Evolution of a Pseudogene: Exclusive Survival of a Functional Mitochondrial nad7 Gene Supports Haplomitrium as the Earliest Liverwort Lineage and Proposes a Secondary Loss of RNA Editing in Marchantiidae

Abstract

Gene transfer from the mitochondrion into the nucleus is a corollary of the endosymbiont hypothesis. The frequent and independent transfer of genes for mitochondrial ribosomal proteins is well documented with many examples in angiosperms, whereas transfer of genes for components of the respiratory chain is a rarity. A notable exception is the nad7 gene, encoding subunit 7 of complex I, in the liverwort Marchantia polymorpha, which resides as a full-length, intron-carrying and transcribed, but nonspliced pseudogene in the chondriome, whereas its functional counterpart is nuclear encoded. To elucidate the patterns of pseudogene degeneration, we have investigated the mitochondrial nad7 locus in 12 other liverworts of broad phylogenetic distribution. We find that the mitochondrial nad7 gene is nonfunctional in 11 of them. However, the modes of pseudogene degeneration vary: whereas point mutations, accompanied by single-nucleotide indels, predominantly introduce stop codons into the reading frame in marchantiid liverworts, larger indels introduce frameshifts in the simple thalloid and leafy jungermanniid taxa. Most notably, however, the mitochondrial nad7 reading frame appears to be intact in the isolated liverwort genus Haplomitrium. Its functional expression is shown by cDNA analysis identifying typical RNA-editing events to reconstitute conserved codon identities and also confirming functional splicing of the 2 liverwort-specific group II introns. We interpret our results 1) to indicate the presence of a functional mitochondrial nad7 gene in the earliest land plants and strongly supporting a basal placement of Haplomitrium among the liverworts, 2) to indicate different modes of pseudogene degeneration and chondriome evolution in the later branching liverwort clades, 3) to suggest a surprisingly long maintenance of a nonfunctional gene in the presumed oldest group of land plants, and 4) to support the model of a secondary loss of RNA-editing activity in marchantiid liverworts.

Organellar genomes of the four-toothed moss, Tetraphis pellucida

“…The pseudogenisation of nad7 in the Tetraphis pellucida chondrome is significant, as while it is also absent or existing only as a non-functional pseudogene in hornworts and in most liverworts [38–40] as well as in the lycopod Huperzia squarrosa [33], it appears to be functionally present in all other known tracheophyte and moss chondromes investigated, including representatives of Takakia , Ulota , Leucobryum and Dichodontium [41] as well as P. patens and A. rugelii . In liverworts, both Haplomitrium [38] and Treubia [27] retain a functional mitochondrial nad7 gene, while all other species investigated have pseudogenised copies, varying greatly in their degrees of degeneration but remarkable for having persisted throughout the long evolutionary history of the group [38].…”

Nuclear DYW-Type PPR Gene Families Diversify with Increasing RNA Editing Frequencies in Liverwort and Moss Mitochondria

“…In the subclass of complex thalloid, marchantiid liverworts no RNA editing has been found. This is evident from the completely sequenced mitochondrial genome of Marchantia polymorpha (Ohyama et al 2009) and from investigations of the mitochondrial genes cox1, cox3, nad5, and nad7 in several other marchantiid liverwort species (Groth-Malonek et al 2007;Malek et al 1996;Sper-Whitis et al 1996;Steinhauser et al 1999). In flowering plants, mitochondrial transcriptomes contain some 300-500 RNA editing sites (Giegé and Brennicke 1999;Handa 2003;Mower and Palmer 2006;Notsu et al 2002) and chloroplast transcriptomes contain approx.…”

“…This phenomenon of correcting genetic information is absent in algae and seems to have emerged concomitant with the water-to-land transition of embryophytes (Covello and Gray 1993;Jobson and Qiu 2008;Maier et al 2008;Steinhauser et al 1999). RNA editing occurs in all land plant clades (Freyer et al 1997;Groth-Malonek et al 2007;Hiesel et al 1994;Malek et al 1996;Sper-Whitis et al 1994;Sper-Whitis et al 1996) with one unique exception. In the subclass of complex thalloid, marchantiid liverworts no RNA editing has been found.…”

“…Studies in Haplomitrium mnioides, however, a member of the basal-most subclass of liverworts (Haplomitriidae), showed RNA editing at more than 20 positions in its nad7 gene alone (Groth-Malonek et al 2007). …”

RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

“…Originally reported in 1989 for mitochondrial mRNAs of angiosperms (Covello and Gray 1989;Gualberto et al 1989;Hiesel et al 1989;Lamattina et al 1989), C-to-U type of RNA editing was discovered in chloroplasts shortly thereafter (Hoch et al 1991;Maier et al 1992). Subsequent work has shown that RNA editing occurs in chloroplasts and mitochondria of all land plant clades with the unique exception of the subclass of complex thalloid marchantiid liverworts (Freyer et al 1997;Groth-Malonek et al 2007;Hiesel et al 1994;Malek et al 1996;Sper-Whitis et al 1994. Some basal land plant clades, most notably the hornworts, lycophytes and ferns, also show a signiWcant amount of "reverse" (termed so for historical reasons alone) U-to-C RNA editing (Groth-Malonek et al 2005;Kugita et al 2003;Malek and Knoop 1998;Vangerow et al 1999;Yoshinaga et al 1996Yoshinaga et al , 1997, a phenomenon that is only very rarely observed in angiosperms (Gualberto et al 1990;Schuster et al 1990a).…”