Search results for "genetic code"
showing 10 items of 26 documents
Inducible Genetic Code Expansion in Eukaryotes
2020
Abstract Genetic code expansion (GCE) is a versatile tool to site‐specifically incorporate a noncanonical amino acid (ncAA) into a protein, for example, to perform fluorescent labeling inside living cells. To this end, an orthogonal aminoacyl‐tRNA‐synthetase/tRNA (RS/tRNA) pair is used to insert the ncAA in response to an amber stop codon in the protein of interest. One of the drawbacks of this system is that, in order to achieve maximum efficiency, high levels of the orthogonal tRNA are required, and this could interfere with host cell functionality. To minimize the adverse effects on the host, we have developed an inducible GCE system that enables us to switch on tRNA or RS expression whe…
Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis)
2021
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural…
Synthesis and Evaluation of Novel Ring‐Strained Noncanonical Amino Acids for Residue‐Specific Bioorthogonal Reactions in Living Cells
2021
Abstract Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels–Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. In combination with genetic code expansion (GCE)‐a method that allows to incorporate noncanonical amino acids (ncAAs) site‐specifically into proteins in vivo. These reactions enable residue‐specific fluorophore attachment to proteins in living mam…
Genes, genomes, and codes : revisiting some key terms with multiple meanings
2015
Is a genome the full complement of an organism?s genes or of its DNA? Is genetics the study of genes or of heredity? Is the genetic code the mechanism for translating nucleotide sequence to amino acid sequence or to phenotype? Does «genetic information» refer to the sequences coding for proteins or to all DNA sequences? Each of these questions stems from an elision between one, concrete, meaning, and another, open-ended and ambiguous. Such elision invites the illusion that the ambiguity of the open-ended term has been resolved, and by implication, that the gap between actual achievement and promise has been closed. Yet, despite the phenomenal progress molecular biology has made, we remain w…
Characterization of a novel open reading frame, urf a, in the mitochondrial genome of fission yeast: correlation of urf a mutations with a mitochondr…
1991
Between the genes for tRNA(gin) and tRNA(ile) an open reading frame of 227 amino acids has been identified which is unique among known mitochondrial genomes and which has been termed urf a (Lang et al. 1983; Kornrumpf et al. 1984). It uses the "mitochondrial" genetic code, i.e., it contains a TGA codon, whereas all other protein-encoding genes, and all but one intronic open reading frame, use the "standard" genetic code (UGG for tryptophan). A previous paper has demonstrated that "mutator" strains show an increased formation of mitochondrial drug-resistant and respiration-deficient mutants (including deletions). In this paper we show that the mutator activity is correlated with mutations in…
Genetic variation in neuromuscular performance.
1973
Using a simple cumulative model of heredity plus environment, based on intrapair differences observed in monozygous (MZ) and dizygous (DZ) twins, the relative contribution of heredity to the interindividual variance in several neuromuscular parameters was determined with 15 pairs of male (8 MZ and 7 DZ) and 14 pairs of female (7 MZ and 7 DZ) twins ranging in age from 10 to 14 years. The data disclosed that in boys the variability in maximal mechanical (anaerobic) power was 99.2% genetically determined under the environmental conditions of the study. The corresponding heritability estimate values for the patellar reflex time and reaction time were 97.5% and 85.7%, respectively. In girls the …
Platyzoan mitochondrial genomes.
2012
Platyzoa is a putative lophotrochozoan (spiralian) subtaxon within the protostome clade of Metazoa, comprising a range of biologically diverse, mostly small worm-shaped animals. The monophyly of Platyzoa, the relationships between the putative subgroups Platyhelminthes, Gastrotricha and Gnathifera (the latter comprising at least Gnathostomulida, "Rotifera" and Acanthocephala) as well as some aspects of the internal phylogenies of these subgroups are highly debated. Here we review how complete mitochondrial (mt) genome data contribute to these debates. We highlight special features of the mt genomes and discuss problems in mtDNA phylogenies of the clade. Mitochondrial genome data seem to be …
Genomic determinants of protein folding thermodynamics in prokaryotic organisms.
2004
Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G+C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical…
Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation
2021
Summary Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use t…
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
2007
Abstract Background Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution. Results Using a variety of statistical null models we find patterns of compressive coding that can not be explained purely in terms of the selective processes favoring genome minimization or translational coupling. The distribution of overlap lengths follows a fat-tailed distribution, in which a significant proportion of overlaps are in excess of 100 base…