Adenosine to inosine mRNA editing in fungi and how it may relate to fungal pathogenesis

Teichert, Ines

doi:10.1371/journal.ppat.1007231

Cited by 15 publications

(10 citation statements)

References 34 publications

(61 reference statements)

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“…Beyond using proteogenomics analysis to refine known genes and to identify hidden genes, the data were mined for peptide sequence variations caused by putative changes at the RNA level, i.e., RNA editing. RNA editing is found in all domains of life, and A-to-I mRNA editing has recently been described in filamentous ascomycetes, where editing frequencies have been linked to sexual development (22–25).…”

Section: Resultsmentioning

confidence: 99%

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications

Blank-Landeshammer

Teichert

Märker

et al. 2019

mBio

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Proteogenomics combines proteomics, genomics, and transcriptomics and has considerably improved genome annotation in poorly investigated phylogenetic groups for which homology information is lacking. Furthermore, it can be advantageous when reinvestigating well-annotated genomes. Here, we applied an advanced proteogenomics approach, combining standard proteogenomics with peptidede novosequencing, to refine annotation of the well-studied model fungusSordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in the detection of 104 so-far hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single-amino-acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Coexpression and phylostratigraphic analysis of the refined proteome suggest that new functions in evolutionarily young genes correlate with distinct developmental stages. In conclusion, our advanced proteogenomics approach supports and promotes functional studies of fungal model systems.IMPORTANCENext-generation sequencing techniques have considerably increased the number of completely sequenced eukaryotic genomes. These genomes are mostly automatically annotated, andab initiogene prediction is commonly combined with homology-based search approaches and often supported by transcriptomic data. The latter in particular improve the prediction of intron splice sites and untranslated regions. However, correct prediction of translation initiation sites (TIS), alternative splice junctions, and protein-coding potential remains challenging. Here, we present an advanced proteogenomics approach, namely, the combination of proteogenomics andde novopeptide sequencing analysis, in conjunction with Blast2GO and phylostratigraphy. Using the model fungusSordaria macrosporaas an example, we provide a comprehensive view of the proteome that not only increases the functional understanding of this multicellular organism at different developmental stages but also immensely enhances the genome annotation quality.

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Section: Resultsmentioning

confidence: 99%

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications

Blank-Landeshammer

Teichert

Märker

et al. 2019

mBio

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“…Besides PSC editing, As in amino acid codons are targeted in fungi, leading to synonymous or nonsynonymous codon changes (Table 2). Interestingly, editing also targets stop codons of correctly annotated functional genes, often changing a UAG into a UGG tryptophan codon, causing translation to run on into the 3′-UTR (stop loss (SL) editing, Table 2) (reviewed in Teichert 2018).…”

Section: Detection Of Mrna Editing In Filamentous Ascomycetesmentioning

confidence: 99%

Fungal RNA editing: who, when, and why?

Teichert

2020

Appl Microbiol Biotechnol

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RNA editing occurs in all kingdoms of life and in various RNA species. The editing of nuclear protein-coding transcripts has long been known in metazoans, but was only recently detected in fungi. In contrast to many metazoan species, fungal editing sites occur mostly in coding regions, and therefore, fungal editing can change protein sequences and lead to modified or new functions of proteins. Indeed, mRNA editing is thought to be generally adaptive on fungi. Although RNA editing has been detected in both, Ascomycota and Basidiomycota, there seem to be considerable differences between these two classes of fungi concerning the types, the timing, and the purpose of editing. This review summarizes the characteristics of RNA editing in fungi and compares them to metazoan species and bacteria. In particular, it will review cellular processes affected by editing and speculate on the purpose of editing for fungal biology with a focus on the filamentous ascomycetes. Key Points • Fungi show various types of mRNA editing in nuclear transcripts. • Fungal editing leads to proteome diversification. • Filamentous ascomycetes may require editing for sexual sporulation. • Wood-degrading basidiomycetes may use editing for adaptation to different substrates.

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“…RNA editing is a modification of transcripts encoded by organellar and nuclear genomes that occurs in various organisms, including animals, plants, fungi, and protists [1,2,3,4]. The modifications of transcripts caused by the RNA editing effect with encoding of alternative amino acid sequences is necessary for correct functioning of some protein-coding genes [5].…”

Section: Introductionmentioning

confidence: 99%

Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends

Myszczyński

Ślipiko

Sawicki

2019

IJMS

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RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.

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Adenosine to inosine mRNA editing in fungi and how it may relate to fungal pathogenesis

Cited by 15 publications

References 34 publications

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications

Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications

Fungal RNA editing: who, when, and why?

Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends

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