scholarly journals Modeling in yeast how rDNA introns slow growth and increase desiccation tolerance in lichens

2021 ◽  
Author(s):  
Daniele Armaleo ◽  
Lilly Chiou
Keyword(s):  
Desiccation Tolerance ◽  
Slow Growth ◽  
Nuclear Ribosomal Dna ◽  
Rrna Genes ◽  
Northern Analysis ◽  
Ribosome Assembly ◽  
Group I Introns ◽  
Group I ◽  
Yeast Mutants ◽  
Splicing Machinery

Abstract We connect ribosome biogenesis to desiccation tolerance in lichens, widespread symbioses between specialized fungi (mycobionts) and unicellular phototrophs. We test whether the introns present in the nuclear ribosomal DNA of lichen mycobionts contribute to their anhydrobiosis. Self-splicing introns are found in the rDNA of several eukaryotic microorganisms, but most introns populating lichen rDNA are unable to self-splice, being either catalytically-impaired group I introns, or spliceosomal introns ectopically present in rDNA. Although the mycobiont’s splicing machinery removes all introns from rRNA, Northern analysis indicates delayed post-transcriptional removal during rRNA processing, suggesting interference with ribosome assembly. To study the effects of lichen introns in a model system, we used CRISPR to introduce a spliceosomal rDNA intron from the lichen fungus Cladonia grayi into all nuclear rDNA copies of Saccharomyces cerevisiae, which lacks rDNA introns. Three intron-bearing yeast mutants were constructed with the intron inserted either in the 18S rRNA genes, the 25S rRNA genes, or in both. The mutants removed the introns correctly but had half the rDNA genes of the wildtype, grew 4.4 to 6 times slower, and were 40 to 1700 times more desiccation tolerant depending on intron position and number. Intracellular trehalose, a disaccharide implicated in desiccation tolerance, was detected at low concentration. Our data suggest that the interference of the splicing machinery with ribosome assembly leads to fewer ribosomes and proteins and to slow growth and increased desiccation tolerance in the yeast mutants. The relevance of these findings for slow growth and desiccation tolerance in lichens is discussed.

scholarly journals Modeling in yeast how rDNA introns slow growth and increase desiccation tolerance in lichens

2021 ◽  
Author(s):  
Daniele Armaleo ◽  
Lilly Chiou
Keyword(s):  
Stress Responses ◽  
Desiccation Tolerance ◽  
Slow Growth ◽  
Nuclear Ribosomal Dna ◽  
Rrna Genes ◽  
Spliceosomal Intron ◽  
Group I Introns ◽  
Spliceosomal Introns ◽  
Group I ◽  
Eukaryotic Microorganisms

AbstractWe define a molecular connection between ribosome biogenesis and desiccation tolerance in lichens, widespread symbioses between specialized fungi (mycobionts) and unicellular phototrophs. Our experiments test whether the introns present in the nuclear ribosomal DNA of lichen mycobionts contribute to their anhydrobiosis. Self-splicing introns are found in the rDNA of several eukaryotic microorganisms, but most introns populating lichen rDNA are unable to self-splice, being either degenerate group I introns lacking the sequences needed for catalysis, or spliceosomal introns ectopically present in rDNA. Using CRISPR, we introduced a spliceosomal intron from the rDNA of the lichen fungus Cladonia grayi into all nuclear rDNA copies of the yeast Saccharomyces cerevisiae, which lacks rDNA introns. Three intron-bearing mutants were constructed with the intron inserted either in the 18S rRNA genes, the 25S rRNA genes, or in both. The mutants removed the introns correctly but had half the rDNA genes of the wildtype strain, grew 4.4 to 6 times slower, and were 40 to 1700 times more desiccation tolerant depending on intron position and number. Intracellular trehalose, a disaccharide implicated in desiccation tolerance, was detected but not at levels compatible with the observed resistance. Extrapolating from yeast to lichen mycobionts we propose that the unique requirement for a splicing machinery by lichen rDNA introns slows down intron splicing and ribosomal assembly. This effect, and the distinctive roles played by group I vs. spliceosomal rDNA introns, lead the environmental stress responses of lichen fungi to generate the twin lichen phenotypes of slow growth and desiccation tolerance.

scholarly journals Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0245714
Author(s):  
Li-hong Chen ◽  
Wei Yan ◽  
Ting Wang ◽  
Yu Wang ◽  
Jian Liu ◽  
...  
Keyword(s):  
18S Rdna ◽  
Large Subunit ◽  
Gc Content ◽  
Nucleotide Sequences ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Rdna Site ◽  
Group I Introns ◽  
Intron Insertion ◽  
Group I

The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secondary structure elements designated P1-P10 helics and loops. We found a 12 nt nucleotide sequences TACCACAGGGAT at site 2 in the 3’-end of 28S rDNA, site 2 introns just insert the upstream or the downstream of the12 nt nucleotide sequences. Afters sequence analysis of all 18S and 28S rDNA introns from tested isolates, three high conserved regions around 30 nt nucleotides (conserved 1, conserved 2, conserved 3) and identical nucleotides can be found. Conserved 1, conserved 2 and conserved 3 regions have high GC content, GC percentage is almost more than 60%. From our results, it seems that the more convenient host sites, intron sequences and secondary structures, or isolates for 18S and 28S rDNA intron insertion and deletion, the more popular they are. No matter 18S rDNA introns or 18S rDNA introns among tested isolates, complementary base pairing at the splicing sites in P1-IGS-P10 tertiary helix around 5’-end introns and exons were weak.

