Molecular mechanisms of bamboo-derived miRNA-mediated gene regulation and dietary adaptation in giant pandas

TL;DR

This study explores how giant pandas adapt to a bamboo-only diet by investigating the role of plant-derived miRNAs in regulating genes related to metabolism and immunity.

Contribution

The study identifies and characterizes bamboo-derived miRNAs in giant pandas and demonstrates their cross-kingdom regulatory effects on host genes.

Findings

67 candidate bamboo-derived miRNAs were identified in giant panda plasma exosomes.

miR166a and miR159 were confirmed to directly suppress the HDAC9 gene through binding to its 3’ untranslated region.

Bamboo miRNAs may regulate key pathways like MAPK and NF-kappa B, influencing metabolism and immune response.

Abstract

Giant pandas subsist almost exclusively on bamboo, a low-nutrient, high-fiber plant. However, the molecular mechanisms underlying their dietary adaptation remain unclear. Recent evidence suggests that dietary plant-derived microRNAs (miRNAs) may influence gene regulation across species boundaries. This study aims to investigate the presence and functional significance of bamboo-derived miRNAs in giant pandas, and to explore their potential regulatory roles through gene expression modulation.

We successfully isolated and characterized plasma exosomes from giant pandas and identified 67 candidate bamboo-derived miRNAs by aligning small RNA sequences with bamboo shoot transcriptomes. Functional annotation revealed that these miRNAs target genes involved in metabolism, immunity, neurodevelopment, and cellular homeostasis. Among them, HDAC9 was identified as a core gene targeted by multiple bamboo-derived miRNAs. Dual-luciferase reporter assays confirmed that two representative miRNAs, miR166a and miR159, directly bind to and suppress HDAC9 3’ untranslated region activity. Additionally, target enrichment analysis showed that these miRNAs may influence key signaling pathways, including MAPK and NF-kappa B. Several core target proteins, such as PRKACB, RAC2, and ADCY6, were implicated in inflammation, energy metabolism, and cardiovascular function. These findings suggest a broad and specific regulatory network mediated by dietary bamboo miRNAs.

Our results demonstrate that bamboo-derived miRNAs are present in the blood of giant pandas and may modulate gene expression through cross-kingdom regulatory mechanisms. These miRNAs potentially contribute to dietary adaptation by regulating genes involved in metabolism, immune response, and reproductive processes. This study provides molecular insights into the unique plant-based diet of giant pandas and suggests that cross-kingdom RNA regulation may represent a widespread adaptive strategy across animal taxa.

The online version contains supplementary material available at 10.1186/s12864-025-12244-y.

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