Recombinant mitochondrial DNA molecules suggest a template switching ability for group-II-intron reverse transcriptase

Artifacts and biases of the reverse transcription reaction in RNA sequencing

RNA sequencing has spurred a significant number of research areas in recent years. Most protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA molecule during the reverse transcription reaction. The resulting cDNA pool is often wrongfully assumed to be quantitatively and molecularly similar to the original RNA input. Sadly, biases and artifacts confound the resulting cDNA mixture. These issues are often overlooked or ignored in the literature by those that rely on the reverse transcription process. In this review, we confront the reader with intra- and intersample biases and artifacts caused by the reverse transcription reaction during RNA sequencing experiments. To fight the reader's despair, we also provide solutions to most issues and inform on good RNA sequencing practices. We hope the reader can use this review to their advantage, thereby contributing to scientifically sound RNA studies.

Group II intron in Bacillus cereus has an unusual 3' extension and splices 56 nucleotides downstream of the predicted site

All group II introns known to date fold into six functional domains. However, we recently identified an intron in Bacillus cereus ATCC 10987, B.c.I4, that splices 56 nt downstream of the expected 3′ splice site in vivo (Tourasse et al. 2005, J. Bacteriol., 187, 5437–5451). In this study, we confirmed by ribonuclease protection assay that the 56-bp segment is part of the intron RNA molecule, and computational prediction suggests that it might form a stable stem-loop structure downstream of domain VI. The splicing of B.c.I4 was further investigated both in vivo and in vitro. Lariat formation proceeded primarily by branching at the ordinary bulged adenosine in domain VI without affecting the fidelity of splicing. In addition, the splicing efficiency of the wild-type intron was better than that of a mutant construct deleted of the 56-bp 3′ extension. These results indicate that the intron has apparently adapted to the extra segment, possibly through conformational adjustments. The extraordinary group II intron B.c.I4 harboring an unprecedented extra 3′ segment constitutes a dramatic example of the flexibility and adaptability of group II introns.

Hybrid mitochondrial plasmids from senescence suppressor isolates of Neurospora intermedia

We analyzed several natural suppressor isolates of the pKalilo-based fungal senescence syndrome of Neurospora intermedia. The pKalilo plasmid did not increase in titer in these isolates. Nor did it show integration "de novo." In at least two of the senescence suppressor isolates, pKalilo had formed stable recombinants with other mitochondrial elements. pKalilo/mtDNA recombination junctions were complete and appeared to have been formed via a nonhomologous recombination mechanism. Further analysis revealed that pKalilo had recombined a novel, 2.6-kb cryptic mitochondrial retroplasmid, similar to the mitochondrial retroplasmid pTHR1 from Trichoderma harzianum and retroplasmids of the "Varkud" homology group. The recombinant molecules consisted of pKalilo, the novel element, and short intervening stretches of mtDNA. The latter stretches clearly corresponded to "in vivo" mitochondrial cDNA, suggesting that the molecules had formed via the action of a template-switching reverse transcriptase. We discuss how different types of mitochondrial plasmids interact and how their detrimental effect on the host may be suppressed.

Down-regulation of mitochondrial cytochrome c oxidase in senescent porcine pulmonary artery endothelial cells

Cellular aging is associated with dysfunction of the mitochondrial respiration chain. Deficiency of mitochondrial cytochrome c oxidase (complex IV) plays a critical role in aging-induced mitochondrial dysfunction. We investigated whether in vitro cellular aging causes the downregulation of complex IV activity and gene expression using senescent (passage 45) and young (passage 3) pulmonary artery endothelial cells (PAEC). In senescent PAEC, the catalytic activity of complex IV decreased 84%, compared to that in young cells. Relative protein levels of complex IV subunits I and IV (complex IV S1 and S4) in senescent cells decreased 91%, compared to those in young cells. This suggests that lack of complex IV S1 and S4 in senescent cells may contribute to the deficiency of complex IV. Total steady state levels of mRNA for complex IV S1 and S4 in senescent cells were decreased to 20% and 18% of those in young cells. The relative rates of mRNA synthesis of complex IV S1 and S4 were decreased 46% and 37% in senescent cells, respectively, compared to young cells. The degradation of complex IV S1 and S4 was increased 76% and 64% in senescent cells, compared to young cells. These data indicate that mitochondrial DNA-encoded subunit I and nuclear DNA-encoded subunit IV of complex IV are downregulated through reduced synthesis and enhanced degradation of their mRNA, which may be responsible for the deficiency of complex IV in replicative senescent PAEC.