Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Genomics

Background:

• Short noncoding RNAs, like microRNAs (miRNAs), are crucial for eukaryotic gene regulation.
• Mito-nuclear crosstalk, the communication between mitochondria and the nucleus, is a key cellular process.
• Mitochondrial-derived small RNAs (smithRNAs) have been identified in bivalves, capable of regulating nuclear genes.

Purpose of the Study:

• To estimate the probability of de novo evolved smithRNAs finding suitable targets in the nuclear transcriptome.
• To investigate the evolutionary potential and significance of smithRNAs in mito-nuclear interactions.

Main Methods:

• Computational simulations using transcriptomes from 12 bivalve species.
• Analysis of potential smithRNA-target interactions, considering mismatches.

Main Results:

• The probability of a novel smithRNA finding a nuclear target is high (1x10^-8 with 5 mismatches).
• This probability is consistent across different bivalve species.
• Mitochondrial RNAs can be exapted to form functional smithRNAs.

Conclusions:

• Novel smithRNAs can readily evolve from existing mitochondrial RNAs.
• The emergence of smithRNAs likely played a significant role in the evolution of mito-nuclear interactions.
• SmithRNAs may have contributed to speciation events in animals.