Protein aggregation in plant mitochondria inhibits translation and induces an NAC017-dependent ethylene-associated unfolded protein response

Abstract

Loss of Lon1 in plant mitochondria led to stunted plant growth and accumulation of nuclear-encoded mitochondrial proteins, including Lon1 substrates, while mitochondrial-encoded proteins typically decreased in abundance. Lon1 mutants contained protein aggregates in the mitochondria matrix which were enriched in PPR-containing proteins and ribosomal subunits of the translation apparatus and were slowed in mitochondrial RNA splicing, editing and general translation rate. Transcriptome analysis showed multiple organellar unfolded protein responses involving ethylene biosynthesis were induced by either Lon1 loss, mitochondrial ribosomal protein loss, translation or respiratory inhibition and most were regulated by the mitochondrial retrograde signaling pathway dependent on the transcription factor NAC017. The short hypocotyl in lon1 mutants during skotomorphogenesis was partially rescued by ethylene inhibitors and mutants showed higher ethylene production rates than wildtype. Together this provides multiple steps in the link between loss of Lon1 and its whole plant phenotype.

Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis

“…The atg5 mutant was utilized to investigate whether im-paired autophagy elicits mitochondrial unfolded protein responses, illuminating the potential contribution of diminished autophagic flux in lon1 mutants to unfolded protein responses. We found that the majority of mitochondrial proteases reported that UPR mt [26,27], UPR cp [28], and UPR er [29] target genes are significantly upregulated in lon1-2 and lon1-2atg5-1 (Figure 3B-E, Supplementary Data S2), particularly pronounced in lon1-2 which was reported recently [20]. However, this phenomenon was not observed in atg5-1, demonstrating that the absence of ATG5 does not significantly induce UPR mt , and the downregulation of autophagy levels in the lon1 mutant is not the main cause of inducing UPRs or mitochondrial protease upregulation.…”

“…The downregulation of autophagy flux in lon1 mutants, as discovered in this study, along with the reported upregulation of unfolded protein responses [20], can lead to changes not only in the abundance of specific proteins but also in the relative proportion of cellular compartments in plants. To investigate the possibility of changes in the relative proportion of cellular compartments, we conducted label-free quantitative mass spectrometry using root total proteins (Supplementary Data S1).…”

“…This raises the question of how autophagy is modulated in lon1 mutant lines. Surprisingly, a reanalysis of reported RNA deep sequencing data [20] found that core autophagy genes were significant downregulated in lon1-2 (Figure 1A). ATG2, ATG8s (ATG8A, E, F, G, and H), VTI12, and CFS1 proteins are involved in the delivery/extension/fusion stage of autophagic degradation.…”

“…Only a few genes, such as ACS4 and DTX3, show the same responses in lon1-2 and atg5-1, with over two-fold changes. Furthermore, we extracted mitochondrial proteases and reported unfolded protein responses genes in lon1 [20] to investigate how dysfunctional autophagy contributes to transcripts responses in lon1. The atg5 mutant was utilized to investigate whether im-paired autophagy elicits mitochondrial unfolded protein responses, illuminating the potential contribution of diminished autophagic flux in lon1 mutants to unfolded protein responses.…”

“…Recently, we previously reported that Lon1 dysfunction leads to unfolded protein responses (UPRs) characterized by enhanced ethylene production in Arabidopsis [20]. In this study, we reanalyzed the transcriptome changes in lon1 mutants and discovered a general downregulation of autophagy core proteins, including ATG8 isoforms, at the transcript level.…”