Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

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

doi:10.1016/j.isci.2023.105965

Cited by 3 publications

(6 citation statements)

References 102 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The next most abundant groups of proteins were transmembrane proteins and the ER-Golgi proteome, which suggests that membrane-forming structures such as ER, Golgi, and plasma membrane are integral parts of the cytomatrix. This hypothesis is supported by GOBP, KEGG, and Reactome pathway analyses (Shaiken et al, 2023). A nuclear connection to the cytomatrix is indicated by the presence of SUN1/2, emerin, and plectin, along with the nucleoporins.…”

Section: Mass-spectrometry Profile Of the Cytomatrix Proteomementioning

confidence: 76%

“…Applying different salt solutions, the nuclear-associated fraction was separated from the cytosol and nucleus (Shaiken and Opekun, 2014). Further, high-throughput methods such as RNA-seq, Ribo-seq, and mass-spectrometry were used to define the nuclear-associated fraction as an elastic solid phase of the cytoplasmthe cytomatrix (Shaiken et al, 2023).…”

Section: Mass-spectrometry Profile Of the Cytomatrix Proteomementioning

confidence: 99%

“…At least three 10 cm dishes were used for the cytomatrix isolation experiment. The detailed procedure of cell fractionation into the cytosol, cytomatrix and core nucleus is described previously (Shaiken et al, 2023). Briefly, cells were lysed in an appropriate volume (0.1 ml per 100 mm dish) of Buffer A: 40 mM HEPES pH 7.4, 120 mM KCl, 0.5% Glycerol, and 0.5% NP-40 with protease and phosphatase (when necessary) inhibitors and rotated for 30 min at 4°C.…”

Section: Cell Fractionationmentioning

confidence: 99%

“…From the physicochemical standpoint, the cytoplasm is a two-phase system that can be separated into an elastic solid (cytomatrix) and viscous fluid (cytosol). We previously provided evidence of compartmentalization of transcriptome, proteome, metabolome, and protein synthesis within the cytomatrix and cytosol (Shaiken et al, 2023). The cytomatrix and extracellular matrix are interconnected, forming a singular integrated system with the receptors and signaling pathways.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Intracellular Cytomatrix, Immobilized Biocatalysis, Matrix Micromechanics and The Warburg Effect: Entanglement of Two Age-Old Mysteries of the Normal and Malignant Cell

Shaiken

Siam

Sederstrom

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

For decades cancer studies have focused on molecular genetics while the role of the cytoplasm has remained obscure. Separation of the viscous fluid cytosol and elastic-solid cytomatrix has offered an opportunity to solve an age-old mystery in biochemistry, how millions of complex chemical reactions can occur simultaneously within the cell cytoplasm. The cytomatrix contains structural proteins, ribosomes, and metabolome enzymes responsible for unique biosynthetic pathways that involve immobilized biocatalysis. Immobilizing these catalytic complexes overcomes the spatial limitations for biochemical processes and allows integration of the intracellular and extracellular matrices and receptors with nuclear processes. Together, the cytosol and cytomatrix produce an interconnected synergistic network that maintains the operational flexibility of healthy cells as well as the survival of malignant cells. The cytomatrix is also responsible for cellular micromechanics and cytoplasmic motion. The combination of mechanical and biocatalytic processes triggered by extracellular signals and gene mutations in malignant cells requires additional energy. Cancer cells, consequently, utilize aerobic glycolysis, the Warburg effect, to meet the energy demands of the matrix mechanics that arise in response to imbalanced signaling and excessive biocatalytic activity. Clinical cancer is a rare event despite a high frequency of mutations, as clinical cancer is limited by the requirement for alterations that result in a high energy production state. Without these transformations, potential cancers can only survive in the quiescent state or will be eliminated. Survival of cancer cells indicates that the cancer cells were able to synchronize energy output for matrix mechanics supplying sufficient energy for tumor growth. Thus, the Warburg effect connects genetic aberrations and intracellular matrix mechanics with the ability to provide the energy supply required for the unprecedented complexity of tumor growth.

show abstract

Section: Mass-spectrometry Profile Of the Cytomatrix Proteomementioning

confidence: 76%

Section: Mass-spectrometry Profile Of the Cytomatrix Proteomementioning

confidence: 99%

Section: Cell Fractionationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Intracellular Cytomatrix, Immobilized Biocatalysis, Matrix Micromechanics and The Warburg Effect: Entanglement of Two Age-Old Mysteries of the Normal and Malignant Cell

Shaiken

Siam

Sederstrom

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Additionally, what we have learned about the interaction of Not proteins with the ribosome comes from purification of Not4‐associated complexes that uses as a starting material soluble cellular extracts (Buschauer et al, 2020 ). We should also keep in mind that the content of soluble cellular extracts can be variable depending upon which conditions were used to prepare such extracts, for instance which conditions of salt or detergent (Shaiken et al, 2023 ) (Figure 4 ).…”

Section: Translation Elongationmentioning

confidence: 99%

Roles of the CCR4‐Not complex in translation and dynamics of co‐translation events

Collart,

Audebert,

Bushell

2023

WIREs RNA

View full text Add to dashboard Cite

The Ccr4‐Not complex is a global regulator of mRNA metabolism in eukaryotic cells that is most well‐known to repress gene expression. Delivery of the complex to mRNAs through a multitude of distinct mechanisms accelerates their decay, yet Ccr4‐Not also plays an important role in co‐translational processes, such as co‐translational association of proteins and delivery of translating mRNAs to organelles. The recent structure of Not5 interacting with the translated ribosome has brought to light that embedded information within the codon sequence can be monitored by recruitment of the Ccr4‐Not complex to elongating ribosomes. Thereby, the Ccr4‐Not complex is empowered with regulatory decisions determining the fate of proteins being synthesized and their encoding mRNAs. This review will focus on the roles of the complex in translation and dynamics of co‐translation events.This article is categorized under: Translation > Mechanisms Translation > Regulation

show abstract

Understanding the nutritional benefits through plant proteins-probiotics interactions: mechanisms, challenges, and perspectives

Wu,

Kan,

Cui

et al. 2024

Critical Reviews in Food Science and Nutrition

View full text Add to dashboard Cite

Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

Cited by 3 publications

References 102 publications

Intracellular Cytomatrix, Immobilized Biocatalysis, Matrix Micromechanics and The Warburg Effect: Entanglement of Two Age-Old Mysteries of the Normal and Malignant Cell

Intracellular Cytomatrix, Immobilized Biocatalysis, Matrix Micromechanics and The Warburg Effect: Entanglement of Two Age-Old Mysteries of the Normal and Malignant Cell

Roles of the CCR4‐Not complex in translation and dynamics of co‐translation events

Understanding the nutritional benefits through plant proteins-probiotics interactions: mechanisms, challenges, and perspectives

Contact Info

Product

Resources

About