US20150315607A1 - Mutated nucleotide molecule, and transformed plant cells and plants comprising the same - Google Patents

Mutated nucleotide molecule, and transformed plant cells and plants comprising the same Download PDF

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US20150315607A1
US20150315607A1 US14/596,419 US201514596419A US2015315607A1 US 20150315607 A1 US20150315607 A1 US 20150315607A1 US 201514596419 A US201514596419 A US 201514596419A US 2015315607 A1 US2015315607 A1 US 2015315607A1
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bhlh142
seq
plant
male sterile
transcription factor
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Swee-Suak Ko
Min-Jeng Li
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Academia Sinica
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8287—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for fertility modification, e.g. apomixis
    • C12N15/8289—Male sterility
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants

Definitions

  • Rice is one of the most important staple crops in the world, feeding almost half of the world's population, and it serves as a model for monocots, which include many important agronomic crops (e.g. wheat, maize, sorghum, millet). Food and Agriculture Organization (FAO) predicts that rice yield will have to be increased 50-70% by 2050 to meet the demands.
  • FEO Food and Agriculture Organization
  • Several approaches are currently adopted to increase rice yields, such as heterosis breeding, population improvement, wide hybridization, genetic engineering, and molecular breeding 1 .
  • hybrid rice is being considered the most promising one (15-20% increases in yield) 2 .
  • Crops produced from F1 hybrid seeds offer significant benefits in terms of yield improvement, agronomic performance and consistency of end-use quality. This is due to the ‘hybrid vigor’ generated by combining carefully selected parent lines. Hybrid crops are responsible for a dramatic increase in global crop yields in the past decades, and male sterility (MS) has played a significant role in this advancement. Male sterile traits can be divided into cytoplasmic male sterility (CMS), which is determined by cytoplasmic factors such as mitochondria, and genetic male sterility (GMS), which is determined by nuclear genes.
  • CMS cytoplasmic male sterility
  • GMS genetic male sterility
  • CMS has long been used in hybrid corn production, while both CMS and GMS are currently used for hybrid rice production 3 , due to the convenience of controlling sterility expression by manipulating the gene-cytoplasm combinations in any selected genotype. Most importantly, it evades the need for emasculation in cross-pollinated species, thus encouraging cross breeding and producing pure hybrid seeds under natural conditions.
  • commercial seed production must be simple and inexpensive, and the requirement for a maintainer line to produce the seed stocks of CMS line increases the production cost for this 3-line hybrid system.
  • GMS genetic MS
  • PGMS photoperiod- or temperature-inducible MS
  • LYP9 4 paternal line 93-11 to generate superhybrid rice
  • PA64S derived from a spontaneous PGMS japonica mutant NK58S (long day->13.5 h; Shi, 1985), is also a TGMS indica rice, whose MS is promoted by temperatures greater than 23.5° C., but recovers its fertility at temperatures between 21 ⁇ 23° C.
  • Recent mapping analyses demonstrate that the P/TGMS in these MS lines is regulated by a novel small RNA 5 .
  • CSA Carbon Starved Anther
  • the mutation on the R2R3 MYB transcription regulator defects pollen development 6 and further study shows that csa is a new photoperiod-sensitive mutant, exhibiting MS under short-day conditions but male fertility under long-day conditions 7 .
  • the molecular basis of its MS sensitivity to day length remains to be addressed.
  • Transgenic male sterility has been generated using a number of transgenes, but its application in commercial production of hybrid seeds is limited due to the lack of an efficient and economical means to maintain the MS lines, or the lack of suitable restorers 8 .
  • a reversible MS system has been demonstrated in transgenic Arabidopsis plants by manipulating a R2R3 MYB domain protein (AtMYB103) 8 . Blocking the function of AtMYB103 using an insertion mutant or an AtMYB103EAR chimeric repressor construct under the control of the AtMYB103 promoter resulted in complete MS without seed setting 8 .
  • a restorer containing the AtMYB103 gene driven by of a stronger anther-specific promoter was introduced into pollen donor plants and crossed into the MS transgenic plants for the repressor. The male fertility of F1 plants is restored.
  • the chimeric repressor and the restorer constitute a reversible MS system for hybrid seed production. The successful application of this system for large scale hybrid seed production depends on whether the MS female parent lines can be multiplied efficiently and economically.
  • an inducible promoter by chemicals or other factors e.g. photoperiod or temperature
  • Rice anthers are composed of four lobes attached to a central core by connective and vascular tissue.
  • microsporocytes form in the middle, surrounded by four anther wall layers: an epidermal outer layer, endothecium, middle layer, and tapetum 9 .
  • the tapetum is located in the innermost cell layer of the anther walls and plays an important role in supplying nutrients such as lipids, polysaccharides, proteins, and other nutrients for pollen development 10 .
  • PCD programmed cell death
  • TFs transcription factors
  • DYSFUNCTIONAL TAPETUM 1 DYSFUNCTIONAL TAPETUM 1
  • TDF1 Defective in Tapetal Development and Function 1
  • MS1 MALE STERILITY 1
  • TDR1 Undeveloped Tapetum1
  • EAT1 ETERNAL TAPETUM 1
  • DTD DELAYED TAPETUM DEGENERATION
  • TDR1 directly binds the promoter of CP1 and C6 for their transcription 14 .
  • C6 encodes a lipid transfer protein that plays a crucial role in the development of lipidic orbicules and pollen exine during anther development 17 .
  • CP1 is involved in intercellular protein degradation in biological system and its mutant shows defected pollen development 25 .
