Perfecting the Genetic Code with an RNP Complex

In this issue of Structure, Sekine et al. (2006) present a splendid example, using glutamyl-tRNA synthetase crystal structures, of the steps potentially taken in the transition from the RNA world to the theater of proteins

Mistranslation and its control by tRNA synthetases

Aminoacyl tRNA synthetases are ancient proteins that interpret the genetic material in all life forms. They are thought to have appeared during the transition from the RNA world to the theatre of proteins. During translation, they establish the rules of the genetic code, whereby each amino acid is attached to a tRNA that is cognate to the amino acid. Mistranslation occurs when an amino acid is attached to the wrong tRNA and subsequently is misplaced in a nascent protein. Mistranslation can be toxic to bacteria and mammalian cells, and can lead to heritable mutations. The great challenge for nature appears to be serine-for-alanine mistranslation, where even small amounts of this mistranslation cause severe neuropathologies in the mouse. To minimize serine-for-alanine mistranslation, powerful selective pressures developed to prevent mistranslation through a special editing activity imbedded within alanyl-tRNA synthetases (AlaRSs). However, serine-for-alanine mistranslation is so challenging that a separate, genome-encoded fragment of the editing domain of AlaRS is distributed throughout the Tree of Life to redundantly prevent serine-to-alanine mistranslation. Detailed X-ray structural and functional analysis shed light on why serine-for-alanine mistranslation is a universal problem, and on the selective pressures that engendered the appearance of AlaXps at the base of the Tree of Life

Active multi-point microrheology of cytoskeletal networks

Active microrheology is a valuable tool to determine viscoelastic properties of polymer networks. Observing the response of the beads to the excitation of a reference leads to dynamic and morphological information of the material. In this work we present an expansion of the well-known active two-point microrheology. By measuring the response of multiple particles in a viscoelastic medium in response to the excitation of a reference particle, we are able to determine the force propagation in the polymer network. For this purpose a lock-in technique is established that allows for extraction of the periodical motion of embedded beads. To exert a sinusoidal motion onto the reference bead an optical tweezers setup in combination with a microscope is used to investigate the motion of the response beads. From the lock-in data the so called transfer tensor can be calculated, which is a direct measure for the ability of the network to transmit mechanical forces. We also take a closer look at the influence of noise on lock-in measurements and state some simple rules for improving the signal-to-noise ratio

Functional and Crystal Structure Analysis of Active Site Adaptations of a Potent Anti-Angiogenic Human tRNA Synthetase

SummaryHigher eukaryote tRNA synthetases have expanded functions that come from enlarged, more differentiated structures that were adapted to fit aminoacylation function. How those adaptations affect catalytic mechanisms is not known. Presented here is the structure of a catalytically active natural splice variant of human tryptophanyl-tRNA synthetase (TrpRS) that is a potent angiostatic factor. This and related structures suggest that a eukaryote-specific N-terminal extension of the core enzyme changed substrate recognition by forming an active site cap. At the junction of the extension and core catalytic unit, an arginine is recruited to replace a missing landmark lysine almost 200 residues away. Mutagenesis, rapid kinetic, and substrate binding studies support the functional significance of the cap and arginine recruitment. Thus, the enzyme function of human TrpRS has switched more to the N terminus of the sequence. This switch has the effect of creating selective pressure to retain the N-terminal extension for functional expansion

Technical assistance to assess the potential of renewable liquid and gaseous transport fuels of non-biological origin (RFNBOs) as well as recycled carbon fuels (RCFs), to establish a methodology to determine the share of renewable energy from RFNBOs as well as to develop a framework on additionality in the transport sector

This report is a summary of the work conducted in Task 1 of the technical assistance to assess the potential of renewable fuels of non-biological origin (RFNBOs) and recycled carbon fuels (RCFs) to establish a methodology to determine the share of renewable energy from RFNBOs as well as to develop a framework on additionality in the transport sector. The goal of Task 1 within the entire project was the assessment of the deployment potential of RFNBOs and RCFs over the period from 2020 to 2050 in the EU transport sector. All relevant transport sub-sectors and modalities are considered: road transport, maritime and inland shipping, aviation, and railway. Furthermore, the competition for RFNBOs and RCFs between the transport sectors and other sectors and applications of RFNBOs is considered. A central result is the potential gross final consumption of RFNBOs and RCFs that would count towards the RES target in the transport sector. In addition, the needed resources and the arising costs for this deployment as well as the impacts on greenhouse gas emissions and local environments are analyzed. Finally, barriers to the deployment and options to overcome these are outlined

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo

Percutaneous coronary intervention of chronic total occlusions involving a bifurcation: Insights from the PROGRESS-CTO registry

BACKGROUND: The impact of bifurcations at the proximal or distal cap on the outcomes of chronic total occlusion (CTO) percutaneous coronary intervention (PCI) has received limited study. METHODS: We analyzed the clinical, angiographic, and procedural data of 4,584 cases performed in patients between 2012 and 2020 in a global CTO PCI registry. We compared 4 groups according to the bifurcation location: proximal cap, distal cap, proximal and distal cap, and no bifurcation. RESULTS: The CTO involved a bifurcation in 67% cases, as follows: proximal cap (n = 1451, 33%), distal cap (n = 622, 14%), or both caps (n = 954, 21%). Proximal and distal cap cases had higher J-CTO compared with proximal cap, distal cap, and no bifurcation cases (2.9 ± 1.1 vs 2.5 ± 1.1 vs 2.4 ± 1.2 vs 2.0 ± 1.2, P \u3c 0.0001), and they were also associated with a lower technical success rate (79% vs 85% vs 85% vs 90%, P \u3c 0.0001), higher pericardiocentesis rate (1% vs 1% vs 0.2% vs 0.3%, P = 0.02), and higher emergency coronary artery bypass graft surgery rate (0.3% vs 0% vs 0% vs 0%, P = 0.01). CONCLUSION: More than two-thirds of CTO PCIs involve a bifurcation, which is associated with lower technical success and higher risk of complications