Biology subjects

Choi, I.-S.

Publications and source records attributed to Choi, I.-S..

5 recordsLinked to original sources

bioRxiv2026

Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

Across eukaryotes, mitochondrial (mt) and nuclear genomes coordinate the expression and interaction of gene products to maintain cellular functions. While mitonuclear coevolution has been widely explored in animals, it remains understudied in plants, despite their utility as model systems due to relatively slow mitochondrial evolutionary rates and the presence of plastids. Plants rely on oxidative phosphorylation (OXPHOS) for ATP conversion, which requires cofunctionality and likely coevolution of mitochondrial and nuclear gene products. Here, we investigated evolutionary rate covariation (ERC) between mitochondrial- and nuclear-encoded OXPHOS genes in papilionoid legumes, where plastid-nuclear coevolution and an inversion in plastid DNA have been documented previously. Using 50 legume species spanning 15 papilionoid clades, we estimated evolutionary rates for five gene sets: mt-encoded OXPHOS genes, nuclear-encoded mitochondrial-targeted (N-mt) OXPHOS genes, and three control nuclear gene sets that lack mitochondrial interactions (glycolysis, cell cycle, and cytosolic ribosomal genes). Both mt and N-mt OXPHOS genes exhibited significantly elevated nonsynonymous (dN) and synonymous substitution rates (dS) in the 50-kb inversion clade relative to other legumes, suggesting accelerated mitochondrial substitution rates. Moreover, elevated dN/dS ratios in mt and N-mt OXPHOS genes in this clade were driven by relaxed purifying, not intensified positive selection. ERCs were highest for OXPHOS complexes and genes with physical mitonuclear interactions, as predicted under mitonuclear coevolution. We discuss how these results compare to other cases of cytonuclear coevolution in plants, including plastid-nuclear coevolution in papilionoids, and why dual-targeted, nuclear-encoded genes that repair mt and plastid DNA may underly patterns of molecular evolution in both organelles. Significance StatementMitonuclear interactions are essential for cellular energy production, yet the evolutionary dynamics of these interactions remain poorly understood in plants. This study highlights papilionoid legumes as an important system for understanding how coordinated evolution between mitochondrial and nuclear genes shapes plant genomes. By identifying signatures of mitonuclear coevolution in the 50-kb inversion clade, this work demonstrates how shifts in selective pressures on mitochondrial processes can influence nuclear gene evolution. These findings advance our understanding of cytonuclear coordination in plants and provide a foundation for future studies exploring how interactions among genomic compartments contribute to plant evolution, adaptation, and resilience in agriculturally important lineages.

evolutionary biology↗

bioRxiv2025

Influenza A Virus infection is associated with TDP-43 pathology and neuronal damage in the brain

Viral pandemics such as COVID-19 have demonstrated long-term neurological consequences, including memory impairment and depression, emphasizing the importance of understanding virus-brain interactions [1]. Similar concerns have been raised for Influenza A virus (IAV), which has been implicated in neurodegenerative disorders [2, 3]. In this study, we investigated the neuropathological effects of highly pathogenic avian influenza (HPAI) H5N1 and H5N8 strains in a mouse model. Although viral RNA was detected in the brain post-infection, no viral proteins were found, suggesting limited or transient brain replication. Despite this, infected brains showed significant neuronal damage, including axonal loss and nuclear condensation, as evidenced by immunofluorescence and Nissl staining. We also observed pathological changes in TDP-43, including conformational alterations and increased phosphorylation, which required antigen retrieval for detection--features reminiscent of those found in frontotemporal dementia and amyotrophic lateral sclerosis [4, 5]. Transcriptomic analysis further revealed strain-specific host responses, including activation of interferon-related genes and downregulation of microtubule-associated pathways. These findings suggest that IAV infection can trigger hallmarks of neurodegeneration in the absence of persistent viral protein expression, possibly through host-driven mechanisms. Our results underscore the need for further investigation into virus-induced molecular pathways contributing to neurodegenerative disease.

neuroscience↗

bioRxiv2024

Well-resolved phylogeny reveals multiple origins of keel flowers during the diversification of papilionoid legumes

O_LIThe butterfly-shaped keel flower is a highly successful floral form in angiosperms. These flowers steer the mechanical interaction with bees and thus are hypothesized to accelerate pollinator-driven diversification. The exceptionally labile evolution of keel flowers in Papilionoideae (Fabaceae) provides a suitable system to test this hypothesis. C_LIO_LIUsing 1,456 low-copy nuclear loci, we confidently resolve the early divergence history of Papilionoideae. Constrained by this backbone phylogeny, we generated a time tree for 3,326 Fabales to evaluate the tempo and mode of diversification within a state-dependent evolutionary framework. C_LIO_LIThe first keel flowers emerged around 59.0 Ma in Papilionoideae, predating the earliest fossil by 3-4 million years. The Miocene diversification of Papilionoideae coincided with rapid evolution of keel flowers. At least six independent origins and thirty-two losses of keel flowers were identified in Papilionoideae, Cercidoideae, and Polygalaceae. However, the state-dependent diversification model was not favored. C_LIO_LILack of radiation associated with keel flowers suggests that diversification within Papilionoideae was not solely driven by pollinator-mediated selection, but instead an outcome of the synergistic effects of multiple innovations including nitrogen fixation and chemical defense as well as dispersal into subtropical and temperate regions. C_LI

evolutionary biology↗

bioRxiv2021

The chicken or the egg? Plastome evolution and a novel loss of the inverted repeat in papilionoid legumes

The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study 33 newly sequenced plastomes of papilionoid legumes and outgroups were evaluated, along with 34 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, just [~]20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the inverted repeat has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in driving plastome change is discussed. Significance statementComparative genomic approaches employing plastid genomes (plastomes) have revealed that they are more variable across angiosperms than previously suggested. This study examined 64 species of Fabaceae and outgroups, including 33 newly sequenced taxa, to explore plastome structural evolution of the subfamily Papilionoideae in a phylogenetic context. Several unusual features of the inverted repeat highlight the importance of recombination in plastomic structural changes within and between individuals and species.

plant biology↗

bioRxiv2020

Fibroblasts close a void in free space by a purse-string mechanism

How stromal cells fill voids in wounded tissue remains one of the most fundamental questions in regenerative medicine. Fibroblasts are known to fill voids by depositing extracellular matrix (ECM) proteins while migrating towards the wound site; however, their ability to adopt an epithelial-like purse-string behaviour remains unexplored. Here, we fabricated an artificial wound with a deep void space to investigate fibroblasts behaviour during gap closure. We found that fibroblasts can form a free-standing bridge on deep microvoids and consequently close the void through the purse-string contraction, which was previously believed to be exclusively an epithelial wound closure mechanism. The results also revealed that the fibroblast gap closure in our fabricated 3D artificial wound depends on myosin II-mediated contractility and intercellular adherent junctions. Our study reveals that stromal cells can gain the structural features of epithelial cells, namely, intercellular contractile rings, to fulfil their functions under the specific microenvironmental conditions of tissue repair. Furthermore, fibroblasts can close artificial wounds with gap widths up to 300 m, approximately twice as large as the critical epithelial gap closure size on non-adherent substrates. Fibroblasts exhibited a zip-up gap closure mechanism with a geometrical size effect. These findings reveal a new mechanism for gap closure by stromal cells during wound healing and pave a way to groundbreaking therapeutic strategies for tissue repair.

biophysics↗