  • EAT1 acts downstream of TDR1 and directly regulates the expression of AP25 and AP37, which encode aspartic proteases involved in tapetal PCD 23 .
  • the basic helix-loop-helix (bHLH) proteins are a superfamily of TFs and one of the largest TF families in plants. There are at least 177 bHLH genes in the rice genome 26,27 and more than 167 bHLH genes in Arabidopsis genome 28,29 .
  • eukaryotic TFs consist of at least two discrete domains, a DNA binding domain and an activation or repression domain that operate together to modulate the rate of transcriptional initiation from the promoter of target genes 30 .
  • the bHLH TFs play many different roles in plant cell and tissue development as well as plant metabolism 3 .
  • the HLH domain promotes protein-protein interaction, allowing the formation of homodimeric or heterodimeric complexes 31 .
  • bHLH TFs bind as dimers to specific DNA target sites and are important regulatory components in diverse biological processes 29 . So far, three of the bHLH TFs have been shown to be involved in rice pollen development—UDT1 (bHLH164), TDR1 (bHLH5), and EAT1/DTD1 (bHLH141).
  • bHLH142 a novel MS-related gene encoding for another member of the bHLH TFs.
  • the molecular mechanism of MS in this mutant is elucidated, and it suggests that bHLH142 is specifically expressed in the anther and bHLH142 coordinates with TDR1 in regulating EAT1 promoter activity in transcription of protease genes required for PCD during pollen development. That is to say, bHLH142 plays an essential role in rice pollen development by controlling tapetal PCD.
  • Both null mutant and overexpression transgenic plants showed a completely male sterile phenotype. Most interestingly, the overexpression plants have restored the fertility under low temperature. Homologs of SEQ ID NO: 2 with high similarity are found in other major cereal crops, and its use may increase the productivity of cereal crops by manipulating the bHLH gene for development of male sterility and production of hybrid crops.
  • the object of the present invention is developing a mutated nucleotide molecule, and a transformed plant cell and a male sterile mutant plant comprising the mutated nucleotide molecule; in which the male sterile mutant plant can be used as a female parent to produce F1 hybrid seeds, thereby improving yield and quality of crops.
  • the present invention provides a mutated nucleotide molecule, comprising a nucleotide sequence of the transcription factor bHLH142 and an inserted T-DNA segment.
  • the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • the T-DNA segment has comprises a single copy of T-DNA.
  • the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2.
  • the present invention provides a transformed plant cell, which comprises the above-mentioned mutated nucleotide molecule.
  • the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2.
  • the present invention also provides a male sterile mutant plant comprising the above-mentioned mutated nucleotide molecule, and the transcription factor bHLH142 is not expressed; particularly, not expressed in anthers.
  • the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2.
  • a polypeptide sequence having at least 80% similarity to SEQ ID No: 2 more preferably, a polypeptide sequence having at least 90% similarity to SEQ ID No: 2; even more preferably, a polypeptide sequence having at least 95% similarity to SEQ ID No: 2; and most preferably, a polypeptide sequence of SEQ ID No: 2.
  • the male sterile mutant plant of the present invention is a homozygous mutant.
  • the plant is a monocot; preferably, the monocot is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
  • the plant is a dicot; preferably, the dicot is Arabidopsis or Brassica species.
  • the present invention also provides a transformed plant cell, which comprises a plasmid comprising the sequence of the transcription factor bHLH142 and a strong promoter.
  • the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • the present invention also provides a reversible male sterile transgenic plant, wherein the transcription factor bHLH142 is overexpressed; particularly, overexpressed in anthers.
  • the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2.
  • the expression of the transcription factor bHLH142 is controlled by a strong promoter; preferably, by an Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • the pollen fertility of the plant is recovered under low temperature.
  • the pollen fertility of the plant is recovered at 21-23° C.
  • the plant is a monocot; preferably, the monocot is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
  • the plant is a dicot; preferably, the dicot is Arabidopsis or Brassica species.
  • the present invention also provides a method for preparing the above-mentioned reversible male sterile transgenic plant, comprising:
  • the DNA sequence of bHLH142 is SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
  • the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • the plasmid is introduced into calli of the target plant via Agrobacterium tumefaciens.
  • FIG. 1 Phenotypic Analyses of ms142 Mutant.
  • A Comparison of the wild-type plant (left) and ms142 mutant (right) after bolting;
  • B comparison of the wild-type panicle (left) and ms142 mutant (right) at heading stage;
  • C comparison of the wild-type panicle (left) and ms142 mutant (right) at seed maturation stage;
  • D phenotype of the wild-type spikelet (left) and ms142 mutant (right) one day before anthesis;
  • E phenotype of the wild-type spikelet (left) and ms142 mutant (right) after anthesis;
  • F comparison of the wild-type grain (left) and ms142 mutant (right) at harvest stage;
  • G phenotype of the wild-type grain (left) and ms142 mutant (right) after removing rice husk;
  • H phenotype of the wild-type anther (left) and ms142 mutant (right) one day before an
  • FIG. 2 Evidences of T-DNA insertion in ms142 mutant.
  • A Southern blotting to hptII probe confirmed single T-DNA insertion (marked with arrow) in ms142 mutant.
  • B T-DNA tagged construction map of pTag4 vector.
  • C Gene structure and T-DNA insertion site in the mutant at 3rd intron (+1257 bp from ATG).
  • D Genotyping heterozygous T4 mutant progeny. Genotype: WT, wild-type like; He, heterozygous; and Ho, homozygous. Grain fertility: F, fertile; and S, sterile.
  • FIG. 3 Transverse anatomical comparison of the anther development in the wild type (TNG67) and ms142 mutant.
