New Method Enhances mRNA Analysis to Reveal Plant-Bacteria Interaction Dynamics

Jenn Hoskins
2nd July, 2024

New Method Enhances mRNA Analysis to Reveal Plant-Bacteria Interaction Dynamics

Image Source: Natural Science News, 2024

Key Findings

  • Researchers at Gyeongsang National University developed a new RNA-seq method to better study plant-bacterial interactions
  • This method enriches bacterial mRNA in plant samples by removing ribosomal RNA, improving the analysis of bacterial gene expression
  • The new method increased the mapping efficiency of bacterial genes in infected plants and identified more differentially expressed genes than conventional methods
Understanding the complex interactions between plants and microbes is crucial for developing resilient agricultural systems. One powerful tool for this purpose is RNA sequencing (RNA-seq), which helps researchers study gene expression. However, RNA-seq faces challenges, particularly in analyzing bacterial transcriptomics within plant-bacterial interactions. This is due to the abundant ribosomal RNA (rRNA) that can overshadow important transcripts. A recent study by Gyeongsang National University[1] aimed to address this issue by modifying a strand-specific dual RNA-seq method to enrich bacterial mRNA in infected plant samples. In this study, researchers focused on various plant-bacterial interactions, including both host and non-host resistance interactions with pathogenic bacteria, as well as interactions with beneficial rhizosphere-associated bacteria in pepper and tomato plants. The enriched method involved sequentially separating plant mRNA through poly A selection and removing rRNA to enhance bacterial mRNA. This was followed by strand-specific RNA-seq library preparation steps. The results were promising. The enriched method showed an increased mapping efficiency in all plant-bacterial interactions examined, although it produced a lower read count. Specifically, in the compatible interaction with Xanthomonas campestris pv. Vesicatoria race 3 (Xcv3), the enriched method increased the mapping ratio of Xcv3-infected pepper samples to its own genome by 1.45-fold and to the coding sequences (CDS) by 1.49-fold. This method consistently identified a greater number of differentially expressed genes (DEGs) than the conventional RNA-seq method, particularly during the early stages of Xcv3 infection in peppers. Gene Ontology (GO) enrichment analysis revealed that these DEGs were predominantly involved in proteolysis, kinase, serine-type endopeptidase, and heme-binding activities. Previous studies have highlighted the advantages of RNA-seq over microarrays in various contexts. For instance, RNA-seq has been shown to identify more differentially expressed genes and provide a wider quantitative range of expression levels compared to microarrays[2]. Additionally, RNA-seq is superior in detecting low-abundance transcripts, differentiating biologically critical isoforms, and identifying genetic variants[3]. These benefits are particularly relevant in the context of plant-microbe interactions, where understanding the nuanced gene expression changes can lead to more effective strategies for enhancing plant resistance to various stresses. The enriched method developed by Gyeongsang National University builds on these advantages by specifically targeting the challenges associated with bacterial transcriptomics in plant samples. By effectively removing rRNA and enriching bacterial mRNA, this method allows for a more comprehensive and detailed analysis of the bacterial transcriptome. This is crucial for understanding the molecular dynamics of plant-bacterial interactions and can provide valuable insights for developing disease-resistant crops. The study also ties into broader research on plant stress responses. For example, RNA-seq analyses have been used to study peppers under various abiotic stresses, providing useful information for developing stress-resistant cultivars[4]. Similarly, a comprehensive RNA-seq dataset across different stress conditions in Capsicum annuum has helped identify critical genetic factors associated with stress responses[5]. The enriched method for bacterial mRNA in plant samples can complement these studies by providing a more detailed understanding of how bacterial interactions influence plant stress responses. In conclusion, the enriched dual RNA-seq method developed by Gyeongsang National University offers a significant improvement over conventional methods for studying plant-bacterial interactions. By enhancing the proportion of bacterial mRNA, this method provides a more detailed and accurate picture of the transcriptomic changes occurring during these interactions. This advancement not only addresses a critical technical challenge in RNA-seq but also opens up new avenues for research into plant resistance mechanisms and the development of resilient agricultural systems.

BiotechGeneticsPlant Science

References

Main Study

1) An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.

Published 1st July, 2024

https://doi.org/10.1186/s13007-024-01227-x

Related Studies

2) Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies.

https://doi.org/10.3389/fgene.2018.00636

3) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells.

https://doi.org/10.1371/journal.pone.0078644

4) Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

https://doi.org/10.1038/s41597-020-0352-7

5) Global co-expression network for key factor selection on environmental stress RNA-seq dataset in Capsicum annuum.

https://doi.org/10.1038/s41597-023-02592-3


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