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Group II intron splicing factors in plant mitochondria.

Brown GG, Colas des Francs-Small C, Ostersetzer-Biran O - Front Plant Sci (2014)

Bottom Line: Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns.In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants.In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory splicing cofactors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, McGill University Montreal, QC, Canada.

ABSTRACT
Group II introns are large catalytic RNAs (ribozymes) which are found in bacteria and organellar genomes of several lower eukaryotes, but are particularly prevalent within the mitochondrial genomes (mtDNA) in plants, where they reside in numerous critical genes. Their excision is therefore essential for mitochondria biogenesis and respiratory functions, and is facilitated in vivo by various protein cofactors. Typical group II introns are classified as mobile genetic elements, consisting of the self-splicing ribozyme and its intron-encoded maturase protein. A hallmark of maturases is that they are intron specific, acting as cofactors which bind their own cognate containing pre-mRNAs to facilitate splicing. However, the plant organellar introns have diverged considerably from their bacterial ancestors, such as they lack many regions which are necessary for splicing and also lost their evolutionary related maturase ORFs. In fact, only a single maturase has been retained in the mtDNA of various angiosperms: the matR gene encoded in the fourth intron of the NADH-dehydrogenase subunit 1 (nad1 intron 4). Their degeneracy and the absence of cognate ORFs suggest that the splicing of plant mitochondria introns is assisted by trans-acting cofactors. Interestingly, in addition to MatR, the nuclear genomes of angiosperms also harbor four genes (nMat 1-4), which are closely related to maturases and contain N-terminal mitochondrial localization signals. Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns. In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants. In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory splicing cofactors.

No MeSH data available.


Related in: MedlinePlus

Plant mitochondria maturases. Plant maturase ORFs are shown as rectangles, with different shadings indicating conserved regions. The three domains typical to group II intron encoded maturases are outlined in the maturase ORFs: A reverse transcriptase (RT); domain X, associated with maturase activity; D, DNA-binding and endonuclease domain (D/En). The organelle-encoded MatR and MatK proteins contain a well conserved domain X, but have degenerate RT motifs and lack the En domain. In angiosperms, four other maturase-related proteins, denoted as nMAT 1–4, are encoded by nuclear genes, but have N-terminal mitochondrial targeting sequences (Keren et al., 2009). Similarly to MatR, the four nMATs have a conserved domain X, but show deviations in the RT domain and lack (type I) or have deviations in the D/En domain (type II), suggesting loss of mobility functions.
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Figure 4: Plant mitochondria maturases. Plant maturase ORFs are shown as rectangles, with different shadings indicating conserved regions. The three domains typical to group II intron encoded maturases are outlined in the maturase ORFs: A reverse transcriptase (RT); domain X, associated with maturase activity; D, DNA-binding and endonuclease domain (D/En). The organelle-encoded MatR and MatK proteins contain a well conserved domain X, but have degenerate RT motifs and lack the En domain. In angiosperms, four other maturase-related proteins, denoted as nMAT 1–4, are encoded by nuclear genes, but have N-terminal mitochondrial targeting sequences (Keren et al., 2009). Similarly to MatR, the four nMATs have a conserved domain X, but show deviations in the RT domain and lack (type I) or have deviations in the D/En domain (type II), suggesting loss of mobility functions.

Mentions: As outlined above, group II introns have diverged considerably from bacteria and plant organellar genomes. These introns in plants sometime lack regions which are considered to be essential for their splicing. Also, the number of maturases has been dramatically reduced during the evolution of organellar genomes in plants. The mitochondrial genomes of bryophytes, as Marchantia polymorpha and Physcomitrella patens, contain a few maturase ORFs, while only a single intron has retained its maturase gene in the mtDNAs in angiosperms: the matR gene encoded within nad1 intron 4 (Wahleithner et al., 1990) (Figures 1,3). MatR proteins contain a well-conserved domain X, but have degenerate RT motifs and lack the En domain (Figure 4). The high conservation of MatR across the plant lineage (Adams et al., 2002) and RNA-editing events which restore conserved amino-acids (Thomson et al., 1994) suggest that matR encodes a functional protein. Preliminary data suggest that MatR binds to several group II introns in vivo, but its putative roles in splicing are yet to be determined. Analogously, MatK protein, encoded within trnK gene in chloroplasts, is associated with numerous group II introns in vivo (Zoschke et al., 2010). Besides MatR there are no splicing factor candidates among the ORFs of angiosperm mitochondrial genomes (although some lower plants may contain a few maturase ORFs in the mtDNAs). The splicing of mitochondrial introns in plants is therefore expected to be facilitated by nuclear-encoded proteins. These are translated by cytosolic ribosomes and subsequently imported into the organelle.


