Biology subjects

Melnikov, S. V.

Publications and source records attributed to Melnikov, S. V..

9 recordsLinked to original sources

bioRxiv2025

The evolution lifecycle of ribosome hibernation factors

Bacteria defend against hostile environments through a variety of molecular mechanisms, including ribosome hibernation. Previously, bacteria were shown to initiate ribosome hibernation by activating protective proteins known as hibernation factors. It was demonstrated that hibernation factors prevent ribosome degradation by nucleases, which allows bacteria to safely store their inactive ribosomes and survive under starvation or persistent stress. Because homologs of hibernation factors were found in diverse lineages of bacteria, it is currently assumed that the mechanism of ribosome hibernation is highly conserved across species. Here, we assess 46,015 complete bacterial genomes to reveal the principles underlying the origin and evolution of these essential proteins in bacterial cells. We find that hibernation factors emerged in ancient bacteria as relatively large proteins that then gradually reduced in size and have undergone complete extinction in over 10% of studied bacteria. We then demonstrate that the degeneration of ancient hibernation factors is often accompanied by "borrowing" hibernation factors from other species via gene transfers, de novo gene birth or fusion of truncated hibernation factors with fragments from other stress-response proteins. These findings reveal a unique evolutionary pathway in which bacteria respond to the reductive evolution of hibernation machinery by inventing novel hibernation mechanisms, thus restoring their capacity to survive starvation and stress. This model implies that most ribosome hibernation factors are yet to be discovered and predicts the organisms that rely on currently unknown hibernation mechanisms.

microbiology↗

bioRxiv2024

Natural variation of the drug-binding residues in eukaryotic ribosomes

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 many eukaryotes possess ribosomal drug-binding sites identical to those in humans, and how many significantly differ from humans. To address this, we traced the evolutionary history of individual ribosomal drug-binding residues from the emergence of eukaryotes to the present day. We found that ribosomal drug-binding sites are divergent across eukaryotic clades, with some of the clades exhibiting more substitutions in their ribosomal drug-binding sites compared to humans than humans do compared to bacteria. Overall, our work provides a resource for understanding the evolutionary divergence of drug-binding sites in eukaryotic ribosomes, which may inform the use of ribosome inhibitors as research tools and lineage-specific drugs against eukaryotic parasites.

microbiology↗

bioRxiv2024

Evolutionary divergence of drug-binding sites in bacterial ribosomes

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 this observed divergence is a rare exception or a common occurrence among bacterial species. Here, we address this question by reconstructing the evolutionary history of drug-binding residues of the ribosome from the origin of bacteria to the present day. This analysis reveals the extent of natural diversity of ribosomal drug-binding sites between bacterial species, which may inform the development of species-specific antimicrobials and a more accurate and personalized choice of ribosome-targeting drugs for a given pathogen.

microbiology↗

bioRxiv2022

Structure of dormant bacterial ribosomes reveals an elusive translation factor with evolutionary connections to eukaryotic protein synthesis factors

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, two major families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats, and environmental stressors has confounded their discovery. In this study, using proteomics and cryo-EM, we identify a new dormancy factor from the psychrophilic bacterium Psychrobacter urativorans. By isolating ribosomes under cold-shock conditions, we observe a previously unknown protein bound to the ribosomal A site, protecting critical elements of both the decoding and peptidyl transferase centers. We show that this new factor, which we term Balon, is a homolog of the archaeo-eukaryotic translation factor aeRF1, providing a long-predicted evolutionary "missing link" between the eukaryotic and bacterial translation machinery. Our structures reveal that Balon is delivered to both vacant and actively translating ribosomes by EF-Tu, highlighting an unexpected and previously unknown role for this elongation factor in the bacterial stress response. We describe several unique structural motifs that allow Balon to bind ribosomes in an mRNA-independent manner, initiating a new mode of ribosome dormancy that can commence while ribosomes are still engaged in protein synthesis. Our bioinformatic analysis shows that putative Balon-encoding genes can be found within stress-response operons in nearly 20 % of all known bacterial species, including many human pathogens. Taken together, our work suggests that Balon/EF-Tu regulated ribosome dormancy is likely to be a ubiquitous stress-response mechanism throughout the bacterial kingdom. These findings call for a revision of our model of bacterial translation inferred from common model organisms and hold numerous implications for how we understand and study ribosome dormancy.

molecular biology↗

bioRxiv2022

Ribosomal protein with conserved function has entirely different structures in different organisms

