Stress-granules, P-bodies, and cell aging: A bioinformatics study

• Published in: Biochemical and biophysical research communications Vol. 694; p. 149404
• Main Authors: Mokin, Yakov I, Ilyinsky, Nikolay S, Nesterov, Semen V, Smirnov, Eugene Y, Sergeeva, Olga S, Romanovich, Anna E, Kuznetsova, Irina M, Turoverov, Konstantin K, Uversky, Vladimir N, Fonin, Alexander V
• Format: Journal Article
• Language: English
• Published: United States 29.01.2024
• Subjects: Cellular Senescence; Computational Biology; Humans; Organelles - metabolism; Processing Bodies; Proteome - metabolism; Stress Granules; Membrane-less organelles; DNA-Binding protein; P-bodies; Protein aggregation; Senescence; Intrinsically disordered proteins; RNA-Binding protein; Intrinsically disordered regions; Aging; Liquid-liquid phase separation; Nucleic acids; Stress granules
• ISSN: 0006-291X; 1090-2104; 1090-2104
• DOI: 10.1016/j.bbrc.2023.149404

At the molecular level, aging is often accompanied by dysfunction of stress-induced membrane-less organelles (MLOs) and changes in their physical state (or material properties). In this work, we analyzed the proteins included in the proteome of stress granules (SGs) and P-bodies for their tendency to transform the physical state of these MLOs. Particular attention was paid to the proteins whose gene expression changes during replicative aging. It was shown that the proteome of the studied MLOs consists of intrinsically disordered proteins, 30-40% of which are potentially capable of liquid-liquid phase separation (LLPS). Proteins whose gene expression changes during the transition of human cells to a senescent state make up about 20% of the studied proteomes. There is a statistically significant increase in the number of positively charged proteins in both datasets studied compared to the complete proteomes of these organelles. An increase in the relative content of DNA-, but not RNA-binding proteins, was also found in the SG dataset with senescence-related processes. Among SGs proteins potentially involved in senescent processes, there is an increase in the abundance of potentially amyloidogenic proteins compared to the whole proteome. Proteins common to SGs and P-bodies, potentially involved in processes associated with senescence, form clusters of interacting proteins. The largest cluster is represented by RNA-binding proteins involved in RNA processing and translation regulation. These data indicate that SG proteins, but not proteins of P-bodies, are more likely to transform the physical state of MLOs. Furthermore, these MLOs can participate in processes associated with aging in a coordinated manner.