scholarly journals In Vivo Measurements of Protein Synthesis Kinetics using Single-Molecule Tracking of E.Coli tRNAS

2016 ◽  
Vol 110 (3) ◽  
pp. 351a
Author(s):  
Ivan Volkov ◽  
Javier Aguirre ◽  
Martin Lindén ◽  
Johan Elf ◽  
Magnus Johansson
2016 ◽  
Vol 44 (21) ◽  
pp. e160-e160 ◽  
Author(s):  
David A Ball ◽  
Gunjan D Mehta ◽  
Ronit Salomon-Kent ◽  
Davide Mazza ◽  
Tatsuya Morisaki ◽  
...  

Abstract In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12–0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.


2020 ◽  
Vol 118 (3) ◽  
pp. 616a
Author(s):  
Yuan-I Chen ◽  
Yin-Jui Chang ◽  
Trung D. Nguyen ◽  
Cong Liu ◽  
Stephanie Phillion ◽  
...  

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Juan A. Varela ◽  
Julien P. Dupuis ◽  
Laetitia Etchepare ◽  
Agnès Espana ◽  
Laurent Cognet ◽  
...  

2012 ◽  
Vol 367 (1-2) ◽  
pp. 205-213 ◽  
Author(s):  
Paul J. McDermott ◽  
Catalin F. Baicu ◽  
Shaun R. Wahl ◽  
An O. Van Laer ◽  
Michael R. Zile

2009 ◽  
Vol 107 (3) ◽  
pp. 645-654 ◽  
Author(s):  
S. M. Phillips ◽  
E. I. Glover ◽  
M. J. Rennie

Unloading-induced atrophy is a relatively uncomplicated form of muscle loss, dependent almost solely on the loss of mechanical input, whereas in disease states associated with inflammation (cancer cachexia, AIDS, burns, sepsis, and uremia), there is a procatabolic hormonal and cytokine environment. It is therefore predictable that muscle loss mainly due to disuse alone would be governed by mechanisms somewhat differently from those in inflammatory states. We suggest that in vivo measurements made in human subjects using arterial-venous balance, tracer dilution, and tracer incorporation are dynamic and thus robust by comparison with static measurements of mRNA abundance and protein expression and/or phosphorylation in human muscle. In addition, measurements made with cultured cells or in animal models, all of which have often been used to infer alterations of protein turnover, appear to be different from results obtained in immobilized human muscle in vivo. In vivo measurements of human muscle protein turnover in disuse show that the primary variable that changes facilitating the loss of muscle mass is protein synthesis, which is reduced in both the postabsorptive and postprandial states; muscle proteolysis itself appears not to be elevated. The depressed postprandial protein synthetic response (a phenomenon we term “anabolic resistance”) may even be accompanied by a diminished suppression of proteolysis. We therefore propose that most of the loss of muscle mass during disuse atrophy can be accounted for by a depression in the rate of protein synthesis. Thus the normal diurnal fasted-to-fed cycle of protein balance is disrupted and, by default, proteolysis becomes dominant but is not enhanced.


eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Thomas J Etheridge ◽  
Desiree Villahermosa ◽  
Eduard Campillo-Funollet ◽  
Alex David Herbert ◽  
Anja Irmisch ◽  
...  

The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.


2019 ◽  
Vol 116 (3) ◽  
pp. 175a
Author(s):  
Janet Y. Sheung ◽  
Pinghua Ge ◽  
Sung Jun Lim ◽  
Sang Hak Lee ◽  
Andrew Smith ◽  
...  

Author(s):  
Adekunle T. Bademosi ◽  
Elsa Lauwers ◽  
Rumelo Amor ◽  
Patrik Verstreken ◽  
Bruno van Swinderen ◽  
...  

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