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 new proteins throughout evolution. Here, to help answer this question, we describe the evolution of the ribosomal protein msL1/msL2 that was recently found in ribosomes from the parasitic microorganism clade, microsporidia. We first show that this protein has a conserved location in the ribosome but entirely dissimilar structures in different organisms: in each of the analyzed species, msL1/msL2 exhibits an altered secondary structure, an inverted orientation of the N- and C-termini on the ribosomal binding surface, and a completely transformed three-dimensional fold. We then show that this evolutionary fold switching is likely caused by changes in the msL1/msL2-binding site in the ribosome; specifically, by variations in microsporidian rRNA. These observations allow us to infer an evolutionary scenario in which a small, positively-charged, de novo-born unfolded protein was first captured by rRNA to become part of the ribosome and subsequently underwent complete fold switching to optimize its binding to its evolving ribosomal binding site. Overall, our work provides a striking example of how a protein can switch its fold in the context of a complex biological assembly while retaining its specificity for its molecular partner. This finding will help us better understand the origin and evolution of new protein components of complex molecular assemblies - thereby enhancing our ability to engineer biological molecules, identify protein homologs, and peer into the history of life on Earth.

evolutionary biology↗

bioRxiv2022

Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins are robust indicators of bacterial adaptation to heat and cold

AO_SCPLOWBSTRACTC_SCPLOWRibosomal 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 organisms optimal growth temperature. Previously, some estimations were made using the average nucleotide content in ribosomal RNA, but the universal application of this approach was prevented by numerous outliers. Here, seeking to bypass this problem, we asked whether ribosomal genes contain additional markers of thermal adaptations, aside from their nucleotide composition. To answer this, we analyzed site-specific variations in sequences of ribosomal proteins from 2,021 bacteria with known optimal growth conditions. We found that ribosomal proteins comprise a few "mutational hotspots"--residues that vary in a temperature-dependent manner and distinguish heat- and cold-adapted bacteria. Most of these residues coordinate metal ions that support protein folding at high temperatures. Using these residues, we then showed that the upper and lower limits of an organisms optimal growth temperatures can be estimated using just 0.001% of the genome sequence or just two amino residues in the cellular proteome. This finding illustrates that laboratory-independent estimation of optimal growth temperatures can be simplified if we abandon the traditional use of rRNA and protein sequences to assess their content and instead focus on those few residues that are most critical for protein structure. This finding may simplify the analysis of unculturable and extinct species by helping bypass the need for laborious, costly, and at times impossible laboratory experiments.

evolutionary biology↗

bioRxiv2021

'Lose-to-gain' adaptation to genome decayin the structure of the smallest eukaryotic ribosomes

AO_SCPLOWBSTRACTC_SCPLOWThe 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 genome decay, an evolutionary process in which an ever-increasing burden of deleterious mutations leads to gene loss and gradual genome reduction. Here, seeking to understand how this interplay occurs at the scale of individual macromolecules, we describe cryo-EM and evolutionary analyses of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the most reduced genomes in nature. We show that E. cuniculi ribosomes, the smallest eukaryotic cytoplasmic ribosomes to be structurally characterized, employ unparalleled structural innovations that allow extreme rRNA reduction without loss of ribosome integrity. These innovations include the evolution of previously unknown rRNA features such as molten rRNA linkers and bulgeless rRNA. Furthermore, we show that E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving a unique ability to effectively trap small molecules and use them as ribosomal building-blocks and structural mimics of degenerated rRNA and protein segments. Overall, our work reveals a recurrent evolutionary pattern, which we term "lose-to-gain" evolution, where it is only through the loss of rRNA and protein segments that E. cuniculi ribosomes evolve their major innovations. Our study shows that the molecular structures of intracellular parasites long viewed as reduced, degenerated, and suffering from various debilitating mutations instead possess an array of systematically overlooked and extraordinary structural features. These features allow them to not only adapt to molecular reduction but evolve new activities that parasites can possibly use to their advantage.

evolutionary biology↗

bioRxiv2020

Exploiting evolutionary trade-offs to combat antibiotic resistance

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-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant E. coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates a potentially generalizable approach for combating therapeutic resistance, prolonging the effectiveness of drugs and enabling the use of drugs that are no longer effective due to the rapid evolution of resistance.

evolutionary biology↗

bioRxiv2019

Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus

AO_SCPLOWBSTRACTC_SCPLOWEukaryotic 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 unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrites, pointing to the ancient origin of NLS-type motifs in the Archaea. Furthermore, by using fluorescence microscopy, we show that the archaeal NLS-type motifs can functionally substitute eukaryotic NLSs and direct the transport of ribosomal proteins into the nuclei of human cells. Collectively, these findings illustrate that the origin of NLSs preceded the origin of the cell nucleus, suggesting that the initial function of NLSs was not related to intracellular trafficking. Overall, our study reveals rare evolutionary intermediates among archaeal cells that can help elucidate the sequence of events that led to the origin of the eukaryotic cell.

evolutionary biology↗