A Group II Intron-encoded Maturase Functions Preferentially In Cis and Requires Both the Reverse Transcriptase and X Domains to Promote RNA Splicing

Cui, Xiaoxu

doi:10.1016/s0022-2836(04)00543-1

Cited by 15 publications

(62 citation statements)

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“…Binding of LtrA to DIVa is considered to be the first contact of LtrA with the intron and impacts splicing efficiency (28). In addition, this interaction represses translation of the LtrA reading frame (29) and has been suggested to be more important for intron mobility than for splicing (30). We see no strong association of the area surrounding the matK start codon or of any sequences between DIII and DIV with tagged MatK (Fig.…”

Section: Peak Enrichment Of Rna Coprecipitated With Matk Is Found Inmentioning

confidence: 80%

“…Thus, if MatK autoregulation is maintained in chloroplasts it is not likely to occur via docking to the translational start of MatK. Possibly, loss of binding in this area was tolerable, because the DIVa-maturase interaction was more important for intron mobility than for splicing (30), a feature definitely lost in chloroplasts.…”

Section: Peak Enrichment Of Rna Coprecipitated With Matk Is Found Inmentioning

confidence: 99%

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An organellar maturase associates with multiple group II introns

Zoschke

Nakamura

Liere

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

156

207

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Bacterial group II introns encode maturase proteins required for splicing. In organelles of photosynthetic land plants, most of the group II introns have lost the reading frames for maturases. Here, we show that the plastidial maturase MatK not only interacts with its encoding intron within trnK-UUU, but also with six additional group II introns, all belonging to intron subclass IIA. Mapping analyses of RNA binding sites revealed MatK to recognize multiple regions within the trnK intron. Organellar group II introns are considered to be the ancestors of nuclear spliceosomal introns. That MatK associates with multiple intron ligands makes it an attractive model for an early trans-acting nuclear splicing activity.roup II introns are highly structured ribozymes, found in bacteria and organellar genomes of plants, fungi, protists, and some animals. They catalyze their own excision from precursor RNAs (1). In addition, bacterial group II introns are mobile genetic elements. These features, as well as structural similarities with nuclear introns, have led to the proposition that ancestors of modern group II introns have crossed kingdoms from prokaryotes to eukaryotes via eubacterial endosymbionts, and eventually evolved into nuclear introns (2). Whereas nuclear introns are removed by a large ribonucleoprotein complex called the spliceosome, each bacterial intron encodes a distinct maturase protein facilitating its splicing. The evolutionary transition from the highly specific, maturase-driven splicing toward the complex transacting spliceosomal machinery is unclear. Without any "living fossils" with a protospliceosome, a key question is how the emerging intron diversification was accompanied by a splicing machinery with the ability to act on multiple targets. At least initially, the already existing splicing factors encoded by the invading group II introns, i.e., modified maturases, may have fulfilled this task.In present day organelles, maturase genes can be found in fungal and plant mitochondria as well as in plant chloroplasts. Although mitochondria are not directly amenable to transgenic studies, there are a number of plant species, foremost tobacco, for which directed mutagenesis of chloroplast genomes is possible (3). All land plant chloroplasts with the exception of some parasitic species in the genus Cuscuta (4, 5) contain a single maturase gene called matK in the intron of the lysine tRNA-K (UUU) gene. matK is expressed at least in green tissue (6-8). Sequence and structural homologies are found to the RNA binding motif (domain X) and the reverse transcriptase domain typically found in bacterial maturases (9, 10). Both domains are involved in splicing. By contrast, domains required for the mobility of group II introns are missing in MatK.The function of matK in chloroplasts is so far unknown, but its position inside the trnK gene suggests a role for splicing the trnK precursor. Importantly, it has been suggested that other chloroplast introns are targeted by MatK as well: firstly, several chloroplast genomes o...

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Section: Peak Enrichment Of Rna Coprecipitated With Matk Is Found Inmentioning

confidence: 80%

Section: Peak Enrichment Of Rna Coprecipitated With Matk Is Found Inmentioning

confidence: 99%

An organellar maturase associates with multiple group II introns

Zoschke

Nakamura

Liere

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

156

207

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“…The Ll.LtrB IEP, denoted LtrA protein, has four domains: RT, which contains the conserved RT sequence blocks and corresponds to fingers and palm regions of retroviral RTs; X, which corresponds to the RT thumb and is a site of mutations affecting RNA splicing activity; D, DNA binding; and En, DNA endonuclease (Cui et al 2004;Blocker et al 2005). The RT and X domains bind the intron RNA to stabilize its active structure for RNA splicing and reverse splicing, while the D and En domains are not required for RNA splicing but instead interact with DNA target sites during intron mobility (San Filippo and Lambowitz 2002;Cui et al 2004;Blocker et al 2005). LtrA appears to be largely monomeric in solution, but binds to the intron RNA with a stoichiometry of 2:1, suggesting that it functions as a dimer, similar to HIV-1 and some other RTs (Saldanha et al 1999;Rambo and Doudna 2004).…”

