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Phylogenetic tree of bacterial, chloroplastic, and mitochondrial ribosomal proteins S2. The analysis was carried out with the program PHYLIP version 3.572c and the tree was generated using the neighbor-joining method. The accession numbers of the sequences are available upon request.
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A gene (rps2) coding for ribosomal protein S2 (RPS2) is present in the mitochondrial (mt) genome of several monocot plants, but absent from the mtDNA of dicots. Confirming that in dicot plants the corresponding gene has been transferred to the nucleus, a corresponding Arabidopsis thaliana nuclear gene was identified that codes for mitochondrial RPS...
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... 5 end of the rps2A 3.0 kb mRNA was mapped by primer extension with oligonucleotide O3 (Fig- ure 5B). A major primer extension run-off product was detected that localized the 5 extremity 1327 nu- cleotides upstream of the initiation codon. This long 5 UTR sequence contains no open reading frame longer than 40 codons and shows no similarity to any known sequence. A larger primer extension product is also visible on the gel, that may correspond to a precursor transcript or to an alternative transcription initiation site. Regarding the 3 end of the rps2A mRNA, it probably coincides with a characteristic double stem- loop structure that is located 70 nucleotides down- stream the stop codon (Figure 2). Similar structures are present downstream of many plant mitochondrial genes ( Schuster et al., 1986) and delimitate the 3 end of the corresponding mRNAs. It has been shown that this structure stabilizes the transcripts against degrada- tion by exonucleases ( Dombrowski et al., ...
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... rps2 gene is absent from the mtDNA of all di- cot plants tested where it has probably migrated to the nucleus. A computer search of the data banks re- vealed a candidate Arabidopsis EST (accession num- ber F19985) that was obtained and sequenced. The 5 end of the corresponding mRNA was determined by 5 -RACE, using total flower Arabidopsis RNA as template, which added 44 additional nucleotides to the 5 sequence of the EST clone. The Arabidopsis sequence (accession number AF273102) codes for a 228 amino acids long protein that is 42-48% identi- cal to the maize, wheat and rice mt RPS2 sequences, but only 24% identical to the Arabidopsis chloro- plast RPS2 (accession number AP000423). It seems therefore that the sequence we have identified truly corresponds to the nuclear sequence that codes for the Arabidopsis mt RPS2 protein. A phylogenetic analysis of bacterial, chloroplastic and mitochondr- ial RPS2 sequences also corroborates that assumption: the Arabidopsis sequence clearly branches out with the mitochondrial RPS2 sequences ( Figure 5). However, contrarily to its monocot counterparts, the nucleus- encoded Arabidopsis RPS2 has no long C-terminal extension (Figure ...
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... 5 end of the rps2A 3.0 kb mRNA was mapped by primer extension with oligonucleotide O3 (Fig- ure 5B). A major primer extension run-off product was detected that localized the 5 extremity 1327 nu- cleotides upstream of the initiation codon. ...
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... seems therefore that the sequence we have identified truly corresponds to the nuclear sequence that codes for the Arabidopsis mt RPS2 protein. A phylogenetic analysis of bacterial, chloroplastic and mitochondr- ial RPS2 sequences also corroborates that assumption: the Arabidopsis sequence clearly branches out with the mitochondrial RPS2 sequences ( Figure 5). However, contrarily to its monocot counterparts, the nucleus- encoded Arabidopsis RPS2 has no long C-terminal extension (Figure 3). ...
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... These features restrict its application in the study of plant phylogeny. However, some studies have shown that mitochondrial genes could provide additional evolutionary information and are useful in reconstructing the plant phylogeny (Norman and Gray, 2001;Perrotta et al., 2002;Guo and Ge, 2004;Qiu et al., 2010;Bock et al., 2014;Sun et al., 2015;Folk et al., 2016). ...
