Suryawanshi, A. | Search bioRxiv

bioRxiv2026

Gene duplication and retrotransposition diversify the antiviral repertoire of macaque IFITM proteins

Interferon-induced transmembrane (IFITM) proteins are broad-spectrum antiviral restriction factors that inhibit viral entry of diverse enveloped viruses. Comparative genomic studies have revealed extensive lineage-specific diversification of IFITM genes, yet the functional consequences of this diversification remain poorly understood. We previously identified an expanded IFITM repertoire in macaques consisting of the canonical IFITM proteins, IFITM1 and IFITM3, a duplicated IFITM3 paralog (IFITM3A), and two retrotransposed IFITM3-derived genes (IFITM3-R1 and IFITM3-R2). Here, we thoroughly characterized the antiviral activities, intracellular localization, and mechanisms of regulation of canonical and non-canonical macaque IFITMs against vesicular stomatitis virus (VSV), influenza A virus (IAV), Sendai virus, and HIV-1. IFITM3A exhibited enhanced antiviral activity relative to IFITM3, particularly against VSV and HIV-1. Comparative mutational analyses identified amino acid substitutions in IFITM3 that contribute to the enhanced antiviral phenotype of IFITM3A. In contrast, the retrocopy IFITM3-R1 exhibited markedly reduced expression due to lysosome-dependent protein turnover mediated by a PPxY motif and a unique lysine residue (K51). Alteration of these determinants increased IFITM3-R1 expression and selectively enhanced restriction of VSV and IAV. Although several macaque IFITMs reduced HIV-1 infectivity when expressed in producer cells, none significantly inhibited HIV-1 infection in target cells. Furthermore, differential incorporation of IFITMs into HIV-1 virions did not consistently correlate with antiviral activity, indicating that virion incorporation alone is insufficient to explain HIV-1 restriction. Together, these findings demonstrate that gene duplication and retrotransposition have generated a functionally diverse IFITM repertoire in macaques and provide insight into how evolutionary diversification expands innate antiviral defenses in primates. ImportanceIFITM proteins are broad-spectrum antiviral restriction factors that inhibit infection of numerous enveloped viruses. Although IFITM genes have undergone extensive diversification during mammalian evolution, the functional consequences of this diversification remain poorly understood. Here, we show that expansion of the macaque IFITM locus through gene duplication and retrotransposition generated proteins with distinct antiviral activities, intracellular localization patterns, and regulatory mechanisms. We identify amino acid determinants that contribute to the enhanced antiviral activity of the duplicated paralog IFITM3A and demonstrate that lysosome-dependent turnover mediated by a PPxY motif and a unique lysine residue limits expression and antiviral activity of the retrocopy IFITM3-R1. We further show that macaque IFITMs inhibit HIV-1 predominantly through producer-cell-dependent mechanisms and reveal that IFITM virion incorporation alone does not predict antiviral potency. These findings provide mechanistic insight into how restriction factor diversification expands innate antiviral defenses and shapes host-virus interactions in primates.

microbiology↗

bioRxiv2026

Dual pathway architecture in songbirds enables robust sensorimotor learning

The acquisition of sensorimotor skills critically depends on basal ganglia (BG)-thalamo-cortical circuits. Prevailing theories propose that the BG optimize motor output through reinforcement learning (RL), using internal performance evaluations to approximate stochastic gradient ascent. However, this framework struggles in non-convex performance landscapes, where local optima hinder efficient learning. Songbirds provide a compelling biological example of robust sensorimotor learning, mastering complex vocalizations through trial-and-error within a specialized BG-thalamo-cortical architecture. Here, we present a computational model constrained by the anatomy, physiology, and developmental trajectory of the zebra finch song system. The model combines a BG-driven RL pathway with a parallel cortical motor pathway that progressively consolidates successful motor patterns via Hebbian plasticity. In addition, we incorporate synaptic volatility within the BG pathway, introducing structured variability across learning. Through simulations of vocal learning using both a biophysical syrinx model and synthetic performance landscapes, we demonstrate that this dual-pathway architecture reliably converges to global optima and outperforms standard and noise-annealed RL approaches. The model reproduces key experimental features of song learning, including non-monotonic learning trajectories, a gradual reduction in motor variability, and the developmental transfer of motor control from subcortical to cortical circuits. Mechanistically, delayed maturation of the cortical pathway provides an implicit regulation of the exploration-exploitation trade-off, while synaptic volatility enables escape from local optima. These results highlight the importance of neural circuit architecture and dynamics in efficient learning, and suggest biologically inspired design principles for improving the robustness and sample efficiency of artificial RL systems in complex sensorimotor domains.

neuroscience↗