Abstract
Bacterial transcriptome profiling in the presence of plant fluids or extracts during microbial growth may provide relevant information on plant–bacteria interactions. Here, RNA sequencing (RNA-Seq) was used to determine the transcriptomic profile of Herbaspirillum seropedicae strain HRC54 at the early stages of response to sugarcane apoplastic fluid. Differentially expressed gene (DEG) analysis was performed using the DESeq2 and edgeR packages, followed by functional annotation using Blast2GO and gene ontology enrichment analysis using the COG and KEGG databases. After 2 h of sugarcane apoplastic fluid addition to the H. seropedicae HRC54 culture, respectively, 44 and 45 genes were upregulated and downregulated. These genes were enriched in bacterial metabolism (e.g., oxidoreductase and transferase), ABC transporters, motility, secretion systems, and signal transduction. RNA-Seq expression profiles of 12 genes identified in data analyses were verified by RT-qPCR. The results suggested that H. seropedicae HRC54 recognized sugarcane apoplastic fluid as the host signal, and some DEGs were closely involved at the early stages of the establishment of plant–bacteria interactions.
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The authors thank the National Council of Scientific and Technological Development—CNPq for the fellowships (Grant number 308818/2016-4 and Doctor's scholarship 154782/2016-5); and Embrapa (project MP2 number 02.13.08.006.00.00) and CNPq/INCT-FBN (No. 573828/2008-3) for the financial support.
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DDVP and JLSA were responsible for the bioinformatic analysis; MZTS and EMS for the RNA-Seq experiment and CMS for the confocal microscopy. DDVP drafted the manuscript and MSV, JIB and JLSA corrected it. The authors are aware of the content and results presented in this publication.
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Pessoa, D.D.V., Dos-Santos, C.M., Vidal, M.S. et al. Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid. 3 Biotech 11, 292 (2021). https://doi.org/10.1007/s13205-021-02848-y
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DOI: https://doi.org/10.1007/s13205-021-02848-y