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
... Between common editing sites, we noticed that the variation of editing extent differed at some sites in each dek53 mutant allele, for example, atp8-76 (0.27 and 0.67 in dek53-ref and dek53-mu1, respectively) ( Fig. 4; Supplementary Table S4). Previous studies reported that growth and development (Bock et al., 1993;Hirose et al., 1996;Perrotta et al., 2002), active photosynthesis (Karcher and Bock, 2002), or genetic/mitochondrial background (Kempken et al., 1995;Bentolila et al., 2005) could also affect RNA editing. In this study, the two mutant alleles were generated from different genetic backgrounds, which already exhibited differences in RNA editing events in WT kernels. ...
Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.
... 1/3 the rate of the chloroplast genome), with sequence variations smaller than chloroplasts and nuclear DNA, providing limited evolutionary information (Norman and Gray, 2001;Perrotta et al., 2002). ...
Cynodon dactylon × Cynodon transvaalensis is one of the most important turfgrasses. Sequencing the C. dactylon × C. transvaalensis mitochondrial genome can help us learn more about its genomic composition and allow further study of the population genetics, taxonomy, and evolutionary biology of Poaceae plants and other related species. Here the C. dactylon × C. transvaalensis mitochondrial genome was sequenced using Illumina HiSeq combined with PacBio sequencing technology, and the map of the mitochondrial genome was constructed after de novo assembly and annotation. The C. dactylon × C. transvaalensis mitochondrial genome has 366,612 bp and contains 53 genes, including 31 protein-coding genes, 3 rRNA genes, and 16 tRNA genes. The result of relative synonymous codon usage (RSCU) showed an A or U preference at the third position of the codons. Thirty-three chloroplast DNA fragments were found in C. dactylon × C. transvaalensis mitochondrial DNA, ranging from 72 to 3003 bp. Phylogenetic trees built based on the chloroplast genome were congruent with the plant taxonomy and NCBI taxonomy common tree, while the phylogenetic trees built based on 9 mitochondrial genes showed some differences from the common tree.
... Protein modifications include various posttranslational covalent, or noncovalent, modifications and, in plant mitochondria, their analysis has only recently been started (Millar et al., 2005). Mitochondrialencoded proteins can also be processed from larger precursors (Figueroa et al., 2000;Perrotta et al., 2002). Protein degradation appears to be a crucial control point in plant mitochondrial genome expression as it is in chloroplasts (Adam, 2000). ...
The sections in this article are
Introduction
Identification of the Pentatricopeptide Repeats Protein Family: A Key Discovery toward the Understanding of Plant Mitochondrial Gene Expression
Transcription in Higher Plant Mitochondria
Splicing
Exchange of Nucleotide Identity by RNA Editing
5′ and 3′ Processing of Plant Mitochondrial Transcripts
Stabilization and Degradation of RNA
Translation and Posttranslational Control
Concluding Remarks
Acknowledgements
... Previous studies have shown that the corresponding mitochondrial rps2 and rps11 genes have been transferred to the nucleus in Arabidopsis, soybean and tomato, suggesting that gene loss events followed by functional transfer to the nucleus (Palmer et al., 2000;Perrotta, Grienenberger & Gualberto, 2002). Most ribosome protein genes are frequently absent in clades of angiosperm mt genomes, which can be considered unnecessary to some extent (Shengxin et al., 2013). ...
Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.
... Intriguingly, the emp16 mutation causes an increase in the transcript abundance of rps2A and rps13, which is consistently observed in two emp16 alleles ( Figure 5). The rps2A gene encodes the only functional version of the ribosomal protein RPS2 (Perrotta et al., 2002), and rps13 is of chloroplast origin and encodes a ribosome protein (Adams et al., 2002). The increased expression of rps2A and rps13 transcripts in emp16 presumably represents an indirect effect of the reduced nad2 splicing defect. ...