  • FIG. 4 TUNEL assay showed defect tapetal program cell death in ms142 mutant.
  • DNA fragmentation signals yellow fluorescence
  • PI propidium iodide
  • FIG. 5 Scheme of bHLH142 gene, multiple alignment, and subcellular localization of bHLH142 fused with GFP.
  • A Scheme of the bHLH142 gene and T-DNA insertion position. Gray boxes represent exons and interventing lines represent introns. The ATG start codon and TGA stop codon are indicated.
  • bHLH basic helix-loop-helix domain (amino acids 182 to 228); NLS, two nuclear localization signals (amino acids 159 to 165 and 235 to 240, respectively).
  • B Alignment of bHLH domains. The bHLH142 protein was aligned with the bHLH domains of the analogous proteins from other species.
  • C Schemes of fusion constructs. P35S, cauliflower mosaic virus 35S promoter; Trios, nopaline synthase gene terminator. The NLS domain of VirD2 fused with mRFP was used as the nuclear marker.
  • FIG. 6 Phylogenetic analysis of bHLH142 related proteins.
  • Aral Arabidopsis lyrata ; Aegt, Aegilops tauschii ; At, Arabidopsis thaliana ; Brad, Brachypodium distachyon ; Os, Oryza sativa ; Sei, Setaria italica ; Sb, Sorghum bicolor ; SeMa, Selaginella moellendorffii ; Triu, Triticum urartu ; and Zm, Zea may.
  • FIG. 7 Spatial and temporal gene expression of bHLH142 in various tissues of TNG67 (WT) by (A) RT-PCR and (B) qRT-PCR, and (C) in TNG67 spikelet at various developmental stages; and (D) ISH of bHLH142 antisense (left panel) and sense (right panel) probes in spikelet of TNG67 at meiosis stage.
  • Scale bar 1 mm in (C), 50 ⁇ m in (D).
  • FIG. 10 Gene hierarchy of bHLH142, as determined by the expression profiles of the key regulatory genes involved in pollen development in ms142 and eat1 mutants.
  • A Phenotype of spikelet in TNG67 (WT) and ms142.
  • B Phenotype of spikelet in Hitomebore and H0530 (eat1 mutant).
  • C Real-time RT-PCR of bHLH142 in ms142 and eat1 mutants and their respective wild-types.
  • MMC meiocyte mother cell; Mei, meiosis; YM, young microspore; and VP, vacuolated pollen.
  • FIG. 11 Coordinated Regulation of EAT1 Promoter by bHLH142 and TDR1.
  • A Schematic diagrams of the reporter, effector, and internal control plasmids used in the transient transactivation assay in rice leaf protoplasts.
  • the reporter plasmid contains the CaMV35S minimal promoter and the EAT1 promoter sequence (2 Kb) fused to the firefly luciferase gene (Luc).
  • bHLH142, TDR1, and EAT1 genes were driven under the control of the CaMV35S promoter. Nos and t35s denote the terminators of nopaline synthase and CaMV35S, respectively.
  • the pBI221 vector contains a CaMV35S promoter driving the expression of GUS as the internal control.
  • B Transactivation of the Luc reporter gene by bHLH142 and TDR in rice protoplasts. Different effectors were co-transfected with the reporter and internal control plasmid (pBI221). The data represent means of three independent transient transformations. Error bars indicate SD. Transient transformation without the effector plastnid (mini35p) was used as a negative control.
  • FIG. 13 The Interactions between bHLH142 Protein and TDR1, and between TDR1 and EAT1.
  • A Yeast two-hybrid (Y2H) assays. Constructs expressing the full length bHLH142 were cloned into the prey vector pGADT7 (AD), and truncated forms of TDR and EAT1 were prepared in the bait vector pGBKT7 (BD).
  • B BiFC in rice protoplasts expressing the indicated constructs. Bars represent 10 ⁇ m.
  • C Co-IP assay of HA fused TDR and bHLH142 recombinant proteins expressed in E. coli using anti-HA antibody.
  • D Co-IP assay of HA fused TDR and bHLH142 recombinant proteins expressed in E. coli using bHLH142 antibody.
  • FIG. 14 RNAi Knockdown (KD) of bHLH142 Inhibited Pollen Development.
  • KD RNAi Knockdown
  • A Construct of RNAi vector.
  • B RT-PCR showed down regulation of bHLH142 in the anthers of four RNAi knock down lines.
  • FIG. 15 Overexpression rice bHLH142 driven by Ubiquitin promoter in transgenic rice.
  • A Construction of bHLH142 (LOC_Os01g18870) driven by Ubiquitin promoter in pCAMBIA1301 vector,
  • B Genomic PCR confirmed T-DNA insertion of target gene (upper panel) and selection marker hygromycin (lower panel) in the transgenic rice.
  • FIG. 16 Phenotype of TNG67 (WT) and Ubi::bHLH142 transgenic lines.
  • A Plant type of WT (left) and transgenic line (right), (13) panicles of WT (bottom) and transgenic line (top panel),
  • C panicles of WT (left) and different transgenic lines,
  • D spikelet of WT (left) and different transgenic lines at one day before anthesis,
  • E mature seed of WT (left) and different transgenic lines, and
  • F removed husk rice seed of WT (left) and different transgenic lines.
  • Scale bars 20 cm in (A), 3 cm in (B), 7 cm in (C) and 1 cm in (F).
  • FIG. 17 Overexpression bHLH142 prematurely up-regulated Udt1 and EAT1 before meiosis stage but significantly down-regulated MS2 that associated in pollen exine development.
