# Advances in molecular tools for elucidating nucleic acid biology in fungal pathogens

**Authors:** Lukas Schrettenbrunner, Neshima Mavani, Slavica Janevska, Matthew G Blango

PMC · DOI: 10.1093/femsml/uqag008 · 2026-03-12

## TL;DR

This paper reviews recent molecular tools for studying nucleic acid biology in fungal pathogens, emphasizing their role in understanding and combating these microbes.

## Contribution

The paper provides a comprehensive overview of how modern DNA, RNA, and chromatin-based technologies are advancing the study of fungal pathogens.

## Key findings

- Advances in genetic engineering and chromatin biology are improving understanding of fungal virulence.
- RNA-based technologies and -omics approaches are enhancing the study of fungal pathogens.
- New molecular tools are expected to lead to novel antifungals and diagnostic strategies.

## Abstract

Throughout the history of molecular biology, surprising advances have come from the study of all sorts of microbes. The first description of DNA polymerase came from the bacterial workhorse Escherichia coli, reverse transcriptase was revealed by studies of the Rous Sarcoma Virus, and even the initial discovery of DNA as the hereditary molecule was determined using strains of pneumococci in the classic Griffith and Avery–MacLeod–McCarty experiments. Here, we build from these foundational discoveries to discuss the rapid development of molecular tools to study microbes themselves, with a focus on nucleic acid biology. We use fungal pathogens as a case study, as their diversity, complexity, and emerging appreciation as a global threat to society makes them particularly compelling and informative. In this review, we will address how advancements in methods to probe nucleic acids are now informing our understanding of fungal pathogens and the way we fight them in both the clinic and agriculture. We begin with DNA, taking a close look at the exciting progress in the fields of genetic engineering and chromatin biology, and their impact on the elucidation of virulence-associated cellular processes. Emerging RNA-based technologies follow, highlighting the value provided by biochemical advances and large-scale -omics approaches. We end by speculating on the future of molecular mycology and how these new approaches may facilitate generation of novel antifungals and diagnostic strategies.

Check out this new review highlighting advances in DNA-, RNA-, and chromatin-based technologies and how they are used to keep pace with the emerging threat of fungal pathogens.

## Linked entities

- **Species:** Escherichia coli (taxon 562), Rous sarcoma virus (taxon 11886)

## Full-text entities

- **Genes:** CLP1 (cleavage polyadenylation factor subunit CLP1) [NCBI Gene 854424], AMA1 (Ama1p) [NCBI Gene 853140] {aka SPO70}, WHI3 (mRNA-binding protein WHI3) [NCBI Gene 855524], tRNA [NCBI Gene 13083864], SHE3 (She3p) [NCBI Gene 852427], TRL1 (tRNA ligase) [NCBI Gene 853358] {aka LIG1, RLG1}, CLN3 (cyclin CLN3) [NCBI Gene 851191] {aka DAF1, FUN10, WHI1}, ACT1 (actin) [NCBI Gene 850504] {aka ABY1, END7}, ASH1 (DNA-binding transcription repressor ASH1) [NCBI Gene 853650], PKC1 (protein kinase C) [NCBI Gene 852169] {aka CLY15, CLY5, CLY7, HPO2, RSF8, STT1}
- **Diseases:** Fungal (MESH:D009181), infection (MESH:D007239), invasive pulmonary aspergillosis (MESH:D055744), bloodstream infections (MESH:D018805), C. immitis (MESH:D003047), opportunistic infections (MESH:D009894)
- **Chemicals:** biotin (MESH:D001710), tDRs (MESH:D013936), carbon (MESH:D002244), chitin (MESH:D002686), poly(A) (MESH:D011061), 5-bromouridine-5'-triphosphate (-), t6A (MESH:C003268), 4-thiouridine (MESH:D013891), sulfur (MESH:D013455), H2O2 (MESH:D006861), formaldehyde (MESH:D005557)
- **Species:** Fusarium verticillioides (species) [taxon 117187], Verticillium dahliae (species) [taxon 27337], Cryptococcus neoformans (Cryptococcus neoformans serotype A, species) [taxon 5207], Batrachochytrium (genus) [taxon 100474], Fungi (kingdom) [taxon 4751], Alternaria brassicicola (species) [taxon 29001], Agaricus bisporus (common mushroom, species) [taxon 5341], Candida albicans (species) [taxon 5476], Histoplasma (genus) [taxon 5036], Aspergillus nidulans (species) [taxon 162425], Coccidioides immitis (species) [taxon 5501], Homo sapiens (human, species) [taxon 9606], Fusarium virguliforme (species) [taxon 232082], Rous sarcoma virus (no rank) [taxon 11886], Glycine max (soybean, species) [taxon 3847], Parastagonospora nodorum (species) [taxon 13684], Beauveria bassiana (species) [taxon 176275], Eremothecium gossypii (species) [taxon 33169], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Fusarium fujikuroi (species) [taxon 5127], Aspergillus terreus (species) [taxon 33178], Tetrahymena (genus) [taxon 5890], Pseudogymnoascus destructans (white nose syndrome fungus, species) [taxon 655981], Fusarium graminearum (species) [taxon 5518], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Botrytis cinerea (gray fruit mold, species) [taxon 40559], Penicillium expansum (species) [taxon 27334], Fragaria vesca (alpine strawberry, species) [taxon 57918], Pyricularia oryzae (rice blast fungus, species) [taxon 318829], Fusarium oxysporum (species) [taxon 5507], Aspergillus fumigatus (species) [taxon 746128], Musa acuminata (banana, species) [taxon 4641], Escherichia coli (E. coli, species) [taxon 562], Fusarium oxysporum f. sp. conglutinans Fo5176 (strain) [taxon 660025], Fusarium oxysporum f. sp. cubense (forma specialis) [taxon 61366], Schizosaccharomyces pombe (fission yeast, species) [taxon 4896], Malus domestica (apple, species) [taxon 3750], Galleria mellonella (greater wax moth, species) [taxon 7137], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Human betaherpesvirus 5 (no rank) [taxon 10359], Mycosarcoma maydis (corn smut, species) [taxon 5270], Fusarium odoratissimum (Foc TR4, species) [taxon 2502994], Hepatitis C virus [taxon 11103], Candidozyma auris (species) [taxon 498019], Aspergillus oryzae (species) [taxon 5062], Mucor circinelloides (species) [taxon 36080], Penicillium rubens (species) [taxon 1108849], Aspergillus niger (species) [taxon 5061], Nakaseomyces nivariensis (species) [taxon 418086]
- **Cell lines:** Af293 — Homo sapiens (Human), Finite cell line (CVCL_R691)

## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13003923/full.md

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Source: https://tomesphere.com/paper/PMC13003923