Ribosomal signatures, idiosyncrasies in the ribosomal RNA (rRNA) and/or proteins, are characteristic of the individual domains of life. As such, insight into the early evolution of the domains can be gained from a comparative analysis of their respective signatures in the translational apparatus. In this work, we identify signatures in both the sequence and structure of the rRNA and analyze their contributions to the universal phylogenetic tree using both sequence- and structure-based methods. Domain-specific ribosomal proteins can be considered signatures in their own right. Although it is commonly assumed that they developed after the universal ribosomal proteins, we present evidence that at least one may have been present before the divergence of the organismal lineages. We find correlations between the rRNA signatures and signatures in the ribosomal proteins showing that the rRNA signatures coevolved with both domain-specific and universal ribosomal proteins. Finally, we show that the genomic organization of the universal ribosomal components contains these signatures as well. From these studies, we propose the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome.
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http://dx.doi.org/10.1073/pnas.0804861105 | DOI Listing |
Sci Total Environ
January 2025
State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, China.
Based on the potential bactericidal properties of borate, we synthesized controlled-release borate (CRB) as a novel biocide to inhibit microbial proliferation in a recirculating cooling water system (RCS). In this study, toxicity experiments of CRB were conducted on the dominant bacteria and algae isolated from an actual RCS. The effects of CRB on biocidal performance and genotoxicity were evaluated in a simulated RCS.
View Article and Find Full Text PDFNat Struct Mol Biol
January 2025
Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
Transfer RNAs (tRNAs) serve as a dictionary for the ribosome translating the genetic message from mRNA into a polypeptide chain. In addition to this canonical role, tRNAs are involved in other processes such as programmed stop codon readthrough (SC-RT). There, tRNAs with near-cognate anticodons to stop codons must outcompete release factors and incorporate into the ribosomal decoding center to prevent termination and allow translation to continue.
View Article and Find Full Text PDFNat Commun
January 2025
Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
Obesity poses a global health challenge, demanding a deeper understanding of adipose tissue (AT) and its mitochondria. This study describes the role of the mitochondrial protein Methylation-controlled J protein (MCJ/DnaJC15) in orchestrating brown adipose tissue (BAT) thermogenesis. Here we show how MCJ expression decreases during obesity, as evident in human and mouse adipose tissue samples.
View Article and Find Full Text PDFNat Commun
January 2025
Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern, Germany.
Molecular chaperones are essential throughout a protein's life and act already during protein synthesis. Bacteria and chloroplasts of plant cells share the ribosome-associated chaperone trigger factor (Tig1 in plastids), facilitating maturation of emerging nascent polypeptides. While typical trigger factor chaperones employ three domains for their task, the here described truncated form, Tig2, contains just the ribosome binding domain.
View Article and Find Full Text PDFMol Biol Rep
January 2025
Department of Molecular Biology Vadi Kampüsü, Istanbul Atlas University, Anadolu Cd., No 40, Kağıthane, Istanbul, 34408, Turkey.
Background: Modulation of protein synthesis according to the physiological cues is maintained through tight control of Eukaryotic Elongation Factor 2 (eEF2), whose unique translocase activity is essential for cell viability. Phosphorylation of eEF2 at its Thr56 residue inactivates this function in translation. In our previous study we reported a novel mode of post-translational modification that promotes higher efficiency in T56 phosphorylation.
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