Protein Synthesis: Twenty Three Amino Acids and Counting

The genetic code can be interpreted during translation as 21 amino acids and three termination signals. Recent advances at the interface of chemistry and molecular biology are extending the genetic code to allow assignment of new amino acids to existing codons, providing new functional groups for protein synthesis

The effect of collagenase, water and calcium chloride on the removal of <i>Salmo salar</i> (salmon) and <i>Oncorhynchus mykiss</i> (trout) pin bones

The aim of this study was to determine the influence of the fillet structure on the deboning force required to remove salmon and trout pin bones. Salmon and trout fillets with differing fillet structure were used, in order to study the importance of the fillet structure on the deboning process. In the first test naturally gaping and non-gaping fillets were compared. To confirm the role that the collagen plays within the fillet structure, the fillets underwent series of treatments. Fillets were put into (i) a collagenase solution to remove the collagen in the fillet (ii) a calcium chloride solution to determine if collagen was the main influential factor. Both treated salmon and trout fillets were again compared to untreated fillets from the same batch. The results indicate that collagenase and calcium chloride have a large interaction on deboning force compared to water or no treatments

The Complex Evolutionary History of Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of \u3e2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code

Development of a gluten free bread enriched with faba bean husk as a fibre supplement

Faba bean husks (FBH) are a high-fibre waste product of faba beans and are primarily used as animal feed with the potential of becoming a fibre supplement. In this study, different levels and particle sizes of FBH flour were used to enhance the fibre content of gluten free bread. Bread properties were evaluated by measuring specific volume, colour (crust and crumb), and crumb texture. The sensory characteristics of breads were assessed by a group of untrained panellists (n = 66) on appearance, aroma, flavour, texture, aftertaste, willingness to buy, and overall acceptability using a nine-point hedonic scale. Volume of bread was affected by the level and particle size of FBH added. Texture analysis showed the importance of level of FBH, and of its particle size in establishing hardness, gumminess, and chewiness (p &lt; 0.05). The added FBH influenced the colour of the crust and crumb. Two formulations of FBH-enriched gluten free bread (particle sizes of 212–300 μm at 5% wheat flour weight substitution, and particle sizes of smaller than 212 μm at 15% wheat four weight substitution) increased the fibre content of the bread, while had no negative impact on sensory evaluation in comparison to control treatment (p &lt; 0.05).</p

Cysteinyl-tRNA formation and prolyl-tRNA synthetase

AbstractAminoacyl-tRNA (AA-tRNA) formation is a key step in protein biosynthesis. This reaction is catalyzed with remarkable accuracy by the AA-tRNA synthetases, a family of 20 evolutionarily conserved enzymes. The lack of cysteinyl-tRNA (Cys-tRNA) synthetase in some archaea gave rise to the discovery of the archaeal prolyl-tRNA (Pro-tRNA) synthetase, an enzyme capable of synthesizing Pro-tRNA and Cys-tRNA. Here we review our current knowledge of this fascinating process

Esophageal and small bowel obstruction by occupational bezoar: report of a case

BACKGROUND: Phytobezoar may be a cause of bowel obstruction in patients with previous gastric surgery. Most bezoars are concretions of poorly digested food, which are usually formed initially in the stomach. Intestinal obstruction (esophageal and small bowel) caused by an occupational bezoar has not been reported. CASE PRESENTATION: A 70-year old male is presented suffering from esophageal and small bowel obstruction, caused by an occupational bezoar. The patient has worked as a carpenter for 35 years. He had undergone a vagotomy and pyloroplasty 10 years earlier. The part of the bezoar, which caused the esophageal obstruction was removed during endoscopy, while the part of the small bowel was treated surgically. The patient recovered well and was discharged on the 8(th )postoperative day. CONCLUSIONS: Since occupational bezoars may be a cause of intestinal obstruction (esophageal and/or small bowel), patients who have undergone a previous gastric surgery should avoid occupational exposures similar to the presented case

Integrated signaling and transcriptome analysis reveals Src family kinase individualities and novel pathways controlled by their constitutive activity

The Src family kinases (SFKs) Lck and Lyn are crucial for lymphocyte development and function. Albeit tissue-restricted expression patterns the two kinases share common functions; the most pronounced one being the phosphorylation of ITAM motifs in the cytoplasmic tails of antigenic receptors. Lck is predominantly expressed in T lymphocytes; however, it can be ectopically found in B-1 cell subsets and numerous pathologies including acute and chronic B-cell leukemias. The exact impact of Lck on the B-cell signaling apparatus remains enigmatic and is followed by the long-lasting question of mechanisms granting selectivity among SFK members. In this work we sought to investigate the mechanistic basis of ectopic Lck function in B-cells and compare it to events elicited by the predominant B-cell SFK, Lyn. Our results reveal substrate promiscuity displayed by the two SFKs, which however, is buffered by their differential susceptibility toward regulatory mechanisms, revealing a so far unappreciated aspect of SFK member-specific fine-tuning. Furthermore, we show that Lck- and Lyn-generated signals suffice to induce transcriptome alterations, reminiscent of B-cell activation, in the absence of receptor/co-receptor engagement. Finally, our analyses revealed a yet unrecognized role of SFKs in tipping the balance of cellular stress responses, by promoting the onset of ER-phagy, an as yet completely uncharacterized process in B lymphocytes

Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis

AbstractWith the exception of the methanogenic archaea Methanococcus jannaschii and Methanobacterium thermoautotrophicum ΔH, all organisms surveyed contain orthologs of Escherichia coli cysteinyl-tRNA synthetase (CysRS). The characterization of CysRS-encoding (cysS) genes and the demonstration of their ability to complement an E. coli cysSts mutant reveal that Methanococcus maripaludis and Methanosarcina barkeri, two other methanogenic archaea, possess canonical CysRS proteins. A molecular phylogeny inferred from 40 CysRS sequences indicates that the CysRS of M. maripaludis and Methanosarcina spp. are specific relatives of the CysRS of Pyrococcus spp. and Chlamydia, respectively. This result suggests that the CysRS gene was acquired by lateral gene transfer in at least one euryarchaeotic lineage

A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine

In many prokaryotes and in organelles asparagine and glutamine are formed by a tRNA-dependent amidotransferase (AdT) that catalyzes amidation of aspartate and glutamate, respectively, mischarged on tRNA(Asn) and tRNA(Gln). These pathways supply the deficiency of the organism in asparaginyl- and glutaminyl-tRNA synthtetases and provide the translational machinery with Asn-tRNA(Asn) and Gln-tRNA(Gln). So far, nothing is known about the structural elements that confer to tRNA the role of a specific cofactor in the formation of the cognate amino acid. We show herein, using aspartylated tRNA(Asn) and tRNA(Asp) variants, that amidation of Asp acylating tRNA(Asn) is promoted by the base pair U(1)–A(72) whereas the G(1)–C(72) pair and presence of the supernumerary nucleotide U(20A) in the D-loop of tRNA(Asp) prevent amidation. We predict, based on comparison of tRNA(Gln) and tRNA(Glu) sequence alignments from bacteria using the AdT-dependent pathway to form Gln-tRNA(Gln), that the same combination of nucleotides also rules specific tRNA-dependent formation of Gln. In contrast, we show that the tRNA-dependent conversion of Asp into Asn by archaeal AdT is mainly mediated by nucleotides G(46) and U(47) of the variable region. In the light of these results we propose that bacterial and archaeal AdTs use kingdom-specific signals to catalyze the tRNA-dependent formations of Asn and Gln