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Published on: September 25, 2021
Identification of lncRNA and weighted gene coexpression network analysis of germinating Rhizopus delemar causing
Barsha Kalita1, Abhijeet Roy1, Aiswarya Jayaprakash1
1Department of Bioinformatics, Pondicherry University, Puducherry, India.
Abstract:
Rhizopus delemar, an opportunistic fungal pathogen, causes a highly fatal disease, mucormycosis. Spore germination is a crucial mechanism for disease pathogenesis. Thus, exploring the molecular mechanisms of fungal germination would underpin our knowledge of such transformation and, in turn, help control mucormycosis. To gain insight into the developmental process particularly associated with cell wall modification and synthesis, weighted gene co-expression network analysis (WGCNA) was performed including both coding and non-coding transcripts identified in the current study, to find out the module of interest in the germination stages. The module-trait relationship identified a particular module to have a high correlation only at the resting phase and further analysis revealed the module to be enriched for protein phosphorylation, carbohydrate metabolic process, and cellular response to stimulus. Moreover, co-expression network analysis of highly connected nodes revealed cell wall modifying enzymes, especially those involved in mannosylation, chitin-glucan crosslinking, and polygalacturonase activities co-expressing and interacting with the novel lncRNAs among which some of them predicted to be endogenous target mimic (eTM) lncRNAs. Hence, the present study provides an insight into the onset of spore germination and the information on the novel non-coding transcripts with key cell wall-related enzymes as potential targets against mucormycosis.
Insights
This study reveals key molecular mechanisms of Rhizopus delemar spore germination, identifying novel non-coding RNAs interacting with cell wall enzymes. These findings offer potential new targets for controlling mucormycosis, a dangerous fungal infection.
Area of Science:
- Mycology
- Molecular Biology
- Pathogenesis
Background:
- Mucormycosis, a severe fungal disease caused by Rhizopus delemar, relies on spore germination for pathogenesis.
- Understanding fungal germination mechanisms is critical for developing effective mucormycosis treatments.
Purpose of the Study:
- To investigate the molecular mechanisms underlying Rhizopus delemar spore germination, focusing on cell wall modification and synthesis.
- To identify novel non-coding transcripts involved in fungal development and pathogenesis.
Main Methods:
- Weighted gene co-expression network analysis (WGCNA) was employed on coding and non-coding transcripts during germination stages.
- Co-expression network analysis focused on highly connected nodes and module-trait relationships.
Main Results:
- A specific gene module correlated with the resting phase was enriched for protein phosphorylation, carbohydrate metabolism, and cellular response pathways.
- Cell wall modifying enzymes (mannosylation, chitin-glucan crosslinking, polygalacturonase) were found to co-express and interact with novel long non-coding RNAs (lncRNAs).
- Some identified lncRNAs were predicted to function as endogenous target mimic (eTM) lncRNAs.
Conclusions:
- The study provides insights into the early stages of Rhizopus delemar spore germination.
- Novel non-coding transcripts interacting with key cell wall enzymes represent potential therapeutic targets for combating mucormycosis.
