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Programmed translational bypassing is a process whereby ribosomes "ignore" a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational blockage at a "takeoff codon" immediately upstream of a stop codon followed by a hairpin, which causes peptidyl-tRNA dissociation and reassociation with a matching "landing triplet" 50 nt downstream, where translation resumes. Here, we report 81 translational bypassing elements (byps) in mitochondria of the yeast Magnusiomyces capitatus and demonstrate in three cases, by transcript analysis and proteomics, that byps are retained in mitochondrial mRNAs but not translated. Although mitochondrial byps resemble the bypass sequence in the T4 gene 60, they utilize unused codons instead of stops for translational blockage and have relaxed matching rules for takeoff/landing sites. We detected byp-like sequences also in mtDNAs of several Saccharomycetales, indicating that byps are mobile genetic elements. These byp-like sequences lack bypassing activity and are tolerated when inserted in-frame in variable protein regions. We hypothesize that byp-like elements have the potential to contribute to evolutionary diversification of proteins by adding new domains that allow exploration of new structures and functions.ribosome hopping | mitochondrial genome | proteome analysis | heterologous expression T he traditional view of translation is that mRNA is read sequentially, one codon at a time. However, low-level nonprogrammed translational bypassing (i.e., the occasional skipping of a few nucleotides) can be triggered by various factors, including tRNA paucity, unusual codons, and homo-polymer sequence tracts (1). In addition, programmed translational bypassing of 50 nt has been demonstrated for the gene 60 transcript of bacteriophage T4 (2-4). In vitro mutagenesis experiments showed that efficient translational "jumping" or "hopping" in T4 requires matching takeoff and landing codons (most effective is the wild-type GGA), a stop codon, and both a hairpin RNA secondary structure directly downstream of the takeoff site, and a Shine-Dalgarno (SD) sequence a few nucleotides upstream of the landing codon. Finally, a particular amino acid sequence in the nascent peptide encoded upstream of the takeoff site confers highest jumping efficiency. Additional cases of programmed bypassing have been postulated but currently lack supporting evidence (e.g., ref. 5), making the T4 gene 60 expression the only confirmed instance.Here, we report the massive occurrence of translational bypassing elements in mitochondria of the opportunistic human pathogen Magnusiomyces (also known as Blastoschizomyces or Geotrichum) capitatus (6), which belongs to a deeply branching lineage of Saccharomycetales (Fig. 1A). Our findings suggest that translational bypassing might be more widespread than previously thought. ResultsProtein-Coding Genes Interrupted by Dozens of In...

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Little is known about establishment success of the arbuscular mycorrhizal fungal (AMF) inocula and their effects on a soil-indigenous community of AMF. In this study, we assessed the effect of introducing Rhizophagus irregularis DAOM-197198 in soil under field condition on the community composition of indigenous AMF in the roots of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum). Three field trials were conducted with inoculated and non-inoculated plots. Four to ten roots and their rhizosphere soil samples of two growth stages for corn and wheat, and one growing stage of soybean, were collected, totalling 122 root and soil samples. Root colonization was measured microscopically, and the fungal communities were determined by paired-end Illumina MiSeq amplicon sequencing using 18S rDNA marker. After quality trimming and merging of paired ends, 6.7 million sequences could be assigned to 414 different operational taxonomic units. These could be assigned to 68 virtual taxa (VT) using the AMF reference sequence database MaarjAM. The most abundant VT corresponded to R. irregularis. The inoculation treatment did not influence the presence of R. irregularis, or AMF community diversity in roots. This seems to indicate that inoculation with R. irregularis DAOM-197198 does not change the indigenous AMF community composition, probably because it is already present in high abundance naturally.