Mapping of the css (chloroplast splicing suppressor) gene(s) to a recombinationally suppressed region of chromosome III in Chlamydomonas reinhardtii

Genome ◽  
2012 ◽  
Vol 55 (7) ◽  
pp. 483-491
Author(s):  
Liming Luo ◽  
Jaesung Lee ◽  
David L. Herrin
Keyword(s):  
Molecular Markers ◽  
Chlamydomonas Reinhardtii ◽  
Large Subunit ◽  
Suppressor Gene ◽  
Group I Introns ◽  
Suppressor Mutations ◽  
Group I ◽  
Nuclear Loci ◽  
Nuclear Locus ◽  
Chromosome Iii

In previous work, three suppressors of defective group I introns (7151, 71N1, 7120) were isolated from a mutant of Chlamydomonas reinhardtii that had a splicing-deficient chloroplast large subunit (LSU) rRNA intron. Genetic analysis indicated that the 7151 and 71N1 suppressor mutations each involved single nuclear loci, and that the 7151 mutation was dominant. Here we present genetic evidence that the 7120 suppressor also involves a single nuclear locus and that the mutation is dominant in vegetative diploids. Moreover, we have employed crosses with the S1D2 strain and molecular markers to map the 7120 and 71N1 suppressors. Based on an analysis of 800 progeny from 7120 × S1D2, the 7120 suppressor is located in a region of ∼400 kb on chromosome III that is devoid of recombination. The ∼400-kb region contains at least 72 genes, about one-third of which (i.e., 22) are predicted to be organelle targeted. Similar analysis of 71N1 × S1D2 using 400 progeny also pointed to the recombination-deficient region of chromosome III, raising the possibility that these mutations could affect the same gene. These efforts lay the foundation for identifying the css (chloroplast splicing suppressor) gene(s), which promotes splicing of multiple chloroplast group I introns.

scholarly journals Mobile Self-Splicing Group I Introns from thepsbA Gene of Chlamydomonas reinhardtii: Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter

2001 ◽  
Vol 21 (10) ◽  
pp. 3472-3481 ◽  
Author(s):  
Obed W. Odom ◽  
Stephen P. Holloway ◽  
Nita N. Deshpande ◽  
Jaesung Lee ◽  
David L. Herrin
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Open Reading Frames ◽  
Group I Introns ◽  
Resistance Marker ◽  
Free Standing ◽  
Spectinomycin Resistance ◽  
Highly Efficient ◽  
Group I ◽  
Short Exon ◽  
Self Splicing

ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.

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 The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e84325 ◽  
Author(s):  
Jean-François Pombert ◽  
Christian Otis ◽  
Monique Turmel ◽  
Claude Lemieux
Keyword(s):  
Mitochondrial Genome ◽  
Large Subunit ◽  
Rrna Gene ◽  
Group I Introns ◽  
Group I ◽  
Large Subunit Rrna

scholarly journals Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing Streptococcus thermophilus Strain

2005 ◽  
Vol 71 (7) ◽  
pp. 4057-4068 ◽  
Author(s):  
Céline Lévesque ◽  
Martin Duplessis ◽  
Jessica Labonté ◽  
Steve Labrie ◽  
Christophe Fremaux ◽  
...  
Keyword(s):  
Large Subunit ◽  
Genomic Analysis ◽  
Streptococcus Thermophilus ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Group I Introns ◽  
Structural Protein ◽  
Flight Mass Spectrometry ◽  
Group I ◽  
Type Phage

ABSTRACT The Streptococcus thermophilus virulent pac-type phage 2972 was isolated from a yogurt made in France in 1999. It is a representative of several phages that have emerged with the industrial use of the exopolysaccharide-producing S. thermophilus strain RD534. The genome of phage 2972 has 34,704 bp with an overall G+C content of 40.15%, making it the shortest S. thermophilus phage genome analyzed so far. Forty-four open reading frames (ORFs) encoding putative proteins of 40 or more amino acids were identified, and bioinformatic analyses led to the assignment of putative functions to 23 ORFs. Comparative genomic analysis of phage 2972 with the six other sequenced S. thermophilus phage genomes confirmed that the replication module is conserved and that cos- and pac-type phages have distinct structural and packaging genes. Two group I introns were identified in the genome of 2972. They interrupted the genes coding for the putative endolysin and the terminase large subunit. Phage mRNA splicing was demonstrated for both introns, and the secondary structures were predicted. Eight structural proteins were also identified by N-terminal sequencing and/or matrix-assisted laser desorption ionization—time-of-flight mass spectrometry. Detailed analysis of the putative minor tail proteins ORF19 and ORF21 as well as the putative receptor-binding protein ORF20 showed the following interesting features: (i) ORF19 is a hybrid protein, because it displays significant identity with both pac- and cos-type phages; (ii) ORF20 is unique; and (iii) a protein similar to ORF21 of 2972 was also found in the structure of the cos-type phage DT1, indicating that this structural protein is present in both S. thermophilus phage groups. The implications of these findings for phage classification are discussed.

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