activation of ABA and energy signaling, strengthening the stress response through the cooperation of two key and complementary pathways.