Biology subjects

Mardones, G.

Publications and source records attributed to Mardones, G..

6 recordsLinked to original sources

bioRxiv2026

Evolutionary history and functional divergence of hydroxycarboxylic acid receptors in primates

Hydroxycarboxylic acid receptors (HCARs) are class A G-protein-coupled receptors that function as metabolic sensors. This receptor family includes three members (HCAR1, HCAR2, and HCAR3) expressed in metabolically active tissues and immune cells, where they link cellular metabolic status to physiological responses. This study aims to elucidate the evolutionary history of the most recently originated members of the HCAR gene family, namely HCAR2 and HCAR3, in primates. According to our phylogenetic analyses, the duplicative history of these genes involved multiple independent duplication events during ape evolution. Thus, most ape lineages possess independently originated duplicated copies, while non-ape primates retain the ancestral condition of a single-copy gene (HCAR2/3). Our analyses further indicate that this single-copy gene in non-ape primates is functionally equivalent to HCAR2, suggesting that the primary functional innovation in apes is associated with the physiological roles of HCAR3. Finally, gene expression analyses reveal that major divergence in tissue expression occurred after the initial duplication event that generated HCAR1 and the HCAR2/3 lineage, whereas HCAR2 and HCAR3 exhibit substantial overlap in their expression profiles. Thus, the more refined and context-dependent regulation of lipid metabolism that provides the HCAR3 receptor seems to have originated multiple times during the evolutionary history of apes.

evolutionary biology↗

bioRxiv2024

Evolutionary and Functional Analysis of Monoamine Oxidase C (MAO C): A Novel Member of the MAO Gene Family

The monoamine oxidase (MAO) gene family encodes for enzymes that perform the oxidative deamination of monoamines, a process required to degrade norepinephrine, serotonin, dopamine, and other amines. While mammalian MAO enzymes, MAO A and MAO B, have been extensively studied, the molecular properties of the other family members are only partly uncovered. This study aims to explore the evolution of monoamine oxidases, emphasizing understanding the MAO gene repertoire among vertebrates. Our analyses show that the duplication that gave rise to MAO A and MAO B occurred in the ancestor of tetrapods, between 408 and 352 million years ago. Non-tetrapod jawed vertebrates possess the ancestral preduplicative condition of MAO A/B. Our results also identified a new family member, MAO C, in non-tetrapod jawed vertebrates. Thus, most jawed vertebrates possess a repertoire of two MAO genes, MAO A and MAO B in tetrapods and MAO A/B and MAO C in non-tetrapod jawed vertebrates, representing different MAO gene lineages. Jawless vertebrates possess the ancestral condition of a single copy gene, MAO A/B/C. Enzymatic assays conducted on the MAO recombinant enzymes of the Indo-Pacific tarpon show that both proteins, MAO A/B and MAO C, have enzymatic and molecular properties more similar to human MAO A, with the former featuring a strikingly higher activity rate when compared to all other MAO enzymes. Our analyses underscore the importance of scanning the tree of life for new gene lineages to understand phenotypic diversity and gain detailed insights into their function.

evolutionary biology↗

bioRxiv2023

The Reelin Receptor ApoER2 is a Cargo for the Adaptor Protein Complex AP-4: Implications for Hereditary Spastic Paraplegia.

Adaptor protein complex 4 (AP-4) is a heterotetrameric complex that promotes protein export from the trans-Golgi network. Mutations in each of the AP-4 subunits cause a complicated form of Hereditary Spastic Paraplegia (HSP). Herein, we report that ApoER2, a receptor in the Reelin signaling pathway, is a cargo of the AP-4 complex. We identify the motif ISSF/Y within the ApoER2 cytosolic domain as necessary for interaction with the canonical signal-binding pocket of the {micro}4 (AP4M1) subunit of AP-4. AP4E1-knock-out (KO) HeLa cells and hippocampal neurons from Ap4e1-KO mice display increased Golgi localization of ApoER2. Furthermore, hippocampal neurons from Ap4e1-KO mice and AP4M1-KO human iPSC-derived cortical i3Neurons exhibit reduced ApoER2 protein expression. Analyses of biosynthetic transport of ApoER2 reveal differential post-Golgi trafficking of the receptor, with lower axonal distribution in KO compared to wild-type neurons, indicating a role of AP-4 and the ISSF/Y motif in the axonal localization of ApoER2. Finally, analyses of Reelin signaling in mouse hippocampal and human cortical KO neurons show that AP4 deficiency causes no changes in Reelin-dependent activation of the AKT pathway and only mild changes in Reelin-induced dendritic arborization, but reduces Reelin-induced ERK phosphorylation, CREB activation, and Golgi deployment. Altogether, this work establishes ApoER2 as a novel cargo of the AP-4 complex, suggesting that defects in the trafficking of this receptor and in the Reelin signaling pathway could contribute to the pathogenesis of HSP caused by mutations in AP-4 subunits.

cell biology↗

bioRxiv2023

Evolution of ion channels in cetaceans a natural experiment in the tree of life

Cetaceans could be seen as a natural experiment within the tree of life in which a mammalian lineage changed from terrestrial to aquatic habitats. This shift involved extensive phenotypic modifications, which represent an opportunity to explore the genetic bases of phenotypic diversity. Furthermore, the availability of whole genome sequences in representative species of all main cetacean groups means that we are in a golden age for such studies. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin (TTX), similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than non-cetacean mammals.

evolutionary biology↗

bioRxiv2021

Identification of multiple TAR DNA Binding Protein retropseudogene lineages during the evolution of primates

The TAR DNA Binding Protein (TARDBP) gene has gained attention in biomedicine after the discovery of several pathogenic mutations. The lack of knowledge about its evolutionary history contrasts with a large number of studies in the biomedical area. This study aimed to investigate the retrotransposition evolutionary dynamics associated with this gene in primates. We identified retropseudogenes that originated in the ancestors of anthropoids, catarrhines, and lemuriformes, i.e. the strepsirrhine clade that inhabit Madagascar. We also found species-specific retropseudogenes in the philippine tarsier, Bolivian squirrel monkey, capuchin monkey and vervet. Although retropseudogenes are not able to produce a functional protein, we can not rule out that they may represent genetic material upon which evolution acts on, especially with regulatory functions.

evolutionary biology↗

bioRxiv2020

The proteasomal deubiquitinating enzyme PSMD14 regulates macroautophagy by controlling Golgi-to-ER retrograde transport

Ubiquitination regulates several biological processes. Here, we search for ubiquitin-related genes implicated in protein membrane trafficking performing a High-Content siRNA Screening including 1,187 genes of the human "ubiquitinome" using Amyloid Precursor Protein (APP) as a reporter. We identified the deubiquitinating enzyme PSMD14, a subunit of the 19S regulatory particle of the proteasome, specific for K63-Ub chains in cells, as a novel key regulator of Golgi-to-endoplasmic reticulum (ER) retrograde transport. Silencing or pharmacological inhibition of PSMD14 caused a robust and rapid inhibition of Golgi-to-ER retrograde transport which leads to a potent blockage of macroautophagy by a mechanism associated with the retention of Atg9A and Rab1A at the Golgi apparatus. Because pharmacological inhibition of the proteolytic core of the 20S proteasome did not recapitulate these effects, we concluded that PSMD14, and their K-63-Ub chains, act as a crucial regulator factor for macroautophagy by controlling Golgi-to-ER retrograde transport.

cell biology↗