Uncovering
            <i>Cis</i>
            -Regulatory Elements Important for A-to-I RNA Editing in Fusarium graminearum

Feng, Chanjing; Cao, Xinyu; Du, Youwei; Chen, Yitong; Xin, Kaiyun; Zou, Jingwen; Jin, Qiaojun; Xu, Jin‐Rong; Liu, Huiquan

doi:10.1128/mbio.01872-22

Cited by 10 publications

(18 citation statements)

References 46 publications

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“…We observed similar nucleotide preference surrounding the editing sites and enrichment of editing sites in hairpin loop structures for the editing sites detected in both INVSc1 and BL21 transformants (Fig. 6D-6E), as previously reported in F. graminearum ( 12 ). Therefore, the FgTad2-FgTad3-Ame1 complex exhibits robust A-to-I mRNA editing activities in heterologous systems.…”

Section: Resultssupporting

confidence: 88%

“…Gene deletion was performed using the split-marker approach ( 35 ). Fragments of approximately 1.0 kb upstream and downstream of the target genes were amplified and connected to the N- and C-terminal regions of either a hygromycin-resistance cassette or a recyclable marker module ( 12 ) that confers resistance to hygromycin and sensitivity to the nucleoside analog 5-fluoro-2’-deoxyuridine (Floxuridine) through overlapping PCR. After transforming PH-1 protoplasts, hygromycin-resistant transformants were screened and confirmed by PCR assays.…”

Section: Methodsmentioning

confidence: 99%

“…The PCR products were confirmed by sequencing analysis and then transformed into protoplasts of the FG1G36140 deletion mutant. Transformants resistant to 25 μg/mL Floxuridine (HY-B0097, MCE, USA) were screened, as described ( 12 ). To overexpress FgTAD3 or FgTAD2 initiated by M 1 or M 4 codons in the FG1G36140 locus of AME1 -oe transformants, two DNA fragments were generated using overlapping PCR.…”

Section: Methodsmentioning

confidence: 99%

“…It appears to be a common feature in Sordariomycetes ( 10 ), one of the largest classes of Ascomycota. More than 40,000 A-to-I mRNA editing sites have been identified in the perithecia (sexual fruiting bodies) of Neurospora crassa and Fusarium graminearum , respectively ( 11, 12 ). As fungi lack orthologs of animal ADARs and the cis -regulatory elements of editing are also distinct from animals ( 12 ), a different A-to-I editing mechanism must exist in fungi.…”

Section: Introductionmentioning

confidence: 99%

“…More than 40,000 A-to-I mRNA editing sites have been identified in the perithecia (sexual fruiting bodies) of Neurospora crassa and Fusarium graminearum , respectively ( 11, 12 ). As fungi lack orthologs of animal ADARs and the cis -regulatory elements of editing are also distinct from animals ( 12 ), a different A-to-I editing mechanism must exist in fungi. Here, we demonstrated that FgTad2-FgTad3 is responsible for A-to-I mRNA editing in F. graminearum, with its capacity relying on the interaction between FgTad3 and a sexual stage-specific protein named Ame1 ( a ctivator of m RNA e diting).…”

Section: Introductionmentioning

confidence: 99%

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Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Feng,

Xin,

et al. 2023

Preprint

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A-to-I mRNA editing occurs during fungal sexual reproduction with an unknown mechanism. Here, we demonstrated that the eukaryotic tRNA-specific heterodimeric deaminase FgTad2-FgTad3, not typically associated with mRNA editing, is responsible for A-to-I mRNA editing in Fusarium graminearum. This editing capacity relies on the interaction between FgTad3 and a sexual stage-specific protein called Ame1. The interaction emerged in Sordariomycetes. Key residues involved in the interaction have been identified. Expression and activity of FgTad2-FgTad3 are regulated through alternative promoters, alternative translation initiation, and post-translational modifications. FgTad2-FgTad3-Ame1 efficiently edits target mRNAs in yeasts, bacteria, and human cells, with significant implications for developing base editors in therapy and agriculture. This study reveals mechanisms, regulation, and evolution of RNA editing in fungi, emphasizing protein-protein interactions in controlling enzyme function.

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Section: Resultssupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Feng,

Xin,

et al. 2023

Preprint

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Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Feng,

Xin,

et al. 2024

Nat Commun

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A-to-I mRNA editing in animals is mediated by ADARs, but the mechanism underlying sexual stage-specific A-to-I mRNA editing in fungi remains unknown. Here, we show that the eukaryotic tRNA-specific heterodimeric deaminase FgTad2-FgTad3 is responsible for A-to-I mRNA editing in Fusarium graminearum. This editing capacity relies on the interaction between FgTad3 and a sexual stage-specific protein called Ame1. Although Ame1 orthologs are widely distributed in fungi, the interaction originates in Sordariomycetes. We have identified key residues responsible for the FgTad3-Ame1 interaction. The expression and activity of FgTad2-FgTad3 are regulated through alternative promoters, alternative translation initiation, and post-translational modifications. Our study demonstrates that the FgTad2-FgTad3-Ame1 complex can efficiently edit mRNA in yeasts, bacteria, and human cells, with important implications for the development of base editors in therapy and agriculture. Overall, this study uncovers mechanisms, regulation, and evolution of RNA editing in fungi, highlighting the role of protein-protein interactions in modulating deaminase function.

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Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi

Xin¹,

Zhang²,

Fan³

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in animals, and it occurs in fungi specifically during sexual reproduction. However, it is debatable whether A-to-I RNA editing is adaptive. Deciphering the functional importance of individual editing sites is essential for the mechanistic understanding of the adaptive advantages of RNA editing. Here, by performing gene deletion for 17 genes with conserved missense editing (CME) sites and engineering underedited (ue) and overedited (oe) mutants for 10 CME sites using site-specific mutagenesis at the native locus in Fusarium graminearum , we demonstrated that two CME sites in CME5 and CME11 genes are functionally important for sexual reproduction. Although the overedited mutant was normal in sexual reproduction, the underedited mutant of CME5 had severe defects in ascus and ascospore formation like the deletion mutant, suggesting that the CME site of CME5 is co-opted for sexual development. The preediting residue of Cme5 is evolutionarily conserved across diverse classes of Ascomycota, while the postediting one is rarely hardwired into the genome, implying that editing at this site leads to higher fitness than a genomic A-to-G mutation. More importantly, mutants expressing only the underedited or the overedited allele of CME11 are defective in ascosporogenesis, while those expressing both alleles displayed normal phenotypes, indicating that concurrently expressing edited and unedited versions of Cme11 is more advantageous than either. Our study provides convincing experimental evidence for the long-suspected adaptive advantages of RNA editing in fungi and likely in animals.

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Uncovering Cis -Regulatory Elements Important for A-to-I RNA Editing in Fusarium graminearum

Abstract: A-to-I RNA editing is a new epigenetic phenomenon that is crucial for sexual reproduction in fungi. Deciphering cis -regulatory elements of A-to-I RNA editing can help us elucidate the editing mechanism and develop a model that accurately predicts RNA editing.

Cited by 10 publications

References 46 publications

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Unveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi

Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi

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