  • SC sporogenous cell
  • MMC meiocyte mother cell
  • Mei meiosis
  • YM young microspore
  • PM pollen mitosis
  • MP mature pollen.
  • FIG. 18 Gene expression pattern of bHLH142 homolog in various organs of maize by using RT-PCR. Floret size by measuring the length of floret. 10G, floret length at 10 mm with green color, 1 DBA, one day before anthesis.
  • FIG. 19 Heterologus overexpressing Ubi::bHLH142 caused male sterility in transgenic maize
  • A The transgenic line has smaller angle of tassel branch (right panel) than the WT (left panel).
  • B Closed up tassel during anthesis stage, WT has large and anther opened during anthesis stage (left panel), while anther of transgenic maize were significantly smaller in size and anther no dehiscence (right panel).
  • C Morphology of spikelet of WT (left panel) and transgenic line (right panel)
  • FIG. 20 The male sterility of Overexpression Ubi::bHLH142 transgenic line is sensitive to environment.
  • the bHLH142 overexpressed lines produced no pollen grains during summer season (Left panel) but had fertile pollens during winter seasons. Pollen grains were stained by I 2 /KI solution.
  • FIG. 21 A proposed model for the molecular function of bHLH142 in rice anther development, relative to other key regulators.
  • bHLH142 is in the downstream of UDT1 but upstream of TDR1, and bHLH142 interacts with TDR1 protein and coordinately regulate the promoter of EAT1.
  • EAT1 regulates AP37 and CP1 and promotes tapetal PCD.
  • Evidences from previous works were indicated by black arrows, while data demonstrated in the present study were indicated by red arrows.
  • the seed of ms142 mutant was obtained from TRIM library. Seedlings of ms142 mutant and its WT (TNG67) were raised in half strength Kimura solution for 3 weeks and then transplanted into soil in AS-BCST GMO screen house located in Tainan, Taiwan.
  • Spikelets and anthers of the WT and ms142 mutant were sampled at various stages of development and fixed overnight in phosphate buffer, pH 7.0, that contained 4% paraformaldehyde and 2.5% glutaraldehyde. They were then rinsed with the same buffer and post fixed for 30 min in phosphate buffer, pH 7.0, containing 1% osmium tetroxide. After dehydration, the specimens were embedded in Spurr's Resin (EMS). The processor, KOS Rapid Microwave Labstation, was chosen for post fixation, dehydration, resin infiltration, and embedding. For TEM, ultrathin sections (90 to 100 nm thick) collected on coated copper grids were stained with 6% uranyl acetated and 0.4% lead citrate and examine using transmission electron microscope.
  • EMS Spurr's Resin
  • Various rice organs at different developmental stages were harvested for RNA isolation: root, shoot, flag leaf, internode, panicles of 0.5 cm, 1 cm, 5 cm, 9 cm, and 20 cm length, spikelet at 1 day before anthesis (1 DBA), lemma, palea, anthers, ovary, seed at 5 days after pollination (S1), 15 days after pollination (S3), 25 days after pollination (S5), and callus.
  • microspore mother cell MMC with spikelet length of approximately 2 mm, meiosis (4 mm), young microspore (YM, 6 mm), vacuolated pollen (VP, 8 mm), mitosis pollen (MP, 8 mm with light green lemma), and mature pollen at one day before anthesis (1 DBA).
  • MMC microspore mother cell
  • VP vacuolated pollen
  • MP mitosis pollen
  • MP 8 mm with light green lemma
  • RT-PCR Fifteen ⁇ L of RT-PCR reaction contained 4 ⁇ L, of 1 ⁇ 4 diluted cDNA, 3 ⁇ M of primers, and 7.5 ⁇ L of 2 ⁇ KAPA SYBR FAST master mix (KAPA Biosystems, USA). Quantitative Real-Time PCR (qRT-PCR) was performed using a CFX96 Real-Time PCR detection system (Bio-Rad, USA). Quantification analysis was carried out using CFX Manager Software (Bio-Rad, USA). Primers used for qPCR are listed in Table 1.
  • Tissue sections were deparaffinized with xylene, rehydrated through an ethanol series, and pre-treated with proteinase K (2 mg/mL) in 1-phosphate buffered saline (PBS) at 37° C. for 30 min.
  • Pre-hybridization additionalally including 25% RNAmate, BioChain
  • Hybridization was performed at 59° C.
  • RNA probes were synthesized by in vitro transcription of the RT-PCR fragment in pGEM-T easy vector using the DIG RNA labeling kit (SP6/T7, Roche).
  • RNA probes were synthesized by SP6 RNA polymerase, while sense RNA probes were synthesized by T7 RNA polymerase and used as control. Sequence of fragment to synthesize RNA probe (SEQ ID No. 119):
  • T-DNA/Tos17 knock out mutant lines in hands such as: in udt1 (TRIM), bHLH142 (ms142, TRIM), and eat1 (bHLH141)
  • Tos17 mutant line H0530 background of Hitomebore
  • Rice Tos17 Insertion Mutant Database http://tos.nias.affrc.go.jp/. Flanking sequences were confirmed by genotyping PCR amplification with specific primers (Table 1). We will verify their gene hierarchy using these mutants. Spikelet samples at various developmental stages were collected, isolated RNA, and performed qRT-PCR analysis.
  • PCD is characterized by cellular condensation, mitochondria and cytoskeleton degeneration, nuclear condensation, and internucleosomal cleavage of chromosomal DNA 33 .
  • TUNEL terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling
  • bHLH142-GFP fusion genes driven by the CaMV 35S promoter.
