Biology subjects

Pandi-Perumal, S. R.

Publications and source records attributed to Pandi-Perumal, S. R..

4 recordsLinked to original sources

bioRxiv2025

Examining Sleep Signals at the Cradle of Life: Can phylogenomic analysis of the Last Universal Common Ancestor (LUCA) reveal the fundamental role of sleep?

In common with most physiological activities, sleep is a highly evolutionarily conserved function. Nevertheless, the purpose of sleep remains inadequately investigated. One possible cause of this deficiency is the limitations of the traditional methods used for examining sleep. Up to this time, the mainstay tool used to look at the evolutionary basis of sleep has been phylogenetic analysis. This approach has provided many valuable insights into sleep, yet it has left many questions unanswered. The present study uses a relatively new hybrid technique at the interface of phylogenetics and genomics, known as phylogenomic analysis. This study is the first to use phylogenomic analysis to investigate the basis of sleep by evaluating the presence and conservation of sleep-related genes in the reconstructed genome of the Last Universal Common Ancestor (LUCA). Our gene set enrichment analysis of humans and LUCA indicates that the conserved sleep genes are linked to signaling, metabolism, and circadian rhythm pathways, suggesting that these genes possess primordial roles in essential physiological functions. These findings indicate that the component genes carry out essential physiological tasks that were subsequently repurposed to regulate sleep in more advanced organisms throughout evolution. This study lays the foundation for a systematic phylogenomic exploration of sleep-related genes, connecting molecular evolution with sleep science. By tracing the biological history of sleep to its deep evolutionary origins, our research presents novel insights into sleeps nature, origin, and evolutionary function, paving the way for further interdisciplinary exploration of the biology of sleep. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/644522v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@17adc89org.highwire.dtl.DTLVardef@124de86org.highwire.dtl.DTLVardef@18d3e5corg.highwire.dtl.DTLVardef@1f93b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Studying sleep orthologs in Epsilonproteobacteria through an evolutionary lens: Investigating sleep mysteries through phylogenomics

The current study employed phylogenomic methods to examine the evolutionary role and significance of sleep-related genes in Sulfurimonas paralvinellae of the Epsilonproteobacteria class. This has facilitated the identification of conserved sleep orthologs, including DnaK, serine hydroxymethyltransferase, and potassium channel family proteins, exhibiting sequence similarities ranging from 39.13% to 61.45%. These findings align with prior research indicating that chaperones and ion channels are conserved during sleep. This was demonstrated by the observation that proteins with fewer domains exhibited more significant conservation than others, such as adenylate kinase, which is substantial under selective pressure. Distinct adaptations in bifunctional protein - serine/threonine kinases and phosphatases were linked to S. paralvinellae, an extremophilic organism adapted to high-pressure and/or high-temperature conditions, indicating functional divergence influenced by the organisms environment. The Gene Ontology study results indicated catalytic activity, potassium channel function, and cellular processes, underscoring the significance of ion channels in regulating the sleep-wake cycle. Furthermore, the categories not recognized as particularly significant for the over-represented genes encompassed metabolic and signal transduction categories, suggesting enhanced functional flexibility within this protein subfamily. The findings emphasize that orthologous interactions are complex and influenced by subfunctionalization and neofunctionalization of ecology and evolution. These findings enhance the existing understanding of the evolution of sleep-related genes and their association with metabolic and environmental changes, providing a foundation for subsequent experimental investigations and cross-taxonomic comparisons.

genomics↗

bioRxiv2024

Unraveling the Mysteries of Sleep: Exploring Phylogenomic Sleep Signals in the Recently Characterized Archaeal Phylum Lokiarchaeota near Loki's Castle

Sleep is a universally conserved behavior with an elusive origin and an uncertain evolutionary purpose. Leveraging phylogenomics, we investigate the evolutionary foundations of sleep by identifying orthologs of Human sleep-related genes in the Lokiarchaeota of the Asgard superphylum. Our findings indicate a conserved suite of genes associated with energy metabolism and cellular repair, suggesting a primordial role of sleep in cellular maintenance. This data lends credence to the idea that sleep improves organismal fitness across evolutionary time by acting as a restorative process. Notably, our approach demonstrates that phylogenomics is more useful than standard phylogenetics for clarifying common evolutionary traits. By offering insight into the evolutionary history of sleep and putting forth a novel model framework for sleep research across taxa, these findings contribute to our growing understanding of the molecular foundation of sleep. This study lays the groundwork for further investigations into the importance of sleep in various organisms, which could have consequences for human health and a deeper comprehension related to the fundamental processes of life. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/621620v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@4dd502org.highwire.dtl.DTLVardef@1db82c5org.highwire.dtl.DTLVardef@6662d3org.highwire.dtl.DTLVardef@1e2268b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Cross-Kingdom Genomic Conservation of Human Sleep-Related Gene Orthologs: Phylogenomic Evidence from Chlamydomonas reinhardtii

Sleep is a widespread and evolutionarily conserved process observed in diverse organisms, from jellyfish to mammals, hinting at its origin as a life-supporting mechanism over 500 million years ago. Although its fundamental purpose and mechanisms remain unclear, the evolution and adaptive significance of sleep continue to be debated. This study explores the evolutionary origins of sleep using Chlamydomonas reinhardtii as a model organism, identifying 145 orthologs analogous to known sleep-related genes across species, highlighting the evolutionary conservation of sleep-regulating pathways. Additionally, discovering uncharacterized proteins with high sequence similarity and significant e-values suggests unexplored roles in sleep regulation, underscoring the potential of C. reinhardtii to reveal new insights into the molecular basis of sleep. This work provides a foundation for identifying previously unknown sleep-associated proteins, particularly within single-celled organisms, which may offer novel perspectives on the biological role of sleep. The study demonstrates that phylogenomic analysis of diverse model organisms can expand our understanding of the evolutionary trajectory of sleep and its fundamental function, paving the way for further research in sleep biology and its health implications. Overall, the fundamental functions of sleep observed in higher animal phyla originated from its primordial activities, demonstrating an evolutionary continuum wherein more specialized tasks were integrated with sleeps essential restorative properties.

bioinformatics↗