The life of an mRNA in space and time

Ben-Ari, Ya'ara; Brody, Yehuda; Kinor, Noa; Mor, Amir; Tsukamoto, Tomoko; Spector, David L.; Singer, Robert H.; Shav‐Tal, Yaron

doi:10.1242/jcs.062638

Cited by 119 publications

(114 citation statements)

References 61 publications

Supporting

Mentioning

103

Contrasting

Order By: Relevance

“…Our setup modulates the osmolarity of media flowing over the cells from isosmotic to either hypoosmotic or hyperosmotic conditions and back within seconds (Methods). Regulatory expression of proteins in response to the volume change is minimal at these times (24,25). However, protein folding and protein-protein interactions, which often occur in seconds or less (36), readily respond to induced volume changes at these timescales (9).…”

Section: Resultsmentioning

confidence: 99%

“…Rapid volume changes (approximately 1-100 s) are driven by water influx or efflux, altering the concentration of all molecular species contained within the cellular matrix (19,22,23). At such short times, regulatory actions taken by the cell to cope with the change in volume, such as synthesizing channels, chaperones, and enzymes are scarcely initiated (24,25). Thus, fast volume change affects viscosity (26), crowding (27,28), protein structure (29,30), activity (31), and quinary interactions within the cell purely by physico-chemical means.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Weak protein–protein interactions in live cells are quantified by cell-volume modulation

Sukenik

Ren

Gruebele

2017

Proc. Natl. Acad. Sci. U.S.A.

123

View full text Add to dashboard Cite

Weakly bound protein complexes play a crucial role in metabolic, regulatory, and signaling pathways, due in part to the high tunability of their bound and unbound populations. This tunability makes weak binding (micromolar to millimolar dissociation constants) difficult to quantify under biologically relevant conditions. Here, we use rapid perturbation of cell volume to modulate the concentration of weakly bound protein complexes, allowing us to detect their dissociation constant and stoichiometry directly inside the cell. We control cell volume by modulating media osmotic pressure and observe the resulting complex association and dissociation by FRET microscopy. We quantitatively examine the interaction between GAPDH and PGK, two sequential enzymes in the glycolysis catalytic cycle. GAPDH and PGK have been shown to interact weakly, but the interaction has not been quantified in vivo. A quantitative model fits our experimental results with log K d = −9.7 ± 0.3 and a 2:1 prevalent stoichiometry of the GAPDH:PGK complex. Cellular volume perturbation is a widely applicable tool to detect transient protein interactions and other biomolecular interactions in situ. Our results also suggest that cells could use volume change (e.g., as occurs upon entry to mitosis) to regulate function by altering biomolecular complex concentrations.quinary interactions | protein-protein interactions | cell volume | FRET | live-cell microscopy F rom forming active enzymatic complexes to facilitating signal transduction in regulatory networks, protein interactions are pivotal to cell function. Strong interactions, with dissociation constants (K d ) of nanomolar and lower (1, 2), can be measured accurately both in vitro and in vivo (3, 4). These interactions are ideal in cases where the complex should form with high fidelity and persist. The downside of strong binding is that its regulation in the cellular environment is limited: Once a complex is formed, it seldom dissociates.Another type of protein complexes relies on weak, transient interactions, collectively termed quinary interactions (5-7). Such interactions, with a K d in the micromolar to millimolar range, are emerging as important components of the cell's signaling, regulatory, and stress adaptation mechanisms (6,8,9). Their transient nature is key to their function: Unlike tightly bound complexes, quinary interactions are highly sensitive to variations in their environment and respond rapidly to changes in temperature, pressure, pH, or the local concentration of surrounding molecules. The sensitivity of quinary interactions makes them important in fine-tuning cellular processes. For example, it has been proposed that sequential metabolic enzymes could associate to improve substrate transfer between catalytic enzymes (10), that weak protein association can mediate cytokine release (11), or that phase-separated protein droplets held together by quinary interactions could serve for cellular storage or stress response (12, 13).Despite growing interest, quantification of quinary inte...

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Weak protein–protein interactions in live cells are quantified by cell-volume modulation

Sukenik

Ren

Gruebele

2017

Proc. Natl. Acad. Sci. U.S.A.

123

View full text Add to dashboard Cite

show abstract

“…The ability and mode of motion of RNAs has implications for how they find nuclear targets on chromatin or cellular sub-compartments and how macromolecular complexes are assembled in vivo. Most importantly, the dynamic nature of RNAs is emerging as a means to control physiological cellular responses and pathways [4]. For example, unexpectedly complicated nuclear egress and nuclear import of small RNAs is more common than previously appreciated [5].…”

Section: Rna Physiologymentioning

confidence: 99%

Models of RNA Interaction from Experimental Datasets: Framework of Resilience

Seffens¹

2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

View full text Add to dashboard Cite

Resilience is a network property of systems responding under stress, which for biomedicine correlates to chronic or acute insults. Current need exists for models and algorithms to study whole transcriptome differences between tissues and disease states to understand resilience. Goal of this effort is to interpret cellular transcription in a dynamic system biology framework of RNA molecules forming an information structure with regulatory properties acting on individual transcripts. We develop and evaluate a bioinformatics framework based on information theory that utilizes RNA expression data to create a whole transcriptome model of interaction that could lead to the discovery of new biological control mechanisms. This addresses a fundamental question as to why transcription yields such a small fraction of protein products. We focus on a transformative concept that individual transcripts collectively form an "information cloud" of sequence words, which for some genes may have significant regulatory impact. Extending the concept of cis-and trans-regulation, we propose to search for RNAs that are modulated by interactions with the transcriptome cloud and calling such examples nebula regulation. This framework has implications as a paradigm change for RNA regulation and provides a deeper understanding of nucleotide sequence structure and -omic language meaning.

show abstract

“…In addition, general inhibitors of cellular metabolism surprisingly caused a decreased mobility of mRNP particles, mostly likely explained by overall restructuring of nuclear organization under these conditions, that was restored when energy levels were reset to normal . At least one new system has been recently developed for examining the trafficking of mRNA (and visualizing its protein product) that is certain to shed light on the spatial and temporal kinetics of synthesis, export, and cytoplasmic transport of mRNA to its cellular location where it is ultimately translated into protein (Ben-Ari, et al, 2010). Our capability for RNA imaging is on the verge of complete transformation due to a newly developed tool for tagging and imaging RNAs in living cells (Paige et al, 2011).…”

Section: Transcription and Rna Processingmentioning

confidence: 99%