INTRODUCTION
The chloroplast is a complex cellular organelle that not only performs photosynthesis but also synthesizes various macromolecules and metabolites including fatty acids, vitamins, tetrapyrroles, and amino acids required for plant growth (Allen, Paula, Puthiyaveetil, & Nield, 2011; Jarvis & Lopez-Juez, 2014). Chloroplasts contain their own DNA and protein-synthesizing apparatus. Many key components of the photosynthetic machinery are encoded by the chloroplast genome (Waters & Langdale, 2009). Mitochondria, which are present in all eukaryotes, are the site of cellular respiration that provides energy in the form of ATP via oxidative phosphorylation for driving cellular metabolism. Endo-symbiotic evolution within higher plants resulted in the emergence of semi-autonomous organelles such as chloroplasts and mitochondria (Rigas, Daras, Tsitsekian, Alatzas, & Hatzopoulos, 2014). Most mitochondrial and chloroplast proteins are encoded by the nuclear genome, expressed in the cytosol, and then imported into the organelles (Yusuke et al., 2014). Although the nucleus regulates the development and function of organelles, signals are also sent to the nucleus by these organelles to deliver information regarding their growth and developmental status to adjust the expression of nuclear genes (Nott, Jung, Koussevitzky, & Chory, 2006). For example, COE1 andCOE2 , which play a role in plastid retrograde signaling, have a significant impact on chloroplast biogenesis and plant growth (Sun, Xu, Liu, Kleine, & Leister, 2016; Wu et al., 2022).
Retrograde signaling modulates nuclear gene expression in response to changes in organellar status. Mitochondria and chloroplasts, the two energy-converting organelles of plants, are closely coordinated to balance their activity (Wang et al., 2020). Likewise, anterograde signaling pathways control the expression of nuclear genes encoding factors involved in plastid gene expression and tetrapyrrole biosynthesis (Woodson & Chory, 2008). Plastids produce retrograde signals to alter the expression of nuclear genes in response to stress-related damage (Inaba, Yazu, Ito-Inaba, Kakizaki, & Nakayama, 2011). Developing chloroplasts in Arabidopsis thaliana are vulnerable to photo-oxidative damage because they lack protective carotenoids. This type of damage perturbs the tetrapyrrole biosynthetic pathway resulting in the accumulation of several tetrapyrrole intermediates and the down-regulation of PhANGs (Strand, Asami, Alonso, Ecker, & Chory, 2003). Various genome-uncoupled(gun ) mutants in which this type of retrograde signaling is impaired (e.g., gun1 – gun6 ) have been identified and characterized in previous studies (Koussevitzky, 2007; Larkin, Alonso, Ecker, & Chory, 2003; Mochizuki, Brusslan, Larkin, Nagatani, & Chory, 2001; Strand et al., 2003; Susek, Ausubel, & Chory, 1993; Woodson, Perez-Ruiz, & Chory, 2011).
In plants, mitochondrial retrograde signaling is associated with reactive oxygen species (ROS) signaling, pathogen sensing, and programmed cell death (Rhoads & Subbaiah, 2007; Woodson & Chory, 2008). Some types of cytoplasmic male sterility in flowering plants are induced by retrograde signaling in response to mitochondrial dysfunction (Sota & Kinya, 2008). Calcium ion signaling, protein kinases, nuclear TFs, and rare protein subunits have been shown to be involved in the mitochondrial retrograde signaling pathway (Guha & Avadhani, 2013; Guha, Srinivasan, Koenigstein, Zaidi, & Avadhani, 2016; Thierry, Sébastien, & Patricia, 2015).
Chloroplasts and mitochondria are metabolically interdependent in the photosynthetic cells of plants (Raghavendra & Padmasree, 2003). Carbon dioxide (CO2) and ATP produced by the mitochondria are used during photosynthesis, and the photosynthetic byproducts oxygen (O2) and malate are used by the mitochondria. Mitochondria also consume the redox products of chloroplasts and protect them from damage caused by over-reduction of the photosynthetic electron transport chain and photoinhibition (Raghavendra & Padmasree, 2003). During photorespiration exchange of serine and glycine between mitochondria and chloroplasts is mediated by peroxidases (Peter et al., 2004).
In plant cells, ATP synthases are present in chloroplasts and mitochondria. The mitochondrial ATP synthase, also known as F1Fo-ATP synthase, catalyzes oxidative phosphorylation and uses the transmembrane proton gradient to synthesize ATP (Stock, Leslie, & Walker, 1999). Mitochondrial ATP synthase consists of two separate parts: F1 and Fo. The F1 portion protrudes into the mitochondrial matrix and consists of the a, b, g and d -subunits. The β -subunit carries the catalytic site for ATP synthesis, and catalysis occurs through highly coordinated conformational changes in the α andβ -subunits (Xu, Pagadala, & Mueller, 2015). Fo acts as a turbine driven by proton flow and is inserted in the inner membrane and linked to the F1 rotor.
The C-terminal domain of the β -subunit consists of a highly conserved helix-turn-helix motif termed “DELSEED-loop,” likely to be involved in the coupling between catalysis and rotation (Mnatsakanyan, Krishnakumar, Suzuki, & Weber, 2009). Loss of the 10 residues of the DELSEED-loop abolishes ATP synthesis (Mnatsakanyan, Kemboi, Salas, & Weber, 2011).
Low levels of ATP are sensed by SnRK1 which phosphorylates the SOG1 protein, thereby increasing the expression of cell cycle-related genes (cyclin-dependent protein kinase 3 ;2, CYCA3 ;2 orcyclin D-type protein 3;3 , CYCD3;3 ) to inhibit plant cell growth (Hamasaki et al., 2019).
Here, we studied a mutant affected in AT5G08670 encoding the mitochondrial ATP synthaseβ- subunit which leads to a decrease in ATP synthase level and activity. Transcriptome analysis revealed that the transcriptome profile of this mutant is significantly altered compared to the wild type. The expression of chloroplast and mitochondrial retrograde signaling-related genes and some TFs are affected in the mutant treated with LIN, an inhibitor of chloroplast protein synthesis. These results indicate that mitochondrial ATP levels affect plastid retrograde signaling.