  • Rice protoplasts were isolated and transformed using the polyethylene glycol (PEG) method following procedures described previously 34 . After incubation at room temperature for 16 h in light, protoplasts were observed with a Zeiss LSM 780 laser scanning confocal microscope.
  • the bHLH142 protein sequence was used to search for the closest homologues from their plant species using BLASTP programs. Multiple sequence alignment of full-length protein sequences was performed using ClustalW online (http://www.ch.embnet.org/software/ClustalW.html), and the alignment was used to perform neighbor-joining analysis using Mega 5.05 35 .
  • the numbers at the nodes represent percentage bootstrap values based on 1000 replications.
  • the length of the branches is proportional to the expected numbers of amino acid substitutions per site.
  • Gene identification numbers used to generate the phylogenetic trees and the alignment are listed in Table 2.
  • Peptide sequence (N′ ⁇ C′) ID BradXP_003567568 myhpqcellmphesldmdavvgqshlaasgvsaipaelnfhllhhsfvdtaaspqpptvdyffpgtdpppaa SEQ ID vqfeqlaatnhhamsmlrdyygqqypaetylrggprtttagssslvfgvahddesaaynmvgpfvesspttr No.
  • the MATCHMAKER GAL4 Two-Hybrid System (Clontech, USA) was used for Y2H assays. Since both full-length EAT1 and TDR1 proteins were reported having self-activation (Ji et al., 2013), we made a truncated EAT1 (EAT1 ⁇ , amino acids 1-254) and a truncated TDR1 (TDR ⁇ , amino acids 1-344) to reduce self activation.
  • the full length cDNA of bHLH142 was cloned into pGAD-T7 (Clontech, USA), and full length bHLH142, EAT1, TDR, EAT1 ⁇ , and TDR ⁇ were cloned into pGBK-T7 (Clontech, USA), respectively.
  • the pairs of constructs to be tested were co-transformed into AH109 yeast cells and selected on plates containing Leu (for pGADT7 plasmid) and Trp (for pGBKT7 plasmid) dropout medium for 3-4 days at 30° C.
  • Transformants were tested for specific protein interactions by growing on SD/-Leu/-Trp/-His plates with 30 mM 3-amino-1,2,4 triazole (3AT), and tested after X- ⁇ -Gal induction to confirm positive interaction.
  • This system provides a transcriptional assay for detecting and confirming protein interactions in vivo in yeast.
  • BiFC assay allows visualization of protein-protein interactions in living cells and the direct detection of the protein complexes in subcellular compartments, providing insights into their functions.
  • Full-length cDNAs of bHLH142, UDT1, TDR1, and EAT1 were independently introduced into pJET1.2 (Thermo Scientific).
  • the sequence for the N-terminal amino acid residues 1-174 of YFP was then in-frame fused to the sequence of the C-terminal region of the tested proteins, while the sequence of the C-terminal amino acid residues 175-239 of YIP was in-frame fused to the sequence of the N-terminal end of the proteins.
  • the tested genes were introduced into pSAT5-DEST_CYN1 and pSAT4(A)-DEST_NYN1.
  • Recombinant proteins of bHLH142 and TDR1 fused with hemagglutinin (HA) tag were expressed in bacteria harboring pET-53-DEST (HIS-tag), and cell extracts after lysis were cleared by centrifugation at 12,000 rpm for 15 min, suspended in binding buffer (20 mM Tris-HCl, pH 7.9, 500 mM NaCl), and sonicated on ice for 30 s using an ultrasonic homogenizer (Misonix XL Sonicator Ultrasonic Cell Processor). The supernatants were purified using Ni 2+ resin.
  • extracts were pre-cleared by 30 min incubation with 20 ⁇ l of Pure Proteome Protein G Magnetic Beads (Millipore Co., Billerica, Mass.) at 4° C. with rotation.
  • the antibodies (anti-bHLH142 or anti-HA) were then added to the pre-cleared extracts. After incubation for 4 h at 4° C., 40 ⁇ L of PureProteome Protein G Magnetic Beads was added, and the extracts were further incubated for 10 min at room temperature with rotation. After extensive washing, bound proteins were analyzed by western blotting.
  • Rabbit antiserum against rice bHLH142 was produced using a synthetic peptide (CSPTPRSGGGRKRSR, SEQ ID No. 116) as antigen (GenScript Co).
  • RNA intereference (RNAi) construct for suppressing the expression of bHLH142
  • a 149 bp fragment from 5′UTR region of bHLH142 was amplified by PCR with specific primers (Table 1) and cloned into pENTR (Invitrogen) to yield an entry vector pPZP200 hph-Ubi-bHLHI42 RNAi-NOS (12,483 bp).
  • the RNAi construct was transformed into WT (TNG67) rice calli via Agrobacterium tumefaciens -mediated transformation system 37 . Transgenic plants were regenerated from transformed calli by selection on hygromycin-containing medium.
  • Taiwan Rice Insertional Mutants http://trim.sinica.edu.tw) lines we identified a T-DNA-tagged rice mutant (denoted ms142) with a completely MS phenotype.
  • this mutant produced no viable seeds but maintained a normal vegetative growth ( FIG. 1A ), with panicles and spikelet developing similarly to those of the wild-type (WT) ( FIGS. 1B to 1E ).
  • the ms142 mutant exhibits normal opening of spikelets and elongation of anther filaments, and its anthers are exerted completely in the husk ( FIG. 1E ). However, the anthers of ms142 were significantly smaller in size and appeared yellowish white ( FIG.
  • the protein encoded by the gene is annotated as a basic helix-loop-helix dimerization region bHLH domain containing protein (RiceXPro Version 3.0).
