Post-transcriptional mending of gene sequences: Looking under the hood of mitochondrial gene expression in diplonemids

Abstract

The instructions to make proteins and structural RNAs are laid down in gene sequences. Yet, in certain instances, these primary instructions need to be modified considerably during gene expression, most often at the transcript level. Here we review a case of massive post-transcriptional revisions via trans-splicing and RNA editing, a phenomenon occurring in mitochondria of a recently recognized protist group, the diplonemids. As of now, the various post-transcriptional steps have been cataloged in detail, but how these processes function is still unknown. Since genetic manipulation techniques such as gene replacement and RNA interference have not yet been established for these organisms, alternative strategies have to be deployed. Here, we discuss the experimental and bioinformatics approaches that promise to unravel the molecular machineries of trans-splicing and RNA editing in Diplonema mitochondria.

Massive mitochondrial DNA content in diplonemid and kinetoplastid protists

“…What might explain the ultra‐high quantity of DNA in the D. papillatum mitochondrion? An adaptive explanation is not obvious; in terms of gene content, it possesses a “typical” coding capacity of just 18 fragmented genes . Even more extreme is the kinetoplast DNA of Perkinsela , which harbors 6.6 times more DNA than its corresponding nucleus, which may be related to the phenomenon of endosymbiont degradation .…”

“…Notably six mitochondrial DNA polymerases have been documented in T. brucei . Alternatively, massive RNA editing and/or trans ‐splicing requiring huge coding space could act as an evolutionary ratchet for CNE . However, this could only be the case if extensive RNA editing existed before, or co‐evolved with, the runaway expansion of mitochondrial DNA (see below and Fig.…”

A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. & sp.

“…The newly described genera are also marine, though their habitats are yet to be clarified (Tashyreva et al 2018a). Some of these diplonemids have been studied mostly due to their relationship to the more famous kinetoplastids, and because of their baroque mitochondrial genome architecture and posttranscriptional editing characteristics (Kiethega et al 2013;Marande et al 2005;Valach et al 2016;Yabuki et al 2016), as well as some curious metabolic and molecular traits (Morales et al 2016;Qian and Keeling 2001). But overall, the group has not been extensively described, with multiple undetermined phylotypes present in environmental molecular surveys (Tashyreva et al 2018a,b).…”

Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine microeukaryotes Diplonemida (Euglenozoa)

“…The availability of a methodology to transfect Diplonema will also facilitate investigation of the machineries that drive the unique post-transcriptional processes in their mitochondria, such as U-appendage RNA editing and trans-splicing of fragmented genes (for reviews see Valach et al, 2016;Faktorov a et al, 2018). For example, fluorescence tagging of terminal uridyl transferases or RNA ligases would identify the respective enzyme that acts in mitochondria, and open the venue for uncovering other components in the hypothetical editosome or trans-spliceosome.…”

“…This species is available from the American Type Culture Collection (ATCC), can be easily cultivated axenically in the laboratory at high cell densities, and can be cryopreserved. The mitochondrial genome and transcriptome have been analyzed in detail, revealing novel modes of posttranscriptional gene expression (Marande and Burger, 2007;Kiethega et al, 2013;Moreira et al, 2016;Valach et al, 2016;Faktorov a et al, 2018). Further, D. papillatum has been investigated regarding its compartmentalization of gluconeogenesis (Makiuchi et al, 2011;Morales et al, 2016).…”