Making Sense of “Nonsense” and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications

The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems

Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.

A Mini Review on SARS-COVID-19-2 Omicron Variant (B.1.1.529)

The current world facing unpredictable problems with different variants of COVID-19; SARS-COV-19 is a significant lung infection caused by a coronavirus. Each type has one or more alterations to distinguish from each other. The viruses, including SARS-COV-19, continuously change the genetic code (mutations) during their genome replication. WHO labelled two variants in that we are experienced with delta (B.1.617.2) variant, now recently the omicron came (B.1.1.529) with highly mutatable strikes on it. So WHO predicted it is more dangerous than previous variants because of its mutatable capability. The mutatable strikes play an essential role in transmissibility. So there is a need to evaluate threatens raised with the new variant, so scientists are working on it. Till now, South Africa noticed major cases positive for the Omicron variant. Based on recent reports, the current paper summarized different properties of the omicron variant with others, including protein structure, diagnosis, spreadability, treatment, and potency of vaccines. Doi: 10.28991/SciMedJ-2021-0304-10 Full Text: PDF

Biosemiotics and Body Signifier Theory: a way to understand High Dilutions

Since the 80´s Madeleine Bastide and Agnès Lagache have worked on the idea of the Body Signifier Theory, in which the living systems could be defined as “sensible” systems not only able to self-organize, but also to receive and process non-molecular information according to the Pierce semiotic triad: matrix, receiver and carrier. These ideas were built along 20 years of experimental observations, whose results presented some kind of stereotyped pattern that emerged from cells or animals exposed to high dilutions, according to the similia principle. Curiously, at the same time, classical scientific communities have developed the concept of biosemiotics after the observation that living systems are semiotics entities able to deal with codes and meanings, even in molecule-driven processes. Not only the genetic code, but all regulatory functions in living systems represent coding processes. The development of methodologies to identify and understand these codes and its outputs is the aim of biosemiotic science. Putting both concepts together (body signifiers and biosemiotics), it is possible to recognize strong similarities between their approaches and methodology, allowing logical connections between non-molecular signals and changes in cell interactions patterns. Thus, the general concept of biosemiotic could be a theoretical platform on which the construction of a solid phenomenological description of high dilutions effects could be done.