scholarly journals Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shu Zhang ◽  
Yong-Jie Zhang
Keyword(s):  
Insertion Site ◽  
Mitochondrial Protein ◽  
Host Gene ◽  
Rrna Genes ◽  
Group I Introns ◽  
Protein Coding ◽  
Standard Nomenclature ◽  
Protein Coding Genes ◽  
Group I ◽  
Mitochondrial Introns

Abstract Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungus Tolypocladium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16 fungi of different phyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.

A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of saccharomyces cerevisiae

1993 ◽  
Vol 13 (2) ◽  
pp. 1023-1033
Author(s):  
D E Muscarella ◽  
V M Vogt
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Dna ◽  
Physarum Polycephalum ◽  
Point Mutations ◽  
Group I Intron ◽  
Yeast Cells ◽  
Nuclear Ribosomal Dna ◽  
Group I Introns ◽  
Recognition Sequence ◽  
Group I

Pp LSU3 is a mobile group I intron in the extrachromosomal nuclear ribosomal DNA (rDNA) of Physarum polycephalum. As found for other mobile introns, Pp LSU3 encodes a site-specific endonuclease, I-Ppo, which mediates "homing" to unoccupied target sites in Physarum rDNA. The recognition sequence for this enzyme is conserved in all eucaryotic nuclear rDNAs. We have introduced this intron into a heterologous species, Saccharomyces cerevisiae, in which nuclear group I introns have not been detected. The expression of Pp LSU3, under control of the inducible GAL10 promoter, was found to be lethal as a consequence of double-strand breaks in the rDNA. However, surviving colonies that are resistant to the lethal effects of I-Ppo because of alterations in the rDNA at the cleavage site were recovered readily. These survivors are of two classes. The first comprises cells that acquired one of three types of point mutations. The second comprises cells in which Pp LSU3 became inserted into the rDNA. In both cases, each resistant survivor appears to carry the same alterations in all approximately 150 rDNA repeats. When it is embedded in yeast rDNA, Pp LSU3 leads to the synthesis of I-Ppo and appears to be mobile in appropriate genetic crosses. The existence of yeast cells carrying a mobile intron should allow dissection of the steps that allow expression of the highly unusual I-Ppo gene.

scholarly journals Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.

1993 ◽  
Vol 13 (12) ◽  
pp. 7531-7539 ◽  
Author(s):  
E L Ellison ◽  
V M Vogt
Keyword(s):  
Gel Filtration ◽  
Dimethyl Sulfate ◽  
Strand Break ◽  
Target Site ◽  
Nuclear Ribosomal Dna ◽  
Group I Introns ◽  
Recognition Sequence ◽  
Mobility Shift ◽  
Intron Insertion ◽  
Group I

Endonucleases encoded by mobile group I introns are highly specific DNases that induce a double-strand break near the site to which the intron moves. I-PpoI from the acellular slime mold Physarum polycephalum mediates the mobility of intron 3 (Pp LSU 3) in the extrachromosomal nuclear ribosomal DNA of this organism. We showed previously that cleavage by I-PpoI creates a four-base staggered cut near the point of intron insertion. We have now characterized several further properties of the endonuclease. As determined by deletion analysis, the minimal target site recognized by I-PopI was a sequence of 13 to 15 bp spanning the cleavage site. The purified protein behaved as a globular dimer in sedimentation and gel filtration. In gel mobility shift assays in the presence of EDTA, I-PpoI formed a stable and specific complex with DNA, dissociating with a half-life of 45 min. By footprinting and interference assays with methidiumpropyl-EDTA-iron(II), I-PpoI contacted a 22- to 24-bp stretch of DNA. The endonuclease protected most of the purines found in both the major and minor grooves of the DNA helix from modification by dimethyl sulfate (DMS). However, the reactivity to DMS was enhanced at some purines, suggesting that binding leads to a conformational change in the DNA. The pattern of DMS protection differed fundamentally in the two partially symmetrical halves of the recognition sequence.

Group-I introns with unusual sequences occur at three sites in nuclear 18S rRNA genes of Acanthamoeba lenticulata

1998 ◽  
Vol 34 (1) ◽  
pp. 71-78 ◽  
Author(s):  
J. M. Schroeder-Diedrich ◽  
Paul A. Fuerst ◽  
T. J. Byers
Keyword(s):  
18S Rrna ◽  
Rrna Genes ◽  
Group I Introns ◽  
Group I ◽  
18S Rrna Genes

scholarly journals Variation andin vitrosplicing of group I introns in rRNA genes ofPneumocystis carinii

1993 ◽  
Vol 21 (10) ◽  
pp. 2415-2421 ◽  
Author(s):  
Yong Liu ◽  
Michael J. Leibowitz
Keyword(s):  
Rrna Genes ◽  
Group I Introns ◽  
Group I
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