Sota Fujii

The University of Tokyo | Todai · Graduate School of Agriculture and Life Sciences

Eukaryotic cells have harbored mitochondria for at least 1.5 billion years in an apparently mutually beneficial symbiosis. Studies on the agronomically important crop trait cytoplasmic male sterility (CMS) have suggested the semblance of a host-parasite relationship between the nuclear and mitochondrial genomes, but molecular evidence for this is l...

The mechanisms by which flowering plants choose their mating partners have interested researchers for a long time. Recent findings on the molecular mechanisms of non-self-recognition in some plant species have provided new insights into self-incompatibility (SI), the trait used by a wide range of plant species to avoid self-fertilization and promot...

Pre-zygotic interspecies incompatibility in angiosperms is a male–female relationship that inhibits the formation of hybrids between two species. Here, we report on the identification of STIGMATIC PRIVACY 1 (SPRI1), an interspecies barrier gene in Arabidopsis thaliana. We show that the rejection activity of this stigma-specific plasma membrane prot...

Selfing is a frequent evolutionary trend in angiosperms, and is a suitable model for studying the recurrent patterns underlying adaptive evolution. Many plants avoid self-fertilization by physiological processes referred to as self-incompatibility (SI). In the Brassicaceae, direct and specific interactions between the male ligand SP11/SCR and the f...

The shift from outcrossing to self-fertilization (selfing) is considered one of the most prevalent evolutionary transitions in flowering plants. Selfing species tend to share similar reproductive traits in morphology and function, and such a set of traits is called the ‘selfing syndrome’. Although the genetic basis of the selfing syndrome has been...

Pollen has an extraordinary ability to convert from a dry state to an extremely rapidly growing state. During pollination, pollen receives water and Ca2+ from the contacting pistil, which will be a directional cue for pollen tube germination. The subsequent rapid activation of directional vesicular transport must support the pollen tube growth, but...

Pre-zygotic interspecies incompatibility in angiosperms is an important mechanism to prevent unfavorable hybrids between species. We used a genome-wide association study to identify Stigmatic privacy 2 (SPRI2), a transcription factor with a zinc-finger domain, which regulates interspecies barriers in Arabidopsis thaliana. CRISPR/Cas9-mediated genom...

ATP acts as the common currency of metabolic activity in all life forms. A recent study uses inter-specific transfer of the self-recognition module in plants to enable live monitoring of the cellular status in vivo, revealing the pivotal role of ATP in signaling.

In various coastal areas of Japan, naturalized radish populations are observed. Radish is a cruciferous plant and exhibits self-incompatibility, involving a system controlled by a single locus with multiple S alleles. Although the S allele diversity of radish cultivars and wild radishes has been characterized, the S allele distribution in naturaliz...

Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica , pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK ( S receptor kinase) and pollen determinant SP11 ( S -locus Protein 11, also named SCR) from the S -locus. Although the structure of the B. rapa S 9 -SRK ectod...

Plants have developed a variety of molecular ways to express self-incompatibility (SI) that promote outcrossing by preventing self-fertilization. A new study reveals that Citrus uses the S-RNase as the key molecule for expressing SI, giving us further evidence that the S-RNase system is widespread and evolved in an early branch of angiosperms.

Self-incompatibility (SI) is a sophisticated system for pollen selectivity to prevent pollination by genetically identical pollen. In Brassica, it is genetically controlled by a single, highly polymorphic S-locus, and the male and female S-determinant factors have been identified as S-locus protein 11 (SP11)/S-locus cysteine-rich protein (SCR) and...

[This corrects the article on p. 186 in vol. 69, PMID: 31086497.].

Homeotic alteration phenotype of the flowers in Daucus carota are widely used for hybrid breeding, consequently molecular markers tightly-linked to such phenotype are in demand. Here we report the identification of a gene locus responsible for the phenotypic expression of stamen conversion into a petal-like structure, or petaloid. Using a segregati...

RNA editing altered the RNA sequence by replacing the C nucleotide to U in the organellar genomes of plants. RNA editing status sometimes differed among distant species. The pattern of conservation and variation of RNA editing status made it possible to evaluate evolutionary mechanisms impacting functional aspects of RNA editing. In this study, div...