  • the bHLH142 gene comprises of four exons and three introns.
  • genotyping by PCR using specific primers acrossing the T-DNA insertion site verified its FST ( FIG. 2 ).
  • heterozygous mutant plants behaved similarly to WT in terms of vegetative and reproductive growth and produced fertile seeds.
  • homozygous ms142 mutant plants exhibited similar plant height, panicle number, and panicle length to the WT, but produced no viable seeds.
  • the WT anther walls contained epidermal cell layer, endothecial cell layer, middle layer and tapetal cell layer ( FIG. 3A ).
  • MMC microspore mother cell
  • the microspore mother cells underwent meiosis to form tetrads of haploid microspores; the tapetal cells differentiated to form large vacuole; and the middle layer cells began to degenerate ( FIG. 3B ).
  • the meiocytes formed tetrads ( FIG. 3C ).
  • the ms142 anther consisted of normal epidermis, endothecium, middle layer and tapetum ( FIG. 3F ).
  • ms142 microspore mother cells did not enter meiosis and formed abnormal organelles ( FIG. 3G , indicated by arrows).
  • Abnormal endoplasmic reticulum structure and apoptosis was also observed by transmission electron microscopy.
  • the ms142 tapetal cells continuously became vacuolated and elongated, with some cells divided into two tapetum layers ( FIG. 3G ).
  • the mid-layers of the mutant tapetum maintained their initial shapes, but failed to divide into four cells at tetrad stage ( FIG. 3H ).
  • the ms142 mutant's microspores finally degenerated during the vacuolated pollen stage.
  • the tapetal and middle layer cells contained a large vacuole, and the middle layer cells did not degenerate ( FIG. 3I ). Consequently, there were no mature pollen grains formed in the locules at the mature stage.
  • the mutant anther wall still retained four to five layers of cells, i.e. epidermis, endothecium, middle layer, and one or two layers of tapetum cells. By contrast, the endothecial cell layer did not become thickened in the mutant even at the latter stage of anther development ( FIG. 3J ).
  • ms142 has abnormal anther morphology and aborted degradation of tapetal cells ( FIG. 3 ).
  • Tapetal PCD is characterized by cellular condensation, mitochondria and cytoskeleton degeneration, nuclear condensation, and internucleosomal cleavage of chromosomal DNA 33 . Therefore, we performed the TUNEL assay to detect DNA fragmentation in the anthers of WT and ms142.
  • a TUNEL positive signal began to appear in the tapetal cells of WT during meiosis and a strong TUNEL signal was detected during the young microspore stages ( FIG. 4 ). In contrast, no DNA fragmentation was observed in the tapetal layer in ms142 throughout anther development ( FIG. 4 ).
  • bHLH142 is a Nuclear Protein
  • bHLH142 The gene structure of bHLH142, shown in FIG. 5A , indicates that bHLH domain contains bipartite nuclear localization signal (NLS), and the gene is predicted to encode a protein of 379 amino acids with a theoretical molecular mass of 40.7 kDa and pI of 6.2.
  • NLS nuclear localization signal
  • bHLH142 The nucleotide sequence of bHLH142 is shown below:
  • amino acid sequence of bHLH142 is shown below:
  • bHLH142 is localized in the nucleus.
  • GFP green fluorescent protein gene
  • bHLH142 under the control of the 35S promoter and the nos terminator for transient expression in rice leaf mesophyll protoplasts.
  • RFP red fluorescent protein
  • Rice bHLH142 shares a high similarity with the related proteins from Brachypodium distachyon , millet ( Setaria italica ), Triticum urartu , maize ( Zea may ), Sorghum ( Sorghum bicolor ) and Aegilops tauschii ( FIG. 6 ).
  • the maize homolog, GRMZM2G021276, is highly expressed in immature tassel and meiotic tassel and anther.
  • bHLH142 mRNA is accumulated in young rice panicle and anther only, but not in other tissues (e.g. root, shoot, leaf, lemma, palea, ovary, and seed).
  • high levels of transcripts were found in developing panicles ( FIGS. 7A and 7B ).
  • bHLH142 transcripts were highly expressed in meiocyte mother cells (MMC) and extremely highly expressed in the anther at meiosis stage ( FIG. 7C ).
  • ISH in-situ hybridization
  • EAT1 was expressed slightly later (at young microspore stage) than bHLH142 (at meiosis stage) ( FIG. 10 ).
  • ms142 anther exhibited a similar amount of EAT1 mRNA to WT anthers at MMC, but tended to decline after young microspore stage ( FIG. 10 ).
  • bHLH142 plays a role in the downstream of UDT1, but upstream of EAT1.
  • EAT1 promoter assays in that both bHLH142 and TDR1 are required for the transcription of EAT1 ( FIG. 11 ).
  • Bimolecular fluorescent complementation (BiFC) assay showed that yellow fluorescent protein (YFP) signals are detected only in the nucleus of the rice cells co-expressing both NYN1-bHLH142 and CYN1-TDR1 and in the cells co-expressing both NYN1-TDR1 and CYN1-EAT1, but not in the cells co-expressing both NYN1-bHLH142 and CYN1-EAT1 ( FIG. 13B ).
  • YFP yellow fluorescent protein
  • RNA interference RNA interference construct to suppress the expression of bHLH142 in rice.
  • the gene specific region from the 5′UTR of bHLH142 was, amplified, fused with ⁇ -glucuronidase (GUS) intron and introduced into WT calli via Agrobacterium tumefaciens .
  • GUS ⁇ -glucuronidase
  • All 16 TO RNAi transgenic lines obtained had a MS phenotype similar to the T-DNA mutant ms142.
