Scientific Reports (Dec 2021)

An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection

  • Ganna Reshetnyak,
  • Jonathan M. Jacobs,
  • Florence Auguy,
  • Coline Sciallano,
  • Lisa Claude,
  • Clemence Medina,
  • Alvaro L. Perez-Quintero,
  • Aurore Comte,
  • Emilie Thomas,
  • Adam Bogdanove,
  • Ralf Koebnik,
  • Boris Szurek,
  • Anne Dievart,
  • Christophe Brugidou,
  • Severine Lacombe,
  • Sebastien Cunnac

DOI
https://doi.org/10.1038/s41598-021-03391-9
Journal volume & issue
Vol. 11, no. 1
pp. 1 – 20

Abstract

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Abstract Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant–microbe interactions.