Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

Tattym E Shaiken; Sandra L Grimm; Mohamad Siam; Amanda Williams; Abdol-Hossein Rezaeian; Daniel Kraushaar; Emily Ricco; Matthew J Robertson; Cristian Coarfa; Antrix Jain; Anna Malovannaya; Fabio Stossi; Antone R Opekun; Alyssa P Price; Julien Dubrulle

doi:10.1016/j.isci.2023.105965

Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

iScience. 2023 Jan 13;26(2):105965. doi: 10.1016/j.isci.2023.105965. eCollection 2023 Feb 17.

Authors

Tattym E Shaiken^{1

2}, Sandra L Grimm³, Mohamad Siam^{1

2}, Amanda Williams^{1

2}, Abdol-Hossein Rezaeian^{2

4}, Daniel Kraushaar³, Emily Ricco³, Matthew J Robertson³, Cristian Coarfa³, Antrix Jain³, Anna Malovannaya³, Fabio Stossi^{3

5}, Antone R Opekun^{1

6}, Alyssa P Price¹, Julien Dubrulle³

Affiliations

¹ Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran's Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA.
² PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA.
³ Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA.
⁴ Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA.
⁵ Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
⁶ Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.

Abstract

Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.

Keywords: Cell biology; Molecular biology; Proteomics; Transcriptomics.

Abstract

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