Identification and Verification of Candidate miRNA Biomarkers with Application to Infection with <i>Emiliania huxleyi</i> Virus

Enquan Zhang; Shumiao Zhang; Guiling Li; Zhengxiao Zhang; Jingwen Liu

doi:10.3390/genes14091716

Genes (Aug 2023)

Identification and Verification of Candidate miRNA Biomarkers with Application to Infection with <i>Emiliania huxleyi</i> Virus

Enquan Zhang,
Shumiao Zhang,
Guiling Li,
Zhengxiao Zhang,
Jingwen Liu

Affiliations

Enquan Zhang: College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China
Shumiao Zhang: College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China
Guiling Li: College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China
Zhengxiao Zhang: College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China
Jingwen Liu: College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China

DOI: https://doi.org/10.3390/genes14091716
Journal volume & issue: Vol. 14, no. 9
p. 1716

Abstract

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The interactions of Emiliania huxleyi and its specific lytic virus (EhV) have a profound influence on marine biogeochemical carbon–sulfur cycles and play a prominent role in global climate change. MicroRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential due to their role in virus–host interactions. However, the application of miRNA signatures as diagnostic markers in marine viral infection has made limited progress. Based on our previous small-RNA sequencing data, one host miRNA biomarker that is upregulated in early infection and seven viral miRNA biomarkers that are upregulated in late infection were identified and verified using qRT-PCR and a receiver operating characteristic curve analysis in pure culture, mixed culture, and natural seawater culture. The host ehx-miR20-5p was able to significantly differentiate infection groups from the control in the middle (24 h post-infection, hpi) and late infection (48 hpi) phases, while seven virus-derived miRNA biomarkers could diagnose the early and late stages of EhV infection. Functional enrichment analysis showed that these miRNAs participated in numerous essential metabolic pathways, including gene transcription and translation, cell division-related pathways, protein-degradation-related processes, and lipid metabolism. Additionally, a dual-luciferase reporter assay confirmed the targeted relationship between a viral ehv-miR7-5p and the host dihydroceramide desaturase gene (hDCD). This finding suggests that the virus-derived miRNA has the ability to inhibit the host sphingolipid metabolism, which is a specific characteristic of EhV infection during the late stage. Our data revealed a cluster of potential miRNA biomarkers with significant regulatory functions that could be used to diagnose EhV infection, which has implications for assessing the infectious activity of EhV in a natural marine environment.

Published in Genes

ISSN: 2073-4425 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://www.mdpi.com/journal/genes/

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