Amino acid deprivation triggers a novel GCN2-independent response leading to the transcriptional reactivation of non-native DNA sequences

• Published in: PloS one 2018-07, Vol.13 (7), p.e0200783-e0200783
• Main Authors: De Vito, Annarosaria, Lazzaro, Massimo, Palmisano, Ilaria, Cittaro, Davide, Riba, Michela, Lazarevic, Dejan, Bannai, Makoto, Gabellini, Davide, Schiaffino, Maria Vittoria
• Format: Article
• Language: English
• Subjects: Acetylation; Acids; Activation; Aging; Amino acids; Amino Acids, Essential - deficiency; Amino Acids, Essential - metabolism; Analysis; Animals; Bioinformatics; Biology; Biology and Life Sciences; Blotting, Western; Cancer; Cell culture; Cell Line; Cellular signal transduction; Cellular stress response; CRISPR-Cas Systems; Cysteine; Cytomegalovirus; Deoxyribonucleic acid; Deprivation; DNA; DNA methylation; DNA sequencing; Endogenous retroviruses; Epigenetics; Extracellular signal-regulated kinase; Food intake; Gene Editing; Gene expression; Gene sequencing; Genetics; Genomes; Genomics; HeLa Cells; Hep G2 Cells; HIV; Human immunodeficiency virus; Humans; Kinases; Life span; Mammalian cells; Mammals; Methionine; Mice; Nucleotide sequence; Parasitic diseases; Parasitics (electronics); Pharmacology; Protein-Serine-Threonine Kinases - genetics; Protein-Serine-Threonine Kinases - metabolism; Proteins; Real-Time Polymerase Chain Reaction; Research and Analysis Methods; Ribonucleic acid; RNA; RNA editing; RNA Interference; RNA-mediated interference; Signal transduction; Signal Transduction - genetics; Signal Transduction - physiology; Starvation; Stem cells; Stress response; TOR protein; Transcription; Transcription (Genetics); Transcriptional Activation - genetics; Transcriptional Activation - physiology; Transgenes; Tyrosine; Vectors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0200783

In a variety of species, reduced food intake, and in particular protein or amino acid (AA) restriction, extends lifespan and healthspan. However, the underlying epigenetic and/or transcriptional mechanisms are largely unknown, and dissection of specific pathways in cultured cells may contribute to filling this gap. We have previously shown that, in mammalian cells, deprivation of essential AAs (methionine/cysteine or tyrosine) leads to the transcriptional reactivation of integrated silenced transgenes, including plasmid and retroviral vectors and latent HIV-1 provirus, by a process involving epigenetic chromatic remodeling and histone acetylation. Here we show that the deprivation of methionine/cysteine also leads to the transcriptional upregulation of endogenous retroviruses, suggesting that essential AA starvation affects the expression not only of exogenous non-native DNA sequences, but also of endogenous anciently-integrated and silenced parasitic elements of the genome. Moreover, we show that the transgene reactivation response is highly conserved in different mammalian cell types, and it is reproducible with deprivation of most essential AAs. The General Control Non-derepressible 2 (GCN2) kinase and the downstream integrated stress response represent the best candidates mediating this process; however, by pharmacological approaches, RNA interference and genomic editing, we demonstrate that they are not implicated. Instead, the response requires MEK/ERK and/or JNK activity and is reproduced by ribosomal inhibitors, suggesting that it is triggered by a novel nutrient-sensing and signaling pathway, initiated by translational block at the ribosome, and independent of mTOR and GCN2. Overall, these findings point to a general transcriptional response to essential AA deprivation, which affects the expression of non-native genomic sequences, with relevant implications for the epigenetic/transcriptional effects of AA restriction in health and disease.