FRILAIR – A new long non-coding RNA helps in strawberry fruit ripening

By | May 21, 2021
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The central dogma of molecular biology states that genetic information present in DNA is passed on in the form of an RNA intermediate, before being translated into proteins. However only a minute fraction of RNA transcribed from DNA, codes for functional proteins.

The RNA molecules which are not translated into proteins but have a function are called as Non-Coding RNAs (ncRNAs). Depending on the size of these RNA molecules they can be classified as :

  1. Small ncRNAs : They are less than 40 nucleotides (not) like microRNA (miRNA), piwi-interacting RNA (piRNA), and tRNA derived small RNA (tsRNA). These small ncRNAs play a pivotal role in chromatin modification, regulating gene expression in development and disease.
  2. ncRNAs shorter than 200 nt but longer than 40 nt, as observed in transfer RNA (tRNA), small nucleolar RNA (snoRNA), and small nuclear ribonucleic acid RNA (snRNA).
  3. ncRNAs longer than 200 nucleotides (nt) – ribosomal RNA (rRNA) and long non-coding RNA (lncRNA).

Similar to small ncRNAs, the long non-coding RNA regulates gene expression at transcriptional and post-transcriptional levels. Thes ncRNAs also have many other physiological functions such as epigenetic regulation, splicing, imprinting, and many more.

Long non-coding RNA and fruit ripening :

Long non-coding RNAs are also present in the plant genome and helps in regulating gene expression during plant development.

Recent work from Tang et al; in the Strawberry plant elucidated the function of a new long non-coding RNA in the ripening of the fruit. Strawberry is a popular fruit and cultivated around the world for its commercial value. The value of the fruit depends a lot on the colour of the strawberry. Dark and uniform red colour fruits hold a special place in the market and fetch a high price.

In a bid to understand the possible role of long ncRNAs in strawberry fruit ripening, the authors did transcriptome sequencing on fruits of the diploid strawberry F. vesca (Hawaii 4) at three developmental stages and further did the analysis. The results yielded a novel long ncRNAs called FRILAIR (FRUIT RIPENING-RELATED LONG INTERGENIC RNA) as a potential candidate. FRILAIR is a 1,520 nucleotide intergenic lncRNA found primarily in the cytoplasm. The interesting aspect of FRILAIR is that it harbors a micro RNA( miR397 ) binding site that is highly conserved in different strawberry species.

FRILAIR competes with miRNA397 target:

miR397 is known for its role in pear fruit development. Since FRILAIR has a miRNA397 binding site, The authors propose that FRILAIR could be competing for miR397 target which might be involved in fruit ripening or development. Further study to decipher targets of miR397 in strawberry fruit ripening resulted in 12 protein-coding genes. From the 12 probable targets, laccase-11-like protein ( LAC11a) expression pattern showed an increase at fruit ripening stages and this is similar to FIRLAIR expression at a similar stage of development.

Expression correlation analysis between FRILAIR, miR397, and LAC11a revealed a positive correlation between expression of FIRLAIR and LAC11a expression, and miR397 has a suppressive effect on LAC11a.

Anthocyanin synthesis is regulated by FRILAIR-miR397-LAC11a interactions:

Genetic studies involving overexpression of LAC11a and FIRLAIR in separate experiments demonstrate the upregulation of genes involved in the anthocyanin pathway. Similar results were observed in knockdown experiments of miR397. This indicates that FIRLAIR indirectly helps in the ripening of strawberry fruits ( indicated by an increase in anthocyanin synthesis) by acting as a target of miR397 and thereby allowing the expression of LAC11a. In absence of FRILAIR, miR397 is free to bind to its other target LAC11a and leads to its degradation.

Functional model for FRILAIR -miR397-LAC11a interplay in fruit ripening:

miR397 can target both FRILAIR and LAC11a for degradation by binding to specific sites.

In abundance of FRILAIR , it saturates available miR297. This allows LAC11a to express at optimal levels to promote expressions of genes involved in anthocyanin biosynthesis pathway, leading to the fastening of strawberry fruit ripening.

In absence of FRILAIR, miR397 is free to bind and cleave LAC11a, thereby affects anthocyanin pathway and hence process of fruit ripening.

Reference and Image credit:

Tang Y, Qu Z, Lei J, He R, Adelson DL, Zhu Y, et al. (2021) The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic. PLoS Genet 17(3): e1009461. https://doi.org/10.1371/journal.pgen.1009461