Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability

The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary signifi-cantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete under-standing of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as transla-tion, being more robust than those linked to regula-tion. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression

The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports

Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed

Translation error clusters induced by aminoglycoside antibiotics

Aminoglycoside antibiotics target the ribosome and induce mistranslation, yet which translation errors induce bacterial cell death is unclear. The analysis of cellular proteins by quantitative mass spectrometry shows that bactericidal aminoglycosides induce not only single translation errors, but also clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row. The downstream errors in a cluster are up to 10,000-fold more frequent than the first error and independent of the intracellular aminoglycoside concentration. The prevalence, length, and composition of error clusters depends not only on the misreading propensity of a given aminoglycoside, but also on its ability to inhibit ribosome translocation along the mRNA. Error clusters constitute a distinct class of misreading events in vivo that may provide the predominant source of proteotoxic stress at low aminoglycoside concentration, which is particularly important for the autocatalytic uptake of the drugs

Bioimpedance Spectroscopy Compared to Ultrasound-derived Measures of Quadriceps Muscle Quality

Muscle quality is often measured using ultrasound-derived echo intensity (EI). Recent works have shown tissue frequency-dependent electrical impedance from bioimpedance spectroscopy may be a modality for assessing tissue quality. PURPOSE: The purpose of the project was to examine the association between ultrasound-derived EI of the quadriceps muscles (i.e., vastus lateralis [VL], vastus medialis [VM], vastus intermedius [VI], rectus femoris [RF]) and measures of thigh tissue frequency-dependent electrical impedance (i.e., R0, R1, C, a, fp). METHODS: Twenty-four participants (13 women; mean ± SD; age: 22 ± 4 years; BMI: 25.47 ± 3.26 kg/m2) were recruited. Participants completed one laboratory visit where quadriceps tissue quality was assessed via ultrasound and bioimpedance spectroscopy (BIS). Participants laid supine on a portable exam table to undergo imaging of the dominant leg VL using ultrasound in conjunction with a multi-frequency linear array probe (L4 – 12t – RS, 4.2-13 MHz, 47.1mm field of view). The VL was marked at the proximal and distal musculo-tendon junctions determined via ultrasound and the length was measured with a tape measure. Participants had cross-sectional scans of the VM, VL, VI, and RF at 25, 50, 75% of the length of the VL. Images were analyzed using the polygon tool in ImageJ to trace the muscles and provide EI values. Subcutaneous fat width was measured using the straight-line tool. Echo intensity was calculated using ImageJ gray-scale analysis and histogram function as well as corrected for subcutaneous fat. For statistical analyses, the average corrected EI for each muscle was created across scan sites. For BIS, participants were seated in a chair with Ag/AgCl electrodes placed above the patella and below the hip. Electrodes were placed 6cm apart and the Cole-impedance model was used to represent frequency-dependent thigh tissue data. Signals were analyzed using a custom-written software program. Pearson’s correlation coefficient (r) was used to determined associations between the VL, VM, VI, RF and BIS variables (R0, R1, C, a, fp). An alpha level of p ≤ 0.05 determined statistical significance. RESULTS: The results suggest that VL, VM, VI and RF echo intensity was significantly related to R0 (r = 0.65 – 0.81; p \u3c 0.01). For VI and RF, they were significantly related to a (r = -0.51 – -0.50; p = 0.01), but not for VL or VM (r = -0.39 - -0.22; p \u3e 0.06). Lastly, R1, C, and fp were not significantly correlated to the quadriceps muscles (r = -0.38 – 0.33; p \u3e 0.07). CONCLUSION: Our findings suggest that BIS-derived R0 may be a metric of muscle quality of the quadriceps as it was significantly related to ultrasound-derived measures of echo intensity of the VL, VM, VI, and RF. Further investigation of other muscle groups may be warranted

Multiple Pathways to the Same End: Mechanisms of Myonuclear Apoptosis in Sarcopenia of Aging

Sarcopenia, the age-related decline in muscle mass and function, represents a significant health issue due to the high prevalence of frailty and disability associated with this condition. Nevertheless, the cellular mechanisms responsible for the loss of muscle mass in old age are still largely unknown. An altered regulation of myocyte apoptosis has recently emerged as a possible contributor to the pathogenesis of sarcopenia. Studies in animal models have shown that the severity of skeletal muscle apoptosis increases over the course of aging and correlates with the degree of muscle mass and strength decline. Several apoptotic pathways are operative in aged muscles, with the mitochondria- and TNF-α-mediated pathways likely being the most relevant to sarcopenia. However, despite the growing number of studies on the subject, a definite mechanistic link between myocyte apoptosis and age-related muscle atrophy has not yet been established. Furthermore, the evidence on the role played by apoptosis in human sarcopenia is still sparse. Clearly, further research is required to better define the involvement of myocyte apoptosis in the pathogenesis of muscle loss at advanced age. This knowledge will likely help in the design of more effective therapeutic strategies to preserve muscle mass into old age, thus fostering independence of the elderly population and reducing the socioeconomic burden associated with sarcopenia

An uncharged amine in the transition state of the ribosornal peptidyl transfer reaction.

The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Bronsted coefficient of the a-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution

A LEED structural analysis of the Co(100) surface

The structure of the clean Co(1010) surface has been analysed by LEED. Application of a recently developed computational scheme reveals the prevalence of the termination A in which the two topmost layers exhibit a narrow spacing of 0.62 Å, corresponding to a 12.8(±0.5)% contraction with respect to the bulk value, while the spacing between the second and third layer is slightly expanded by 0.8(±0.2)%

An Uncharged Amine in the Transition State of the Ribosomal Peptidyl Transfer Reaction

The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Brønsted coefficient of the α-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution