<i>Euglena gracilis</i>chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III

Christopher, David A.; Hallick, Richard B.

doi:10.1093/nar/17.19.7591

Cited by 91 publications

(44 citation statements)

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“…A total of 105 dpm of 3zP-labeled primer was co-precipitated with either chloroplast RNA (2.05 x 106 plastidslreaction) or with total cellular RNA (12 to 14 pg). The annealing and primer extension reactions were conducted as described in Christopher and Hallick (1989), except final deoxynucleotide triphosphate concentration was 400 pM.…”

Section: Primer Extension Analysismentioning

confidence: 99%

A novel light-regulated promoter is conserved in cereal and dicot chloroplasts.

1992

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The chloroplast psbD-psbC genes encode D2 and cp43, a reaction center protein and chlorophyll-binding antenna protein of photosystem II, respectively. We have previously shown that differential accumulation of light-induced psbD-psbC mRNAs in barley chloroplasts is due to transcription from a blue light-responsive promoter (LRP). It is hypothesized that the light-induced mRNAs help to maintain levels of the D2 polypeptide, which is photodamaged and degraded in illuminated plants. To determine if light-induced accumulation of psbD-psbC mRNAs was a conserved phenomenon in chloroplasts, the expression of psbD-psbC operons from five cereals (barley, wheat, rice, maize, and sorghum) and three dicot (tobacco, spinach, and pea) species was examined. Cereal and dicot psbD-psbC operons differ due to several DNA rearrangements that moved psbK-psbl proximal to psbD-psbC, allowing cotranscription of these genes and production of several unique transcripts in cereals. Despite differences in the structure and expression of the cereal and dicot psbDpsbC operons, the accumulation of light-induced psbD-psbC mRNAs was conserved in all species studied. An unusual feature of the light-induced mRNAs was the occurrence of 5'end microheterogeneity. The multiple 5'termini were mapped to several consecutive nucleotides (8 to 25 bp) within a highly conserved (61%) DNA region that represents the transcription initiation site for the mRNAs in barley and tobacco. The nove1 LRP differs in sequence from typical plastid promoters that have prokaryotic "-10" and "-35" elements and is centered 570 bp (cereals), 900 bp (tobacco, spinach), or 1100 bp (pea) upstream from the psbD translational start codon. We propose that physiological and gene regulatory demands of the chloroplast act as constraints that preserved the linkage of the LRP with psbD despite DNA inversions involving the psbD upstream region.

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Section: Primer Extension Analysismentioning

confidence: 99%

A novel light-regulated promoter is conserved in cereal and dicot chloroplasts.

1992

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“…Most of the introns are degenerate lacking elements of the conserved group II intron RNA structure, including entire RNA domains, and only two contain intact ORFs that could potentially encode functional proteins (49,118). The smallest of these introns, referred to as group III introns, consist only of DI and DVI and lack DV, which is essential for ribozyme activity (117,119). Comparisons of cpDNA sequences of different euglenoid species show that early branching species contain fewer introns and suggest at least two bursts of intron proliferation (120,121).…”

Section: Group II Intron Proliferation To High Copy Numbermentioning

confidence: 99%

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

2015

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This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.

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“…These introns do not have a domain V but retain group II-like 5' splice boundaries (Christopher and Hallick 1989). These introns have a domain VI that is used during lariat formation (Copertino et al 1994), and some may also contain subdomain ID …”

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confidence: 99%

“…These introns are divided into two categories, group II and group III (Christopher and Hallick 1989;Copertino and Hallick 1993). Most of the 74 group II introns, which range in size from 277 to 671 nucleotides, have the secondary structures of the subgroup IIB introns (Michel et al 1989).…”

mentioning

confidence: 99%

A group III intron is formed from domains of two individual group II introns.

Li¹,

Hallick²

1994

Genes Dev.

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A 1352-nucleotide intron within the Euglena gracilis chloroplast ycf8 gene has been characterized as a complex twintron with overlapping internal introns and alternative splicing pathways. Partially spliced pre-mRNAs were characterized by a combination of cDNA cloning and sequencing, Northern hybridization, and $1 nuclease protection analyses. In the predominant pathway, two internal group II introns (601 and 392 nucleotides} are spliced from subdomain ID of an external group II intron (359 nucleotides). In an alternative pathway, following excision of the 601-nucleotide intron, splicing of a group III intron occurs. This group IlI intron is recruited from sequences of the external intron and the 392-nucleotide intron. This is the first evidence that a group III intron can be derived from portions of existing group II introns. The mechanism of group III intron formation may also be relevant to the evolution of nuclear introns from putative group II intron ancestors.[Key Words: Complex twintron; alternative splicing; group III intron evolution; nuclear intron evolution; Euglena gracilis; chloroplast] Received April 15, 1994; revised version accepted May 18, 1994.Group II introns are present in prokaryotic, fungal and plant mitochondria, and plant chloroplast genomes (Michel et al. 1989;Ferat and Michel 1993). Group II introns have a conserved secondary structure. Several tertiary interactions are involved in formation of the catalytic core, such as exon binding site-intron binding site (EBS-IBS) pairing, guided pair, ~/~', e/~' and ~/~' interactions (Jacquier andMichel 1987, 1990;Michel et al. 1989;Jacquier and Jacquesson-Breuleux 1991; HarrisKerr et al. 1993). Splicing of group II introns occurs by two transesterification reactions (Peebles et al. 1986;Schmelzer and Schweyen 1986;van der Veen et al. 1986). In the first reaction, the 2' hydroxyl group of the unpaired adenosine in domain VI makes a nucleophilic attack on the first nucleotide of the intron, generating a free 5' exon and an intron lariat-3' exon intermediate. In the second reaction, the 3' hydroxyl of the 5' exon makes a nucleophilic attack on the first nucleotide of the 3' exon, resulting in exon ligation and release of the intron as a lariat RNA.The Euglena gracilis chloroplast genome contains at The E. gracilis chloroplast genome also contains short (91-119 nucleotides), A + U-rich group III introns. These introns do not have a domain V but retain group II-like 5' splice boundaries (Christopher and Hallick 1989). These introns have a domain VI that is used during lariat formation (Copertino et al. 1994), and some may also contain subdomain ID

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Euglena gracilischloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III

Cited by 91 publications

References 46 publications

A novel light-regulated promoter is conserved in cereal and dicot chloroplasts.

A novel light-regulated promoter is conserved in cereal and dicot chloroplasts.

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

A group III intron is formed from domains of two individual group II introns.

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