scholarly journals Group I Self-Splicing Intron in the recA Gene of Bacillus anthracis

2002 ◽  
Vol 184 (14) ◽  
pp. 3917-3922 ◽  
Author(s):  
Minsu Ko ◽  
Hyang Choi ◽  
Chankyu Park
Keyword(s):  
Bacillus Anthracis ◽  
Group I Intron ◽  
Reca Gene ◽  
Trna Genes ◽  
Group I Introns ◽  
Protein Coding ◽  
E Coli ◽  
Coding Regions ◽  
Group I ◽  
Self Splicing

ABSTRACT Self-splicing introns are rarely found in bacteria and bacteriophages. They are classified into group I and II according to their structural features and splicing mechanisms. While the group I introns are occasionally found in protein-coding regions of phage genomes and in several tRNA genes of cyanobacteria and proteobacteria, they had not been found in protein-coding regions of bacterial genomes. Here we report a group I intron in the recA gene of Bacillus anthracis which was initially found by DNA sequencing as an intervening sequence (IVS). By using reverse transcriptase PCR, the IVS was shown to be removable from the recA precursor mRNA for RecA that was being translated in E. coli. The splicing was visualized in vitro with labeled free GTP, indicating that it is a group I intron, which is also implied by its predicted secondary structure. The RecA protein of B. anthracis expressed in E. coli was functional in its ability to complement a recA defect. When recA-negative E. coli cells were irradiated with UV, the Bacillus RecA reduced the UV susceptibility of the recA mutant, regardless of the presence of intron.

scholarly journals A Unique Group I Intron in Coxiella burnetii Is a Natural Splice Mutant

2009 ◽  
Vol 191 (12) ◽  
pp. 4044-4046 ◽  
Author(s):  
Rahul Raghavan ◽  
Linda D. Hicks ◽  
Michael F. Minnick
Keyword(s):  
Coxiella Burnetii ◽  
Group I Intron ◽  
23S Rrna ◽  
Rrna Gene ◽  
Group I Introns ◽  
Group I ◽  
23S Rrna Gene ◽  
Self Splicing

ABSTRACT Cbu.L1917, a group I intron present in the 23S rRNA gene of Coxiella burnetii, possesses a unique 3′-terminal adenine in place of a conserved guanine. Here, we show that, unlike all other group I introns, Cbu.L1917 utilizes a different cofactor for each splicing step and has a decreased self-splicing rate in vitro.

scholarly journals A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages

2004 ◽  
Vol 186 (23) ◽  
pp. 8153-8155 ◽  
Author(s):  
Richard P. Bonocora ◽  
David A. Shub
Keyword(s):  
Dna Polymerase ◽  
Group I Intron ◽  
Group I Introns ◽  
Homing Endonucleases ◽  
Structural Element ◽  
Group I ◽  
Close Relatives ◽  
Self Splicing

ABSTRACT Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.

Group I intron-like insertions in SSU rDNA of Cladonia gracilis and C. rangiferina

2004 ◽  
Vol 36 (6) ◽  
pp. 365-380 ◽  
Author(s):  
Michele D. PIERCEY-NORMORE ◽  
Georg HAUSNER ◽  
Ewan A. GIBB
Keyword(s):  
Rna Structure ◽  
Group I Intron ◽  
Group I Introns ◽  
16S Rdna Gene ◽  
E Coli ◽  
Group I ◽  
History Of ◽  
First Time ◽  
Large Groups ◽  
Rna Fold

During a study on population genetics of three species of Cladonia using the nuclear ribosomal 18S DNA, two species contained group I intron-like sequences located in positions 788 and 940 with reference to the E. coli 16S rDNA gene. The intron in position 940 was not typical of group I introns and had previously been described only from the Parmeliaceae and Lecanoraceae, but here we report the occurrence of this intron in the Cladoniaceae. The intron in position 788 had characteristics of group I introns and had previously been reported from the Physciaceae. In this paper we provide for the first time a putative RNA fold for the nS788 intron, compare the secondary RNA structure of the Cladonia group I introns (nS788 and nS940) to that of other taxa, and infer a phylogenetic history among 15 members of the Lecanorales based on the evolutionary history of the nS788 group I intron. The RNA fold for nS788 contained two optional hairpins, P2.1 and a potentially newly described hairpin referred to as P5.1. The phylogenetic hypothesis supports the monophyly of the genus Cladonia. It also supports the separation of two large groups in the Physciaceae; the Buellia-group and the Physcia-group.

scholarly journals A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron

2007 ◽  
Vol 189 (14) ◽  
pp. 5293-5301 ◽  
Author(s):  
David Nord ◽  
Eduard Torrents ◽  
Britt-Marie Sjöberg
Keyword(s):  
Bacillus Anthracis ◽  
Homing Endonuclease ◽  
Insertion Site ◽  
Group I Intron ◽  
Coding Region ◽  
Recognition Sequence ◽  
Intron Insertion ◽  
Group I ◽  
Serovar Typhimurium ◽  
Self Splicing

ABSTRACT The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a putative homing endonuclease belonging to the GIY-YIG family. Here, we show that the nrdE pre-mRNA is spliced and that the homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt) upstream of the intron insertion site, producing 2-nt 3′ extensions. We also show that the sequence required for efficient cleavage spans at least 4 bp upstream and 31 bp downstream of the cleaved coding strand. The position of the recognition sequence in relation to the cleavage position is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE genes from several other Bacillaceae were also susceptible to cleavage, with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B. anthracis, and Bacillus thuringiensis serovar konkukian being better substrates than those of Bacillus subtilis, Bacillus lichenformis, and S. epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and Corynebacterium ammoniagenes were not cleaved. Intervening sequences (IVSs) residing in protein-coding genes are often found in enzymes involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is a frequent target for self-splicing IVSs. A comparison of nrdE genes from seven gram-positive low-G+C bacteria, two bacteriophages, and Nocardia farcinica showed five different insertion sites for self-splicing IVSs within the coding region of the nrdE gene.

scholarly journals CBP2 protein promotes in vitro excision of a yeast mitochondrial group I intron.

1989 ◽  
Vol 9 (12) ◽  
pp. 5424-5433 ◽  
Author(s):  
A Gampel ◽  
M Nishikimi ◽  
A Tzagoloff
Keyword(s):  
Splice Site ◽  
Group I Intron ◽  
Nuclear Gene ◽  
Group I Introns ◽  
Wild Type ◽  
Group I ◽  
Mitochondrial Cytochrome B ◽  
High Concentrations ◽  
Self Splicing

The terminal intron (bI2) of the yeast mitochondrial cytochrome b gene is a group I intron capable of self-splicing in vitro at high concentrations of Mg2+. Excision of bI2 in vivo, however, requires a protein encoded by the nuclear gene CBP2. The CBP2 protein has been partially purified from wild-type yeast mitochondria and shown to promote splicing at physiological concentrations of Mg2+. The self-splicing and protein-dependent splicing reactions utilized a guanosine nucleoside cofactor, the hallmark of group I intron self-splicing reactions. Furthermore, mutations that abolished the autocatalytic activity of bI2 also blocked protein-dependent splicing. These results indicated that protein-dependent excision of bI2 is an RNA-catalyzed process involving the same two-step transesterification mechanism responsible for self-splicing of group I introns. We propose that the CBP2 protein binds to the bI2 precursor, thereby stabilizing the catalytically active structure of the RNA. The same or a similar RNA structure is probably induced by high concentrations of Mg2+ in the absence of protein. Binding of the CBP2 protein to the unspliced precursor was supported by the observation that the protein-dependent reaction was saturable by the wild-type precursor. Protein-dependent splicing was competitively inhibited by excised bI2 and by a splicing-defective precursor with a mutation in the 5' exon near the splice site but not by a splicing-defective precursor with a mutation in the core structure. Binding of the CBP2 protein to the precursor RNA had an effect on the 5' splice site helix, as evidenced by suppression of the interaction of an exogenous dinucleotide with the internal guide sequence.

scholarly journals Precise mapping of new group I introns in tRNA genes

2020 ◽  
Author(s):  
Kelly P. Williams
Keyword(s):  
Splice Site ◽  
Group I Intron ◽  
Trna Genes ◽  
Group I Introns ◽  
Covariance Model ◽  
Software Module ◽  
Catalytic Core ◽  
Group I ◽  
Precise Mapping ◽  
New Type

ABSTRACTBacterial tRNA have been found interrupted at various positions in the anticodon loop by group I introns, in four types. The primary bioinformatic tool for group I intron discovery is a covariance model that can identify conserved features in the catalytic core and can sometimes identify the typical uridine residue at the -1 position, preceding the 5-prime splice site, but cannot identify the typical guanidine residue at the omega position, preceding the 3-prime splice site, to achieve precise mapping. One approach to complete the automation of group I intron mapping is to focus instead on the exons, which is enabled by the regularity of tRNAs. We develop a software module, within a larger package (tFind) aimed at mapping bacterial tRNA and tmRNA genes precisely, that expands this list of four known classes of intron-interrupted tRNAs to 21 cases. A new covariance model for these introns is presented. The wobble base pair formed by the -1 uridine is considered a determinant of the 5-prime splice site, yet one reasonably large new type bears a cytidine nucleotide at that position.

CBP2 protein promotes in vitro excision of a yeast mitochondrial group I intron

1989 ◽  
Vol 9 (12) ◽  
pp. 5424-5433
Author(s):  
A Gampel ◽  
M Nishikimi ◽  
A Tzagoloff
Keyword(s):  
Splice Site ◽  
Group I Intron ◽  
Nuclear Gene ◽  
Group I Introns ◽  
Wild Type ◽  
Group I ◽  
Mitochondrial Cytochrome B ◽  
High Concentrations ◽  
Self Splicing

The terminal intron (bI2) of the yeast mitochondrial cytochrome b gene is a group I intron capable of self-splicing in vitro at high concentrations of Mg2+. Excision of bI2 in vivo, however, requires a protein encoded by the nuclear gene CBP2. The CBP2 protein has been partially purified from wild-type yeast mitochondria and shown to promote splicing at physiological concentrations of Mg2+. The self-splicing and protein-dependent splicing reactions utilized a guanosine nucleoside cofactor, the hallmark of group I intron self-splicing reactions. Furthermore, mutations that abolished the autocatalytic activity of bI2 also blocked protein-dependent splicing. These results indicated that protein-dependent excision of bI2 is an RNA-catalyzed process involving the same two-step transesterification mechanism responsible for self-splicing of group I introns. We propose that the CBP2 protein binds to the bI2 precursor, thereby stabilizing the catalytically active structure of the RNA. The same or a similar RNA structure is probably induced by high concentrations of Mg2+ in the absence of protein. Binding of the CBP2 protein to the unspliced precursor was supported by the observation that the protein-dependent reaction was saturable by the wild-type precursor. Protein-dependent splicing was competitively inhibited by excised bI2 and by a splicing-defective precursor with a mutation in the 5' exon near the splice site but not by a splicing-defective precursor with a mutation in the core structure. Binding of the CBP2 protein to the precursor RNA had an effect on the 5' splice site helix, as evidenced by suppression of the interaction of an exogenous dinucleotide with the internal guide sequence.

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.

Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria

Science ◽  
1990 ◽  
Vol 250 (4987) ◽  
pp. 1566-1570 ◽  
Author(s):  
M. Xu ◽  
S. Kathe ◽  
H. Goodrich-Blair ◽  
S. Nierzwicki-Bauer ◽  
D. Shub
Keyword(s):  
Group I Introns ◽  
Bacterial Origin ◽  
Group I ◽  
Self Splicing
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