Time-dependent oscillation of pre-MiRNAs, mature MiRNAs and MiRNA targets in tomato plants subjected to varying abiotic stress conditions

Abstract

Miniature non-coding RNAs known as MicroRNAs (MiRNA) are transcribed from their independent genes. MiRNAs bind to and regulate various transcripts. They have been linked to a number of biological processes ranging from organ growth, senescence, and pathogen response. We used model crop tomato to study how miRNA genes respond to a variety of abiotic stress, e.g. salt, drought and cold temperature. Precursor-miRNA (pre-miR) levels of six highly conserved plant miRNAs were monitored over 24 h time period. Expression of pre-miR159, −160, −162 and −397 were induced, while pre-miR171a and −319 levels were down regulated as a reaction to a variety of stress treatments. The expression profiles related to miRNA precursors exhibit unique expression pattern to the stress subjected. We followed expression of three mature miRNAs, namely, miR159, miR160 and miR171 upon stress treatment and these exhibited expression profiles similar to their corresponding precursors. Moreover, modulation in mature miRNA levels affected expression of their target transcripts. Prediction of promoter sequences of various tomato pre-miRNAs revealed several cis-elements that may have functional consequence on the gene expression as a consequence of stress. Together, these findings indicate that miRNA genes are sensitive to stress induced due to abiotic factors (climatic stress caused due to drought and cold as well as salt). They demonstrated drastic expression changes to most of the stress examined, a strategy to fine tune transcriptome in a time-efficient manner.