多くの被子植物はなんらかの手段により自己と非自己とを識別し，交配の相手として非自己を選択する．これは短期的には自殖劣勢を回避する意味あいがあり，長期的には集団の多様性を維持する効果があると考えられている．この研究分野においては，1990 年代から最近にいたるま で，自己と非自己を識別する分子機構について多くの報告がなされてきた．その結果，植物は進化の過程において自己と非自己とを識別する分子機構の獲得と損失をくり返 してきたことが明らかにされた．このレビューにおいては，植物がどのようにして多様な生殖システムを形成するにいたったのか，この研究分野における議論の経緯や，近年，解明されてきた分子機構をもとに解説する．そして，この 研究分野における進化の動態モデルの重要性や，残された 重要な課題および...

Key message: Epigenetic dominance modifier. In polymorphic loci, complex genetic dominance relationships between alleles are often observed. In plants, control of self-incompatibility (SI) expression via allelic interactions in the Brassicaceae is the best-known example of such mechanisms. Here, with emphasis on two recently published papers, we r...

In diploid organisms, phenotypic traits are often biased by effects known as Mendelian dominant-recessive interactions between inherited alleles. Phenotypic expression of SP11 alleles, which encodes the male determinants of self-incompatibility in Brassica rapa, is governed by a complex dominance hierarchy(1-3). Here, we show that a single polymorp...

Dioecy is a plant mating system in which individuals of a species are either male or female. Although many flowering plants evolved independently from hermaphroditism to dioecy, the molecular mechanism underlying this transition remains largely unknown. Sex determination in the dioecious plant Asparagus officinalis is controlled by X and Y chromoso...

Self-incompatibility (SI) in flowering plants is a genetic reproductive barrier to distinguish self- and non-self pollen to promote outbreeding. In Solanaceae, self-pollen is rejected by the ribonucleases expressed in the styles (S-RNases), via its cytotoxic function. On the other side, male-determinant is the S-locus F-box proteins (SLFs) expresse...

Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial RNA m...

Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in the mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial R...

Self-incompatibility in the Brassicaceae is controlled by multiple haplotypes encoding the pollen ligand (S-locus protein 11, SP11, also known as S-locus cysteine-rich protein, SCR) and its stigmatic receptor (S-receptor kinase, SRK). A haplotype-specific interaction between SP11/SCR and SRK triggers the self-incompatibility response that leads to...

Pentatricopeptide repeat (PPR) proteins bind RNA and act in multiple eukaryotic processes, including RNA editing, RNA stability, and translation. Here, we investigated the mechanism underlying the functional versatility of Arabidopsis thaliana PROTON GRADIENT REGULATION3 (PGR3), a chloroplast protein harboring 27 PPR motifs. Previous studies sugges...

PPR proteins form a huge family in flowering plants and are involved in RNA maturation in plastids and mitochondria. These proteins are sequence-specific RNA-binding proteins that recruit the machinery of RNA processing. We summarize progress in the research on the functional mechanisms of divergent RNA maturation and on the mechanism by which RNA...

RNA editing in plants is an essential post-transcriptional process that modifies the genetic information encoded in organelle genomes. Forward and reverse genetics approaches have revealed the prevalent role of pentatricopeptide repeat (PPR) proteins in editing in both plastids and mitochondria confirming the shared origin of this process in both o...

Plants possess compartmentalized genomes that are distributed in the nucleus and in two organelles: the mitochondria (mt) and plastids (pt). The crucial functions of these organelles require interaction between products encoded by the organelle genome and the nucleus. Hence, coadaptation contributes to the evolution of plant genomes, leading to a c...

Correlations between amino acids at positions 6, 1′ and aligned nucleotides. The tables show frequencies of co-occurrence of amino acids and nucleotides from the alignments in Figure 2 and Figure S1. A. P motifs, positions 6, 1′ versus each nucleotide. B. S motifs, positions 6, 1′ versus each nucleotide. C. P motifs, position 6 versus purines (R),...

Alignments of PPR editing factors to their target sites. For each factor, the name of the protein and its editing site are listed, then successively the types of PPR motif, the amino acids at position 6, the amino acids at position 1′, an indication of the degree to which these amino acids ‘match’ the RNA using the code developed in this work, and...

Alignments of PPR10 to the PPR10 RNA footprint ranked by p-value. The table shows the top 100 alignments out of the 29400 possible. The two alignments shaded in yellow correspond to the alignments depicted in Figure 2. Orientation: forward indicates N->C, 5′-3′; reverse indicates N->C, 3′-5′. Offset: distance from start of RNA sequence to first PPR...

Frequency of 6,1′ combinations in Arabidopsis PPR proteins. The most frequent combinations are shown (all those observed more than 30 times). Only tandem pairs of motifs (5362 in total) were considered in this analysis, where the first motif was either a P or S motif. Combinations observed in P motifs are shown in blue, those in S motifs in green....