  • These RNAi lines showed reduced expression of bHLH142, as examined by RT-PCR, and produced poorly developed anthers without pollen grains ( FIG. 14 ). This result further supports the notion that bHLH142 plays a key role in rice anther and pollen development.
  • the RNAi fragment SEQ ID No. 120:
  • bHLH142 shares high identity with maize 38 , and gene specific primer sets were designed from homolog of maize ZmLOC100283549 (denoted Zm-142). RT-PCR indicated that Zm-142 was not expressed in vegetative organs of maize such as leaf, root, shoot, and stamen. Interestingly, Zm-142 specifically expressed in floret of 1 mm to 7 mm length but not detectable at later stage and in the mature pollen ( FIG. 18 ). The expression pattern of Zm-142 was similar to bHLH142 38 .
  • FIG. 15A we use the similar construct of overexpression bHLH142 in FIG. 15A was transformed into maize (in cultivar Crystal White background) using agrobacterium -mediated pollen transformation method.
  • One transgenic maize showed obvious male sterility phenotype with smaller angle of tassel branch ( FIG. 19A , right panel) than the WT ( FIG. 19A , left panel). Closed up tassel during anthesis stage, WT has larger anther than transgenic line and it has normal opening of spikelets and elongation of anther filaments during anthesis stage ( FIG. 19B , left panel). Whilst, anther of transgenic maize were significantly smaller in size and anther was completely no elongation of anther filaments ( FIG.
  • FIG. 19B right panel
  • Morphology of spikelet of WT at one day before anthesis was shown in FIG. 19C (left panel) with long and fat anther, but anther of transgenic line was short and shrinkage ( FIG. 19C , right panel).
  • pollens of transgenic line could not be stained and transparent due to no starch accumulation. That implied transgenic line was male sterile ( FIG. 19D ).
  • bHLH142-overexpressed plants also showed a completely male sterile phenotype during summer season ( FIG. 20 , left panel).
  • anthers of overexpression transgenic line produce many pollen grains inside the locules and their pollen grains can be stained by I 2 /KI solution, indicating that the plants have restored the fertility ( FIG. 20 , right panel). Therefore, this novel functionality nature of our target bHLH142 has a big advantage over other genetic MS (GMS) genes for hybrid crop production.
  • GMS genetic MS
  • This reversible pollen fertility trait makes it more desirable in producing hybrid crop seeds just in one cross without the need to maintain the seed stocks of the MS lines as with cytoplasmic MS (CMS).
  • CMS cytoplasmic MS
  • biotech companies are known to prefer adopting overexpression over suppression approach in generating transgenic lines because overexpression lines are more stable than RNAi or antisense knock-down lines.
  • Rice bHLH142 have homologous in maize, sorghum and wheat, and they share more than 70% similarity in amino acid sequence to the rice counterpart (Table 3). This will benefit to genetic engineering male sterile for F1 hybrid seed production and generating hybrid vigor (heterosis) in terms of growth and grain yield in cereal crops.
  • bHLH142 is a New Major Regulator of Rice Anther Development
  • bHLH142 as another critical factor in the bHLH TF family for pollen development, besides UDT1 (bLHL164), TDR1 (bLHL5) and EAT1 (bHLH141).
  • UDT1 bLHL164
  • TDR1 bLHL5
  • EAT1 bHLH141
  • FIG. 10 and FIG. 9 show that the gene hierarchy of bHLH142 is in the downstream of UDT1 (bHLH164) but upstream of TDR1 (bHLH5) and EAT1 (bHLH141) ( FIG. 10 and FIG. 9 ).
  • all these 4 bHLH TFs are tissue specifically expressed in the anther and participate in the important process of sequential pollen development events, particularly in tapetal PCD.
  • bHLH142 Functions Coordinately with TDR1 to Regulate EAT1 Promoter
  • TDR1 and EAT1 mRNA are both down-regulated in ms142, we hypothesize that TDR1 interacts with bHLH142 and positively regulate EAT1 promoter for transcriptional activities of AP25 and AP37, encoding aspartate proteases for tapetal PCD.
  • Our promoter transient assay provides solid evidence that bHLH142 and TDR1 work coordinately in regulating EAT1 promoter ( FIG. 11 ).
  • EAT1 protein significantly reduced EAT1-Luc promoter strength from a 30 fold down to 18 fold increase ( FIG. 11 ), which may be attributed to the competition between bHLH142 and EAT to interact with TDR1.
  • EAT1 favors TDR1-EAT1 interaction and might consequently reduce the interaction between bHLH142 and TDR1, therefore reducing EAT1 transcriptional activation ( FIG. 11 ). It is likely that bHLH142 interacts with TDR1 and TDR1 in turn interacts with EAT1 and bHLH142 does not directly interact with EAT1 ( FIG. 13 ). Whether some other TFs may be required to regulate the transcription of bHLH142 is worth further investigation to unravel the entire regulatory gene hierarchy.
  • N-terminal truncated forms of TDR ⁇ aa(1-344) and EAT1 ⁇ aa(1-254) were used in our experiment to reduce self activation. These two N-terminal truncated protein forms did not exhibit self activation in yeast cells ( FIG. 12A ). Therefore, we are confident that bHLH142 interacts with TDR1 by using these truncated proteins to eliminate the bias ( FIG. 13 ).
  • Our data indicate that bHLH142 interacts with TDR1 in the C-terminal ( FIG. 13 ), and support the conclusion of the previous study in that DTD/EAT1 (bHLH141) interacts with TDR1 in the C-terminal region 24 .
