Sergey Melnikov
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View article: Evolution of drug-binding residues in eukaryotic ribosomes
Evolution of drug-binding residues in eukaryotic ribosomes Open
Drugs that target eukaryotic ribosomes are becoming increasingly important as research tools and potential therapies against cancer and pathogenic eukaryotes. However, in the absence of comparative studies, we currently do not know how man…
View article: Extensive natural variation in bacterial ribosomal drug-binding sites
Extensive natural variation in bacterial ribosomal drug-binding sites Open
Ribosomes from certain bacteria possess divergent drug-binding sites compared to those of Escherichia coli, leading to natural evasion or hypersensitivity to antibiotics. However, in the absence of systematic studies, it is unknown whether…
View article: Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells
Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells Open
Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that structurally distinct pools of ribosomes have diffe…
View article: Evolution of drug-binding residues in eukaryotic ribosomes
Evolution of drug-binding residues in eukaryotic ribosomes Open
Drugs that target eukaryotic ribosomes are becoming increasingly important as research tools and potential therapies against cancer and pathogenic eukaryotes. However, in the absence of comparative studies, we currently do not know how man…
View article: Evolution of drug-binding residues in bacterial ribosomes
Evolution of drug-binding residues in bacterial ribosomes Open
Ribosomes from certain bacteria possess divergent drug-binding sites compared to those of Escherichia coli, leading to natural evasion or hypersensitivity to antibiotics. However, in the absence of systematic studies, it is unknown whether…
View article: Hibernating ribosomes as drug targets?
Hibernating ribosomes as drug targets? Open
When ribosome-targeting antibiotics attack actively growing bacteria, they occupy ribosomal active centers, causing the ribosomes to stall or make errors that either halt cellular growth or cause bacterial death. However, emerging research…
View article: Rippling life on a dormant planet: hibernation of ribosomes, RNA polymerases, and other essential enzymes
Rippling life on a dormant planet: hibernation of ribosomes, RNA polymerases, and other essential enzymes Open
Throughout the tree of life, cells and organisms enter states of dormancy or hibernation as a key feature of their biology: from a bacterium arresting its growth in response to starvation, to a plant seed anticipating placement in fertile …
View article: Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins
Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins Open
Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number…
View article: A new family of bacterial ribosome hibernation factors
A new family of bacterial ribosome hibernation factors Open
To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage 1,2 . In bacteria, two families of hibernation factors have been described…
View article: tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut
tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut Open
Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA syntheta…
View article: A Conserved Ribosomal Protein Has Entirely Dissimilar Structures in Different Organisms
A Conserved Ribosomal Protein Has Entirely Dissimilar Structures in Different Organisms Open
Ribosomes from different species can markedly differ in their composition by including dozens of ribosomal proteins that are unique to specific lineages but absent in others. However, it remains unknown how ribosomes acquire new proteins t…
View article: Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA
Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA Open
Ribosomal genes are widely used as ‘molecular clocks’ to infer evolutionary relationships between species. However, their utility as ‘molecular thermometers’ for estimating optimal growth temperature of microorganisms remains uncertain. Pr…
View article: Supplementary Data for "Gosha: a database of organisms with experimentally defined optimal growth temperatures"
Supplementary Data for "Gosha: a database of organisms with experimentally defined optimal growth temperatures" Open
The data provided in this document are associated with the manuscript initially published as a BioRxiv preprint, which can be accessed at: https://www.biorxiv.org/content/10.1101/2021.12.21.473645v1.abstract The dataset "all_species_tempe…
View article: Supplementary Data for "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold"
Supplementary Data for "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold" Open
This data complement the manuscript "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold".
View article: A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis
A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis Open
During starvation and stress, virtually all organisms arrest protein synthesis to conserve energy. Inactive ribosomes are converted into a dormant state, in which they are protected from damage by hibernation factor proteins. In bacteria, …
View article: A conserved ribosomal protein has entirely dissimilar structures in different organisms
A conserved ribosomal protein has entirely dissimilar structures in different organisms Open
Ribosomes from different species can markedly differ in their composition by including dozens of ribosomal proteins that are unique to specific lineages but absent in others. However, it remains unknown how ribosomes acquire and specialize…
View article: Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins are robust indicators of bacterial adaptation to heat and cold
Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins are robust indicators of bacterial adaptation to heat and cold Open
A bstract Ribosomal genes are widely used as “molecular clocks” to infer the evolutionary relatedness of species. It is unclear, however, whether these genes can also serve as “molecular thermometers” to precisely estimate an organism’s op…
View article: Adaptation to genome decay in the structure of the smallest eukaryotic ribosome
Adaptation to genome decay in the structure of the smallest eukaryotic ribosome Open
The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious mutations. Here, to understand how this coun…
View article: Gosha: a database of organisms with defined optimal growth temperatures
Gosha: a database of organisms with defined optimal growth temperatures Open
Currently, we are witnessing an explosive accumulation of genomic sequences for organisms across all branches of life. However, typically the genomic data lack the information about optimal growth conditions of corresponding organisms. As …
View article: 'Lose-to-gain' adaptation to genome decay in the structure of the smallest eukaryotic ribosomes
'Lose-to-gain' adaptation to genome decay in the structure of the smallest eukaryotic ribosomes Open
The evolution of microbial parasites involves the interplay of two opposing forces. On the one hand, the pressure to survive drives parasites to improve through Darwinian natural selection. On the other, frequent genetic drifts result in g…
View article: Bacterial translation machinery for deliberate mistranslation of the genetic code
Bacterial translation machinery for deliberate mistranslation of the genetic code Open
Significance Aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are essential enzymes that mediate accurate expression of the genetic code. More than 96% of analyzed species possess duplicated aaRSs genes, which are presumed to encode canon…
View article: Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations
Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations Open
Significance The therapeutic use of drugs against microbial pathogens and cancer is currently undergoing a paradigm shift from traditional therapies toward adaptive therapies, which attempt to minimize the risk of the evolution of drug res…
View article: Exploiting evolutionary trade-offs to combat antibiotic resistance
Exploiting evolutionary trade-offs to combat antibiotic resistance Open
Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics…
View article: Supplementary Data for "Exploiting evolutionary trade-offs for management of drug-resistant populations"
Supplementary Data for "Exploiting evolutionary trade-offs for management of drug-resistant populations" Open
These dataset contains sequencing data and plasmid maps for the manuscript entitled "Exploiting evolutionary trade-offs for management of drug-resistant populations".
View article: Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus
Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus Open
Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features …
View article: Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus
Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus Open
A bstract Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as…
View article: Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal?
Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal? Open
In the past two decades, tRNA molecules and their corresponding aminoacyl-tRNA synthetases (aaRS) have been extensively used in synthetic biology to genetically encode post-translationally modified and unnatural amino acids. In this review…
View article: Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia
Muller’s Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia Open
Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasite…