RNA Splicing in the Chloroplast

Herrin, David L.; Kuo, Tai-Chih; Goldschmidt-Clermont, Michel

doi:10.1007/0-306-48204-5_11

Cited by 4 publications

(7 citation statements)

References 59 publications

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“…For example, the Chlamydomonas chloroplast genome sequence reveals group I and II introns located in the psbA, psaA and 23S rRNA genes. Splicing of the group I introns is through a guanosinedependent mechanism (Herrin et al 1990) likely to be similar to that reported for the Tetrahymena rRNA intron. At physiological temperatures, splicing in vitro is much slower than splicing in vivo.…”

Section: Chloroplast Gene Expression and Controlsupporting

confidence: 69%

Organization and expression of organellar genomes

Barbrook

Howe

Kurniawan

et al. 2010

Phil. Trans. R. Soc. B

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Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana . In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a ‘viral-type’ RNA polymerase, although a ‘bacterial-type’ enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.

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Section: Chloroplast Gene Expression and Controlsupporting

confidence: 69%

Organization and expression of organellar genomes

Barbrook

Howe

Kurniawan

et al. 2010

Phil. Trans. R. Soc. B

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“…The relative paucity of autocatalytic group II introns from chloroplasts may be because most of the known ones are from vascular plants and euglenoids, which appear to rely mainly on protein-dependent splicing (Jenkins et al 1997). The Chs.psbA1 intron is also the first cis-spliced group II intron from Chlamydomonas, and it is not closely related to the two trans-spliced group II introns in the psaA1 gene (for review, see Herrin et al 1998).…”

Section: Discussionmentioning

confidence: 99%

“…The chloroplast genomes of Chlamydomonas spp. (mostly mesophilic) are excellent sources of group I intron ribozymes (Herrin et al 1998), but for unknown reasons, typical cis-spliced group II introns have not been reported. To identify a ribozyme from a psychrophilic organism, we searched chloroplast psbA and 23S rRNA genes of snow/ice Chlamydomonas by PCR, expecting to find group I introns.…”

Section: Introductionmentioning

confidence: 99%

A horizontally acquired group II intron in the chloroplastpsbAgene of a psychrophilicChlamydomonas: In vitro self-splicing and genetic evidence for maturase activity

Odom¹,

Shenkenberg²,

Garcia³

et al. 2004

RNA

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The majority of known group II introns are from chloroplast genomes, yet the first self-splicing group II intron from a chloroplast gene was reported only recently, from the psbA gene of the euglenoid, Euglena myxocylindracea. Herein, we describe a large (2.6-kb) group II intron from the psbA gene (psbA1) of a psychrophilic Chlamydomonas sp. from Antarctica that self-splices accurately in vitro. Remarkably, this intron, which also encodes an ORF with putative reverse transcriptase, maturase, and endonuclease domains, is in the same location, and is related to the E. myxocylindracea intron, as well as to group IIB2 introns from cyanobacteria. In vitro self-splicing of Chs.psbA1 occurred via a lariat, and required Mg 2+ (>12 mM) and NH 4 + . Selfsplicing was improved by deleting most of the ORF and by using pre-RNAs directly from transcription reactions, suggestive of a role for folding during transcription. Self-splicing of Chs.psbA1 pre-RNAs showed temperature optima of ∼44°C, but with a broad shoulder on the low side of the peak; splicing was nearly absent at 50°C, indicative of thermolability. Splicing of wild-type Chs.psbA1 also occurred in Escherichia coli, but not when the ORF was disrupted by mutations, providing genetic evidence that it has maturase activity. This work provides the first description of a ribozyme from a psychrophilic organism. It also appears to provide a second instance of interkingdom horizontal transfer of this group IIB2 intron (or a close relative) from cyanobacteria to chloroplasts.

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“…VOL. 21,2001 HOMING OF EXOGENOUS psbA INTRONS 3477 tifs located further downstream, including one that is 30 bp into the ORF. Interestingly, there is also a possible alternative start codon, ATT (i.e., AUU), 26 bp downstream of the putative Ϫ10 motif in the ORF.…”

Section: Fig 2 Pcr Analysis Ofmentioning

confidence: 99%

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

Odom

Holloway

Deshpande

et al. 2001

Molecular and Cellular Biology

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Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 and Cr.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 (16S rrn). 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. The Cr.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/g 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.Some group I introns are characterized by the ability to self-splice in vitro and to promote their insertion into intronless copies of the host gene in vivo (reviewed in references 10 and 29). The latter process is a type of homologous recombination known as intron homing. Such mobile introns typically contain a large open reading frame (ORF) that codes for a site-specific endonuclease. The endonuclease promotes homing by producing a double-strand break in the intronless allele near the site of intron insertion. A popular model for the subsequent events is based on the double-strand break repair model of DNA recombination in Saccharomyces cerevisiae (36), a postulate of which is that coconversion of flanking exon sequences accompanies intron acquisition.Mobile group I introns have been found in phylogenetically diverse eucaryotes and in certain bacteriophages (29). In eucaryotes, they occur in mitochondrial, chloroplast, and nuclear genes but are typically more common in the organelles. Group I intron homing has been studied intensively, however, only in bacteriophage T4, which has provided an elegant viral-procaryotic system for studying homing mechanism...

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RNA Splicing in the Chloroplast

Cited by 4 publications

References 59 publications

Organization and expression of organellar genomes

Organization and expression of organellar genomes

A horizontally acquired group II intron in the chloroplastpsbAgene of a psychrophilicChlamydomonas: In vitro self-splicing and genetic evidence for maturase activity

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

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