Evolutionary and Functional Genomics of Mitochondria

Mitochondria (mts) are a fundamental component of eukaryotic life, but current knowledge about their biology and function is largely incomplete. The animal mitochondrial DNA (mtDNA) is very compact, with few short intergenic regions (besides the Control Region), so that one may consider that there is little space for functions other than the usual content of 36-37 genes. The role of mitochondria on shaping nuclear gene expression has been hypothesized only recently, and few lines of evidence are present. At the moment, mitochondria have been proven to produce small interfering RNAs (RNAi), long non-coding RNAs (lncRNAs) and peptides, all of them suggested or proved to interact via different pathways with the nucleus. The possibility that mtDNA can act on nuclear genes regulation is likely to open a new avenue in mitochondrial studies, adding new functions to mitochondria, and producing brand-new research lines of eukaryote biology and evolution.

Such a complex crosstalk between nucleus and mitochondria also creates the condition for a close co-evolution between them at many levels, as well as the evolution of mito-nuclear genomic conflicts.

Finally, as mitochondria are proven to derive from free-living a-proteobacteria, which are known to interact with their host and change their gene expression (see f.i. Wolbachia), it would be interested to understand what kind of mechanisms have been inherited from the free living proteobacteria, hence the role of these mechanisms in eukaryogenesis, i.e., the evolution of the eukaryotic cell.

Mitochondria to Nucleus RNA trafficking

Although mitochondria appear to be a major destination for nuclear-encoded RNAs, far less is known about RNAs coded by the mitochondrion and delivering their activities in the cytoplasm and nucleus. In fact, data are arising that either small (sncRNAs) and long noncoding RNAs (lncRNAs) are produced by the mitochondrial DNA and delivered outside the organelles, thus realizing a form of RNA-mediated retrograde signaling (i.e., organelle-to-nucleus) (Weber-Lotfi & Dietrich, 2018).

We recently discovery of a new class of small non-coding RNAs (sncRNAs), called smithRNAs, coded by the mitochondrial genome (mtDNA) and predicted to regulate nuclear gene expression.  We now know that they are found in other animals as well, and that they could be involved in additional functions besides sex determination, but many aspects of their biology remain totally unstudied (biogenesis, target genes, taxonomic distribution, evolutionary conservation). Indeed, the smithRNAs may be regarded as a generalized new form of retrograde signaling (i.e., the mitochondria-to-nucleus signaling) and, potentially, a common feature among animals.

In our Lab we are now characterizing these sncRNAs by:

1) an in-depth characterization of smithRNAs in R. philippinarum with selected functionality tests;

2) exploring their biogenesis, to assess if they pertain to siRNA, miRNA or piRNA, or rather to a new alternative class of small non-coding RNAs;

3) further assessing their presence in selected metazoan species and their evolutionary conservation; and

4) analyze the a-proteobacterium Wolbachia, known to be a sex distorter in arthropods, to assess whether a similar RNA interference mechanism is present in a-proteobacteria that are regarded as the closest “free-living” relatives of mitochondria.

This research has been funded by the Italian Ministry of Research grant PRIN2020 (MitoMicro – Mitochondrial MicroRNAs, a new perspective for mitochondrial function and their role in Eukaryotic evolution). This ERC research proposal aims to a more in-depth and wider characterization of these small non-coding RNAs among selected metazoans (see below).