In higher plants, chloroplast and mitochondrial transcripts contain a number of group II introns that need to be precisely spliced before translating into functional proteins. However, the mechanism of splicing and the factors involved in this process is not well understood. By analyzing a seed mutant in maize, we report here the identification of Empty pericarp16 (Emp16) that is required for nad2 intron 4 splicing in mitochondria. Disruption of Emp16 function causes embryo and endosperm development arrest, giving rise to an empty pericarp phenotype in maize. Differentiation of the basal endosperm transfer layer cells is severely affected. Molecular cloning indicates that Emp16 encodes a P-type PPR protein with 11 PPR motifs and is localized in the mitochondrion. Transcript analysis revealed that the mitochondrial nad2 intron 4 splicing is abolished in the emp16 mutants, which leads to severely reduced complex I assembly and activity. In response, the mutant dramatically increases the accumulation of mitochondrial complex III and the expression of alternative oxidase AOX2. These results implicate that EMP16 is specifically required for the mitochondrial nad2 intron 4 cis-splicing, essential for complex I assembly, and the embryogenesis and endosperm development in maize. This article is protected by copyright. All rights reserved.
... The two corresponding mt genes (rps2 and rps11), missing in dicots, probably have been transferred to nuclear genomes. That means that the loss of proteincoding genes may be associated with functional transfer to nuclear genomes [60,61]. Compared with other dicots, Fabales (G. ...
Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb) in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense) than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.
... Of the plant mitochondrial rps3 we have examined, C. revoluta has the largest gene with 1740 bp, whereas the smallest is now found in A. capillus-veneris (1365 bp) ( Table 2). However, this result is not so surprising because size diversity is a widespread feature among plant mitochondrial genes (Kubo et al. 1996;Perrotta et al. 2002). It is noteworthy to point out that scattered in-frame insertions of more than 100 nucleotide, with no significant similarity to any other known DNA sequences, elongate to 295 bp the rps3 exon 2 of A. capillus-veneris ( Fig. 2 and Supplemental S2, Table 2). ...
Ferns are a large and evolutionarily critical group of vascular land plants for which quite limited mitochondrial gene content and genome organization data are, currently, available. This study reports that the gene for the ribosomal protein S3 (rps3) is preserved and physically clustered to an upstream rps19 and a downstream overlapping rpl16 locus in the mitochondrial DNA of the true fern Adiantum capillus-veneris L. Sequence analysis also revealed that the rps3 gene is interrupted by two cis-splicing group II introns, like the counterpart in lycopod and gymnosperm representatives. A preliminary polymerase chain reaction (PCR) survey confirmed a scattered distribution pattern of both the rps3 introns also in other fern lineages. Northern blot and reverse transcription (RT)-PCR analyses demonstrated that the three ribosomal protein genes are co-transcribed as a polycistronic mRNA and modified by RNA editing. Particularly, the U-to-C type editing amends numerous genomic stop codons in the A. capillus-veneris rps19, rps3 and rpl16 sequences, thus, assuring the synthesis of complete and functional polypeptides. Collectively, the findings from this study further expand our knowledge of the mitochondrial rps3 architecture and evolution, also, bridging the significant molecular data gaps across the so far underrepresented ferns and all land plants.
... The phylogenetic trees were reconstructed mainly on the nad7 (Hashimoto and Sato 2001), ribosomal protein genes, such as rps2 (Perrotta et al. 2002), rpl10 (Kubo and Arimura 2010) previously. Based on plastid genome (Moore et al. 2007), subtotal plastid genes (Moore et al. 2010) or partial mitochondrial genes (Ma et al. 2012) phylogeny of angiosperms has been constructed recently. ...
... Extensive mitochondrial genomic variation within a single plant species derives largely from double-strand break (DSB) activity and its repair in Arabidopsis (Davila et al. 2011; Galtier 2011), opening new perspectives on the long-term evolution of this intriguing genome. The phylogenetic trees were reconstructed mainly on the nad7 (Hashimoto and Sato 2001), ribosomal protein genes, such as rps2 (Perrotta et al. 2002), rpl10 (Kubo and Arimura 2010) previously. Based on plastid genome (Moore et al. 2007), subtotal plastid genes (Moore et al. 2010) or partial mitochondrial genes (Ma et al. 2012) phylogeny of angiosperms has been constructed recently. ...
