Biology subjects

Toledo-Patino, S.

Publications and source records attributed to Toledo-Patino, S..

4 recordsLinked to original sources

bioRxiv2026

Hidden diversity and host specificity of Cladocopium symbionts revealed by phylotranscriptomics in giant sea anemones.

Giant sea anemones form an intricate, metabolically linked symbiosis with anemonefish (genus Amphiprion) and dinoflagellates (family Symbiodiniaceae). While the association between fish and anemone is well documented, the identity and distribution of resident Symbiodiniaceae remains poorly characterized. Here, we used RNA-sequencing of anemone tentacles and post-assembly filtering to recover Symbiodiniaceae sequences from Japanese anemones. Using transcriptome-wide phylogenetic approaches, we identified distinct Symbiodiniaceae strains in seven sea anemone species and four cryptic lineages of Entacmaea quadricolor. Phylogenies of 1300 and 214 nuclear genes resolved relationships among these symbionts with greater sensitivity than traditional molecular markers such as the Internal Transcribed Spacer 2 (ITS2) or partial 28S ribosomal DNA. Marker-based assessments indicate these Symbiodiniaceae as novel and specific to sea anemone hosts. Our transcriptome-wide phylogenies reveal previously undescribed Cladocopium (Clade C) strains associated with giant sea anemones, with symbionts clustering according to host species and lineage. Cophylogenetic analysis revealed significant phylogenetic congruence between anemone and Symbiodiniaceae, indicating a nonrandom association between host and symbiont evolutionary histories. Two sympatric cryptic lineages of E. quadricolor previously identified through host transcriptomics harbor distinct, specific Symbiodiniaceae assemblages. Analysis of genes under positive selection indicates functional divergence between these Symbiodiniaceae; three-dimensional reconstructions of symbiont cells using serial block-face scanning electron microscopy show consistent differences in cellular organization between two strains, further supporting their distinct functional identity. Together, our results uncover a hidden diversity of host-specific Symbiodiniaceae and suggest that cryptic diversification in giant sea anemones is mirrored by diversification of their algal symbionts within this tripartite symbiosis.

evolutionary biology↗

bioRxiv2024

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases

At the heart of many nucleoside triphosphatases is a conserved sequence motif that binds phosphate. A current model of early enzyme evolution proposes that this 6-8 residue motif could have sparked the emergence of the very first nucleoside triphosphatases - a striking example of evolutionary continuity from simple beginnings, if true. To test whether this provocative evolutionary model holds for the ancient and ubiquitous P-Loop NTPases, the properties of seven disembodied Walker A-derived peptides were extensively characterized by Hamiltonian replica exchange molecular dynamics simulations. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected - even in the presence of orthophosphate or a nucleotide. Simulations suggest that phosphate binding is non-specific, with a slight preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides with respect to conformational dynamics and phosphate binding, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-Loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family, and the environmental context within which it emerged, must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils - the true nature of which have been eroded by time. Significance StatementThe first proteins were undoubtedly small, but when did those seeds emerge, and what did they look like? It is widely believed that the Walker A P-loop motif is a seed for the emergence of phosphate binding proteins, snugly binding phosphate in a structurally conserved nest. We probe this hypothesis through detailed computational characterization of disembodied Walker A and control peptides, showing that any nest formation is transient, and phosphate binding is weak and non-specific. Thus, we do not find structural continuity represented in the conserved Walker A motif, and current models of early P-loop evolution require revision. Further, care is required when interpreting highly conserved sequence fragments more broadly, as these may merely represent eroded molecular fossils.

biophysics↗

bioRxiv2022

Insertions and deletions mediated functional divergence of Rossmann fold enzymes

Nucleobase-containing coenzymes are considered the relics of an early RNA-based world that preceded the emergence of protein domains. Despite the importance of coenzyme-protein synergisms, their emergence and evolution remain poorly understood. An excellent target to address this issue is the Rossman fold, the most catalytically diverse and abundant protein architecture in Nature. Here, we investigatedted the two largest Rossman lineages, namely the nicotinamide adenine dinucleotide phosphate (NAD(P))-binding and the S-adenosyl methionine (SAM)-dependent superfamilies. With the aim to identify the evolutionary changes that lead to a switch in coenzyme specificity on these superfamilies, we performed structural and sequence-based Hidden Markov Models to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed how insertions and deletions (InDels) reshaped the ancient {beta}1-loop-1 coenzyme-binding structure of NAD(P) into the well-defined SAM-binding {beta}1-loop-1 structure. To prove this observation experimentally, we removed an InDel of three amino acids from the NAD(P) coenzyme pocket and solved the structure of the resulting mutant, revealing the characteristic features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements, validating the successful coenzyme switch. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD-binding and acquiring SAM binding. Our results uncovered how Nature utilized insertions and deletions to switch coenzyme specificity, and in turn, functionalities between these superfamilies. This work also establishes how protein structures could have been recycled through the course of evolution to adopt different coenzymes and confer different chemistries. Significance StatementCofactors are ubiquitous molecules necessary to drive about half of the enzymatic reactions in Nature. Among them, organic cofactors (coenzymes) that contain nucleotide moieties are believed to be relics of a hypothetical RNA world. Understanding coenzyme-binding transitions sheds light onto the emergence of the first enzymes and their chemical diversity. Rossmann enzymes bind to 7 out of 10 nucleotide coenzymes, representing an ideal target to study how different coenzyme specificities emerged and evolved. Here we demonstrated how insertions and deletions reshape coenzyme-specificity in Rossmann enzymes by retracing the emergence of the SAM-binding function from an NAD-binding ancestor. This work constitutes the first example of an evolutionary bridge between redox and methylation reactions, providing a new strategy to engineer coenzyme specificity.

evolutionary biology↗

bioRxiv2020

A highly diverged ancient interface plays a key role in the origin and evolution of Methionine AdenosylTransferase superfamily

Methionine adenosyltransferase (MAT), which catalyzes the biosynthesis of S-adenosylmethionine from L-methionine and ATP, is an ancient, highly conserved enzyme present in all three domains of life. Although the MAT enzymes of each domain are believed to share a common ancestor, the sequences of archaeal MATs show a high degree of divergence from the sequences of bacterial and eukaryotic MATs. However, the structural and functional consequences of this sequence divergence are not well understood. Here, we use structural bioinformatics analysis and ancestral sequence reconstruction to highlight the consequences of archaeal MAT divergence. We show that the dimer interface containing the active site, which would be expected to be well conserved across all three domains, diverged considerably between the bacterial/eukaryotic MATs and archaeal MATs. Furthermore, the characterization of reconstructed ancestral archaeal MATs showed that they probably had low substrate specificity which expanded during their evolutionary trajectory hinting towards the observation that all the modern day MAT enzymes from the three-kingdom probably originated from a common specific ancestor and then archaea MATs diverged in sequence, structure and substrate specificity. Altogether, our results show that the archaea MAT is an ideal system for studying an enzyme family which evolved to display high degrees of divergence at the sequence/structural levels and yet are capable of performing the same catalytic reactions as their orthologous counterparts.

evolutionary biology↗