Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns
Abstract Background Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonu...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-10-01
|
| Series: | Mobile DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13100-022-00280-4 |
| _version_ | 1811194923292033024 |
|---|---|
| author | Kjersti Lian Betty M. N. Furulund Anders A. Tveita Peik Haugen Steinar D. Johansen |
| author_facet | Kjersti Lian Betty M. N. Furulund Anders A. Tveita Peik Haugen Steinar D. Johansen |
| author_sort | Kjersti Lian |
| collection | DOAJ |
| description | Abstract Background Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes. Results A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3′ polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3′ overhang at the intron insertion site. Conclusions The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus. |
| first_indexed | 2024-04-12T00:35:22Z |
| format | Article |
| id | doaj.art-87bd7cf93d3c45e2b8ec62bdaa2aa6e5 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-04-12T00:35:22Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-87bd7cf93d3c45e2b8ec62bdaa2aa6e52022-12-22T03:55:11ZengBMCMobile DNA1759-87532022-10-0113111610.1186/s13100-022-00280-4Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal intronsKjersti Lian0Betty M. N. Furulund1Anders A. Tveita2Peik Haugen3Steinar D. Johansen4Nofima ASGenomics division, Faculty of Biosciences and Aquaculture, Nord UniversityMedical Department, Bærum Hospital, Vestre Viken Hospital TrulstDepartment of Chemistry and Center for Bioinformatics, Faculty of Science and Technology, UiT-The Arctic University of NorwayGenomics division, Faculty of Biosciences and Aquaculture, Nord UniversityAbstract Background Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes. Results A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3′ polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3′ overhang at the intron insertion site. Conclusions The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.https://doi.org/10.1186/s13100-022-00280-4AntisenseDidermaDidymiumHoming endonucleaseIntron evolutionMobile DNA |
| spellingShingle | Kjersti Lian Betty M. N. Furulund Anders A. Tveita Peik Haugen Steinar D. Johansen Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns Mobile DNA Antisense Diderma Didymium Homing endonuclease Intron evolution Mobile DNA |
| title | Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| title_full | Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| title_fullStr | Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| title_full_unstemmed | Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| title_short | Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| title_sort | mobile group i introns at nuclear rdna position l2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns |
| topic | Antisense Diderma Didymium Homing endonuclease Intron evolution Mobile DNA |
| url | https://doi.org/10.1186/s13100-022-00280-4 |
| work_keys_str_mv | AT kjerstilian mobilegroupiintronsatnuclearrdnapositionl2066harborsenseandantisensehomingendonucleasegenesintervenedbyspliceosomalintrons AT bettymnfurulund mobilegroupiintronsatnuclearrdnapositionl2066harborsenseandantisensehomingendonucleasegenesintervenedbyspliceosomalintrons AT andersatveita mobilegroupiintronsatnuclearrdnapositionl2066harborsenseandantisensehomingendonucleasegenesintervenedbyspliceosomalintrons AT peikhaugen mobilegroupiintronsatnuclearrdnapositionl2066harborsenseandantisensehomingendonucleasegenesintervenedbyspliceosomalintrons AT steinardjohansen mobilegroupiintronsatnuclearrdnapositionl2066harborsenseandantisensehomingendonucleasegenesintervenedbyspliceosomalintrons |