Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

Abstract

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

The Evolution and Functional Roles of miR408 and Its Targets in Plants

“…The IbKCS cleavage sites guided by miR408 are located at the 5th and 10th nucleotides from the 5′ end, which are non-canonical and canonical cutting sites, respectively [ 44 ]. In S. officinarum , the Diphenol oxidase laccase cleavage sites guided by miR408 are located at the second to third nucleotides from the 5′ end [ 64 ]. In M. truncatula , m iR408 cleaved PLC at the 10th–11th nucleotides from the 5′ end [ 41 ].…”

The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops

“…In addition to genetic mechanisms, diazotrophic bacteria can trigger specific epigenetic modifications that regulate development [ 171 ] and cell wall lignification [ 101 , 172 ]. Epigenetic studies on sugarcane plants have revealed the differential expression of miR408 in response to either diazotrophic bacteria, G. diazotrophicus PAL5, or the pathogenic bacteria Acidovorax avenae [ 172 ].…”

“…In addition to genetic mechanisms, diazotrophic bacteria can trigger specific epigenetic modifications that regulate development [ 171 ] and cell wall lignification [ 101 , 172 ]. Epigenetic studies on sugarcane plants have revealed the differential expression of miR408 in response to either diazotrophic bacteria, G. diazotrophicus PAL5, or the pathogenic bacteria Acidovorax avenae [ 172 ]. MiR408 was induced in response to beneficial association and repressed upon pathogenic infection, regulating the expression of mRNA encoding laccase, a multicopper enzyme involved in lignin biosynthesis [ 172 ].…”

“…Epigenetic studies on sugarcane plants have revealed the differential expression of miR408 in response to either diazotrophic bacteria, G. diazotrophicus PAL5, or the pathogenic bacteria Acidovorax avenae [ 172 ]. MiR408 was induced in response to beneficial association and repressed upon pathogenic infection, regulating the expression of mRNA encoding laccase, a multicopper enzyme involved in lignin biosynthesis [ 172 ]. The same expression pattern was found in maize plants inoculated with H. seropedicae [ 101 ].…”

Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots

“…Several publications reported the identification of miRNAs in biofuel crops such as Miscanthus giganteus(Jha & Shankar, 2013), Setaria italica(Yadav, Muthamilarasan, Pandey, Khan, & Prasad, 2014;Yi, Xie, Liu, Qi, & Yu, 2013), Sorghum bicolor(Calviño, Bruggmann, & Messing, 2011), Z. mays(Aravind et al, 2017;Liu et al, 2019), and Saccharum sp. (Gentile, Dias, Mattos, Ferreira, & Menossi, 2015 and references therein;Li et al, 2017;Thiebaut et al, 2017;Su et al, 2017;Yang et al, 2017). However, only a few of them addressed specific miR-NAs predicted to be involved in cell wall construction or remodeling.In the present work, we identified 39 miRNAs expressed within the roots of the biofuel crop sugarcane undergoing cell wall changes due to aerenchyma formation.…”