Correlations between amino acids at specific positions within PPR motifs and aligned nucleotides. Contingency tables (amino acids versus nucleotides) were constructed from the alignments in Figure 2 and Figure S1. Each 20×4 table was tested for independent assortment of amino acids and nucleotides using a chi-squared test (after first removing any...

Author Summary RNA binding proteins dictate RNA fate and function by modulating RNA processing, localization, translation, and stability. The consequences of RNA/protein interactions are determined, in part, by the position at which the protein binds the RNA. However, it is impossible to predict the target sites of most RNA binding proteins or to d...

Pentatricopeptide repeat (PPR) proteins are involved in the modification of organelle transcripts. In this study, we investigated the molecular function in rice of the mitochondrial PPR-encoding gene MITOCHONDRIAL PPR25 (MPR25), which belongs to the E subgroup of the PPR family. A Tos17 knockout mutant of MPR25 exhibited growth retardation and pale...

The pentatricopeptide repeat (PPR) is a degenerate 35-amino-acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis thaliana. From the wealth of sequence information now available from plant genomes, the PPR protein family is now known to be one of the largest families in angiosperm species, as most gen...

RT-PCR analysis of genes 10 iORFs and eight ncRNAs. RT-PCR analysis was performed using RNA isolated from calli, etiolated seedlings and green seedlings. rrn18, 18 S ribosomal RNA.

Multiple alignment of deduced amino acid sequences of iORF_487 and iORF_502 with known transposable elements. Upper, alignment of iORF_487 with retroviral aspartyl protease domain of Arabidopsis thaliana Athila transposable element (AC022456_8). Lower, alignment of iORF_502 with part of reverse transcriptase domain of Phyllostachys edulis (ADB85398...

Summary of mitochondrial genome size of different species. Values on vertical scale are the number of base pairs in each organelle. For metazoans, the average mitochondrial genome size of 1104 species is presented. Chloroplast genome size of Cucumis melo is unknown; however, given the constant chloroplast size in angiosperms it is estimated at arou...

Northern blot analysis of orf181 and orf490 in calli (C) and seedlings (S). RNA expression was undetectable in orf490 or orf181, the two genes used as untranscribed background region. Hybridization signal of nad4 is shown as the positive control.

Summary of inter-genic ORF (iORF) expression. Values are given as the mean of all probes within each iORF region.

Spreadsheet information of primers used for RT-PCR analysis. TU, name of the transcriptional unit; Start, start position of TU; End, end position of TU; Primer 1 and Primer 2, sequence information of primer pair sequences used for RT-PCR analysis.

Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of Oryza sativa japonica (rice) mitochondria, which was predicted to be approximately 490-kb long. Whereas statisti...

Cytoplasmic male sterility (CMS) is associated with a mitochondrial mutation that causes an inability to produce fertile pollen. The fertility of CMS plants is restored in the presence of a nuclear-encoded fertility restorer (Rf) gene. In Lead Rice-type CMS, discovered in the indica variety 'Lead Rice', fertility of the CMS plant is restored by the...

Over 20 proteins of the pentatricopeptide repeat (PPR) family have been demonstrated to be involved in RNA editing in plant mitochondria and chloroplasts. All of these editing factors contain a so-called 'E' domain that has been shown to be essential for editing to occur. The presumption has been that this domain recruits the (unknown) editing enzy...

Since the endosymbiotic origin of chloroplasts from cyanobacteria 2 billion years ago, the evolution of plastids has been characterized by massive loss of genes. Most plants and algae depend on photosynthesis for energy and have retained ∼110 genes in their chloroplast genome that encode components of the gene expression machinery and subunits of t...

Cytoplasmic male sterility (CMS) is a maternally inherited trait that results in the inability of plants to produce functional pollen. CMS is considered as a phenomenon caused by aberrant mitochondrial genomes. In BT-type CMS of rice (Oryza sativa L.), a CMS-associated mitochondrial gene has been reported to be an orf79 gene. To confirm the effect...

Validation of contig linkage by PCR analysis. Lane numbers refer to primer pairs in Additional file 8.

Information on the primers used for the PCR analysis to validate the linkage between the contigs. Information on the primers used for the PCR analysis in Additional file 7.

Possible linkages of the contigs validated by PCR analysis for the LD-CMS mitochondrial genome. See the legend for Additional file 9 for descriptions.

Lists of genes and the corresponding primers used for the northern blot analysis. Lists of mitochondrial genes in Nipponbare and the primers used for the northern blot analysis in Figure 6 and Additional file 6.

