Biology subjects

Helena-Bueno, K.

Publications and source records attributed to Helena-Bueno, K..

4 recordsLinked to original sources

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

Genome sequences hot and cold: a database of organisms with defined optimal growth temperatures

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 a result, it becomes challenging to use the genomic data for studying the adaptations of organisms and biological molecules to diverse environments. To address this problem, we have created a database Gosha, available at http://melnikovlab.com/gshc. This database brings together information about the genomic sequences and optimal growth temperatures for 25,324 species, including [~]89% of the bacterial species with known genome sequences. Using this database, one can annotate genomic sequences from thousands of species and correlate variations in genes and genomes with optimal growth temperatures. The database interface allows users to retrieve optimal growth temperatures for bacteria, eukaryotes and archaea, providing a tool to explore how organisms, genomes, and individual proteins and nucleic acids adapt to certain temperatures. We hope that this database will contribute to medicine and biotechnology by helping to create a better understanding of molecular adaptations to heat and cold, leading to new ways to preserve biological samples, engineer useful enzymes, and develop biological materials and organisms with the desired tolerance to heat and cold. GRAPHICAL ABSTRACTGosha (available at www.melnikovlab.com/gshc) is a database that collects information about the optimal growth temperatures of living species. This database aims to facilitate studies of molecular adaptation to specific temperatures. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/473645v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@17b949dorg.highwire.dtl.DTLVardef@5a0271org.highwire.dtl.DTLVardef@1566cccorg.highwire.dtl.DTLVardef@100e590_HPS_FORMAT_FIGEXP M_FIG C_FIG

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↗