Section: Introductionmentioning

confidence: 99%

“…DIVa is thought to contribute to the intron specificity of binding, but if DIVa is deleted, LtrA can still promote RNA splicing at reduced efficiency by binding directly to the catalytic core Matsuura et al 2001). Notably, LtrA functions preferentially in cis to promote the splicing of the intron that encodes it (Cui et al 2004), and the binding of LtrA to DIVa down-regulates its own translation (Singh et al 2002). Although not always a site of translation initiation, a predicted DIVa stem-loop structure is present in most group II introns that encode IEPs, and the yeast aI2 IEP has also been shown to bind both DIVa and catalytic core regions, suggesting that this mode of interaction is conserved among group II IEPs (Singh et al 2002;Huang et al 2003).…”

Section: Introductionmentioning

confidence: 99%

“…Previously, we used a genetic assay in which the splicing of the Ll.LtrB intron is linked to the expression of GFP in conjunction with a high-throughput genetic method termed ''unigenic evolution'' to identify regions of LtrA required for RNA splicing (Cui et al 2004). Mapping of these regions onto a three-dimensional model of LtrA suggested an extended RNA-binding surface that spans the RT and X/thumb domains and includes the N-terminal extension, regions in and around the template-primer binding track, and patches on the back of the molecule (Blocker et al 2005).…”

Section: Introductionmentioning

confidence: 99%

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Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase

Gu¹,

Cui²,

Mou³

et al. 2010

RNA

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Mobile group II introns encode a reverse transcriptase that binds the intron RNA to promote RNA splicing and intron mobility, the latter via reverse splicing of the excised intron into DNA sites, followed by reverse transcription. Previous work showed that the Lactococcus lactis Ll.LtrB intron reverse transcriptase, denoted LtrA protein, binds with high affinity to DIVa, a stem-loop structure at the beginning of the LtrA open reading frame and makes additional contacts with intron core regions that stabilize the active RNA structure for forward and reverse splicing. LtrA's binding to DIVa down-regulates its translation and is critical for initiation of reverse transcription. Here, by using high-throughput unigenic evolution analysis with a genetic assay in which LtrA binding to DIVa down-regulates translation of GFP, we identified regions at LtrA's N terminus that are required for DIVa binding. Then, by similar analysis with a reciprocal genetic assay, we confirmed that residual splicing of a mutant intron lacking DIVa does not require these N-terminal regions, but does require other reverse transcriptase (RT) and X/thumb domain regions that bind the intron core. We also show that N-terminal fragments of LtrA by themselves bind specifically to DIVa in vivo and in vitro. Our results suggest a model in which the N terminus of nascent LtrA binds DIVa of the intron RNA that encoded it and nucleates further interactions with core regions that promote RNP assembly for RNA splicing and intron mobility. Features of this model may be relevant to evolutionarily related non-long-terminal-repeat (non-LTR)-retrotransposon RTs.

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Unraveling the role of the enigmatic MatK maturase in chloroplast group IIA intron excision

2020

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Maturases are prokaryotic enzymes that aid self‐excision of introns in precursor RNAs and have evolutionary ties to the nuclear spliceosome. Both the mitochondria and chloroplast, due to their prokaryotic origin, encode a single intron maturase, MatR for the mitochondria and MatK for the chloroplast. MatK is proposed to aid excision of seven different chloroplast group IIA introns that reside within precursor RNAs for essential elements of chloroplast function. We have developed an in vitro activity assay to test chloroplast group IIA intron excision. Using this assay, we demonstrate self‐excision of the group IIA intron of the second intron of rps12 and the group IIA intron of rpl2. We further show that the addition of heterologously expressed MatK protein increases efficiency of group IIA intron self‐splicing for the second intron of rps12 but not the group IIA intron of rpl2. These data, to our knowledge, provide the first direct evidence of MatK’s maturase activity.

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A Group II Intron-encoded Maturase Functions Preferentially In Cis and Requires Both the Reverse Transcriptase and X Domains to Promote RNA Splicing

Cited by 15 publications

References 0 publications

An organellar maturase associates with multiple group II introns

An organellar maturase associates with multiple group II introns

Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase

Unraveling the role of the enigmatic MatK maturase in chloroplast group IIA intron excision

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