Comparison of InDel and segmental sequence variation (SSV) genotypes among japonica mitochondrial genomes Nipponbare, PA64S, and indica 93-11. Nucleotide positions in 93-11 are displayed. Genotypes are: j, japonica type; 9, 93-11 type; n, Nipponbare type; p, PA64S type; c, CMS specific. Sequence variations in the genic regions are given in the last...

Transcript detection of genes involved in the evolution of the CW-orf307 locus. Transcripts were detected by northern blot analysis using mitochondrial RNA extracted from calli. Genes involved in the rpl5 region (orf165, orf284, cox1, pseudo-rps14, rpl5, and rps2) and genes involved in CW-orf307 (atp1, orf288, orf224, cox2, and trnR). C-terminal re...

Order and position of the contigs aligned in the master circles. Sequences in this order were deposited to DDBJ (CW-CMS, AP011076; LD-CMS, AP011077).

Comparison of SNP genotypes among japonica mitochondrial genomes Nipponbare, PA64S, and indica 93-11. Nucleotide positions in 93-11 are displayed. Genotypes in CMS are: j, japonica type; 9, 93-11 type; n, Nipponbare type; p, PA64S type; cms, CMS specific; -, no syntenic region present in the CMS lines. SNPs in the genic regions are given in the las...

Phylogenetic relationship of the five rice mitochondrial genomes. All of the sequence variations were used to generate the maximum-likelihood inference-based dendrogram. Bar indicates the rate of nucleotide substitution per site.

PCR amplification of the CMS unique genomic structure and genes. PCR amplification positive (+) and negative (-) in each rice core-collection accession for each primer pair. * Refer to Figure 2, Additional files 8 and 11 for information on the primers. ** Refer to [28] for details.

Possible linkage of the contigs validated by PCR analysis for the CW-CMS mitochondrial genome. Numbers within the arrows indicate the contig accession numbers, whereas numbers above indicate the sequence depth of each contig. The yellow color indicates the contigs that appear twice in our master circle, and the blue color indicates the contigs that...

Cytoplasmic male sterility (CMS) is one of the most ideal phenomena known in higher plants to describe the incompatibilities between mitochondrial-nuclear genomic interactions. To elucidate the dependency of pollen development on mitochondrial genotypes and cytoplasmic-nuclear genomic barriers, we employed five CMS isogenic lines of rice, CW-, W11-...

Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS) is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact seque...

Conflict/reconciliation between mitochondria and nuclei in plants is manifested by the fate of pollen (viable or nonviable) in the cytoplasmic male sterility (CMS)/fertility restoration (Rf) system. Through positional cloning, we identified a nuclear candidate gene, RETROGRADE-REGULATED MALE STERILITY (RMS) for Rf17, a fertility restorer gene for C...

OsNek3 (Oryza sativa L. NIMA-related kinase) and DCW11 encoding a mitochondrial putative protein phosphatase 2C were found in our previous microarray study as down-regulated genes in the rice CW-CMS line, which lacked pollen germination ability. Further analysis of DCW11 revealed that DCW11 is strongly correlated with CW-CMS occurrence. Here we sho...

Since plants retain genomes of an extremely large size in mitochondria (200–2,400 kb), and mitochondrial protein complexes are comprised of chimeric structures of nuclear- and mitochondrial-encoded subunits, coordination of gene expression between the nuclei and mitochondria is indispensable for sound plant development. It has been well documented...

Causes of cytoplasmic male sterility (CMS) in plants have been studied for two decades, and mitochondrial chimeric genes have been predicted to induce CMS. However, it is unclear what happens after CMS-associated proteins accumulate in mitochondria. In our previous study of microarray analysis, we found that 140 genes are aberrantly regulated in an...

Cytoplasmic male sterility (CMS) is a maternally inherited trait that results in the inability to produce fertile pollen, and is widely known in higher plants. Recent studies have identified that an aberrant chimeric gene in mitochondria possibly causes CMS in various plant species. In some CMS lines, pollen fertility is recovered by a nuclear-enco...

The CW-cytoplasmic male sterility (CMS) line has the cytoplasm of Oryza rufipogon Griff, and mature pollen is morphologically normal under an optical microscope but lacks the ability to germinate; restorer gene Rf17 has been identified as restoring this ability. The difference between nuclear gene expression in mature anthers was compared for the C...

Cytoplasmic male sterility (CMS) of rice (Oryza sativa L.) was first reported using the cytoplasm of a Chinese wild rice, Oryza rufipogon Griff. strain W1. However, it was not possible to characterize this ms-CW-type CMS in more detail until a restorer line had been developed due to the lack of restorer genes among cultivars thus far tested. The br...