Group II intron splicing factors in plant mitochondria.

Brown GG, Colas des Francs-Small C, Ostersetzer-Biran O - Front Plant Sci (2014)

Plant mitochondria maturases. Plant maturase ORFs are shown as rectangles, with different shadings indicating conserved regions. The three domains typical to group II intron encoded maturases are outlined in the maturase ORFs: A reverse transcriptase (RT); domain X, associated with maturase activity; D, DNA-binding and endonuclease domain (D/En). The organelle-encoded MatR and MatK proteins contain a well conserved domain X, but have degenerate RT motifs and lack the En domain. In angiosperms, four other maturase-related proteins, denoted as nMAT 1–4, are encoded by nuclear genes, but have N-terminal mitochondrial targeting sequences (Keren et al., 2009). Similarly to MatR, the four nMATs have a conserved domain X, but show deviations in the RT domain and lack (type I) or have deviations in the D/En domain (type II), suggesting loss of mobility functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927076&req=5

Figure 4: Plant mitochondria maturases. Plant maturase ORFs are shown as rectangles, with different shadings indicating conserved regions. The three domains typical to group II intron encoded maturases are outlined in the maturase ORFs: A reverse transcriptase (RT); domain X, associated with maturase activity; D, DNA-binding and endonuclease domain (D/En). The organelle-encoded MatR and MatK proteins contain a well conserved domain X, but have degenerate RT motifs and lack the En domain. In angiosperms, four other maturase-related proteins, denoted as nMAT 1–4, are encoded by nuclear genes, but have N-terminal mitochondrial targeting sequences (Keren et al., 2009). Similarly to MatR, the four nMATs have a conserved domain X, but show deviations in the RT domain and lack (type I) or have deviations in the D/En domain (type II), suggesting loss of mobility functions.
Mentions: As outlined above, group II introns have diverged considerably from bacteria and plant organellar genomes. These introns in plants sometime lack regions which are considered to be essential for their splicing. Also, the number of maturases has been dramatically reduced during the evolution of organellar genomes in plants. The mitochondrial genomes of bryophytes, as Marchantia polymorpha and Physcomitrella patens, contain a few maturase ORFs, while only a single intron has retained its maturase gene in the mtDNAs in angiosperms: the matR gene encoded within nad1 intron 4 (Wahleithner et al., 1990) (Figures 1,3). MatR proteins contain a well-conserved domain X, but have degenerate RT motifs and lack the En domain (Figure 4). The high conservation of MatR across the plant lineage (Adams et al., 2002) and RNA-editing events which restore conserved amino-acids (Thomson et al., 1994) suggest that matR encodes a functional protein. Preliminary data suggest that MatR binds to several group II introns in vivo, but its putative roles in splicing are yet to be determined. Analogously, MatK protein, encoded within trnK gene in chloroplasts, is associated with numerous group II introns in vivo (Zoschke et al., 2010). Besides MatR there are no splicing factor candidates among the ORFs of angiosperm mitochondrial genomes (although some lower plants may contain a few maturase ORFs in the mtDNAs). The splicing of mitochondrial introns in plants is therefore expected to be facilitated by nuclear-encoded proteins. These are translated by cytosolic ribosomes and subsequently imported into the organelle.

Bottom Line: Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns.In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants.In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory splicing cofactors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, McGill University Montreal, QC, Canada.

ABSTRACT
Group II introns are large catalytic RNAs (ribozymes) which are found in bacteria and organellar genomes of several lower eukaryotes, but are particularly prevalent within the mitochondrial genomes (mtDNA) in plants, where they reside in numerous critical genes. Their excision is therefore essential for mitochondria biogenesis and respiratory functions, and is facilitated in vivo by various protein cofactors. Typical group II introns are classified as mobile genetic elements, consisting of the self-splicing ribozyme and its intron-encoded maturase protein. A hallmark of maturases is that they are intron specific, acting as cofactors which bind their own cognate containing pre-mRNAs to facilitate splicing. However, the plant organellar introns have diverged considerably from their bacterial ancestors, such as they lack many regions which are necessary for splicing and also lost their evolutionary related maturase ORFs. In fact, only a single maturase has been retained in the mtDNA of various angiosperms: the matR gene encoded in the fourth intron of the NADH-dehydrogenase subunit 1 (nad1 intron 4). Their degeneracy and the absence of cognate ORFs suggest that the splicing of plant mitochondria introns is assisted by trans-acting cofactors. Interestingly, in addition to MatR, the nuclear genomes of angiosperms also harbor four genes (nMat 1-4), which are closely related to maturases and contain N-terminal mitochondrial localization signals. Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns. In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants. In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory splicing cofactors.

No MeSH data available.


Related in: MedlinePlus