  • both bHLH142 and EAT1 can interact with TDR1 in the C′ terminal of TDR1.
  • This finding also supports the result of our EAT1 promoter assay, where additional EAT1 protein reduces EAT1 promoter activity, presumably due to the competition between bHLH142 and EAT1 proteins in the C′ terminal of TDR1.
  • the current regulatory network for rice pollen development is presented in FIG. 21 .
  • Previous works with various rice MS mutants suggest that UDT1 and GAMYB may positively regulate the transcription of TDR1 22 and TDR1 in turn controls the transcription of C6 and CP1 14 .
  • TDR1 interacts with EAT1 for its direct regulation of the expression of two aspartate proteinase genes for initiation of tapetal PCD 23 .
  • bHLH142 acts downstream of UDT1 but upstream of TDR1 and EAT1, and then bHLH142 interact with TDR1 in activating EAT1 transcription (indicated by red arrows in FIG. 21 ).
  • EAT1 also positively regulate the transcription of AP37 and CP1 directly, two proteins involved in tapetal PCD at late pollen development stage.

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Abstract

The present invention relates to a method for producing male sterile plant, a mutated nucleotide molecule comprising a nucleotide sequence of the transcription factor bHLH142 and an inserted T-DNA segment, and a novel transformed plant cell and a male-sterile mutant plant comprising the mutated nucleotide molecule, in which the transcription factor bHLH142 is not expressed. The present invention also relates to a novel reversible male sterile transgenic plant, wherein the transcription factor bHLH142 is overexpressed, and its preparation method. The bHLH gene is tissue specifically expresses in the anther and it plays a pivotal role in pollen development. Both the male sterile and reversible male sterile transgenic plants showed a completely male sterile phenotype, but the fertility of the reversible male sterile transgenic plant can be restored under low temperature.

Description

    BACKGROUND OF THE INVENTION
  • Rice (Oryza sativa) is one of the most important staple crops in the world, feeding almost half of the world's population, and it serves as a model for monocots, which include many important agronomic crops (e.g. wheat, maize, sorghum, millet). Food and Agriculture Organization (FAO) predicts that rice yield will have to be increased 50-70% by 2050 to meet the demands. Several approaches are currently adopted to increase rice yields, such as heterosis breeding, population improvement, wide hybridization, genetic engineering, and molecular breeding1. Among these, hybrid rice is being considered the most promising one (15-20% increases in yield)2. Crops produced from F1 hybrid seeds offer significant benefits in terms of yield improvement, agronomic performance and consistency of end-use quality. This is due to the ‘hybrid vigor’ generated by combining carefully selected parent lines. Hybrid crops are responsible for a dramatic increase in global crop yields in the past decades, and male sterility (MS) has played a significant role in this advancement. Male sterile traits can be divided into cytoplasmic male sterility (CMS), which is determined by cytoplasmic factors such as mitochondria, and genetic male sterility (GMS), which is determined by nuclear genes. CMS has long been used in hybrid corn production, while both CMS and GMS are currently used for hybrid rice production3, due to the convenience of controlling sterility expression by manipulating the gene-cytoplasm combinations in any selected genotype. Most importantly, it evades the need for emasculation in cross-pollinated species, thus encouraging cross breeding and producing pure hybrid seeds under natural conditions. However, commercial seed production must be simple and inexpensive, and the requirement for a maintainer line to produce the seed stocks of CMS line increases the production cost for this 3-line hybrid system.
  • On the other hand, genetic MS (GMS), controlled by nuclear genes, offers an alternative hybrid seed production system. For the two-line hybrid system, it is beneficial to use photoperiod- or temperature-inducible MS (PGMS or TGMS) mutants to maintain seed stocks for hybrid seed production. Currently, in China, PA64S is the most widely used maternal line in two-line hybrid rice breeding, and it is crossed with paternal line 93-11 to generate superhybrid rice, LYP94. PA64S, derived from a spontaneous PGMS japonica mutant NK58S (long day->13.5 h; Shi, 1985), is also a TGMS indica rice, whose MS is promoted by temperatures greater than 23.5° C., but recovers its fertility at temperatures between 21˜23° C. Recent mapping analyses demonstrate that the P/TGMS in these MS lines is regulated by a novel small RNA5. In the case of another rice genic MS mutant discovered recently, Carbon Starved Anther (CSA), the mutation on the R2R3 MYB transcription regulator defects pollen development6 and further study shows that csa is a new photoperiod-sensitive mutant, exhibiting MS under short-day conditions but male fertility under long-day conditions7. The molecular basis of its MS sensitivity to day length remains to be addressed.
  • Transgenic male sterility has been generated using a number of transgenes, but its application in commercial production of hybrid seeds is limited due to the lack of an efficient and economical means to maintain the MS lines, or the lack of suitable restorers8. Recently, a reversible MS system has been demonstrated in transgenic Arabidopsis plants by manipulating a R2R3 MYB domain protein (AtMYB103)8. Blocking the function of AtMYB103 using an insertion mutant or an AtMYB103EAR chimeric repressor construct under the control of the AtMYB103 promoter resulted in complete MS without seed setting8. A restorer containing the AtMYB103 gene driven by of a stronger anther-specific promoter was introduced into pollen donor plants and crossed into the MS transgenic plants for the repressor. The male fertility of F1 plants is restored. The chimeric repressor and the restorer constitute a reversible MS system for hybrid seed production. The successful application of this system for large scale hybrid seed production depends on whether the MS female parent lines can be multiplied efficiently and economically. Alternatively, an inducible promoter by chemicals or other factors (e.g. photoperiod or temperature) can be directly used to regulate the expression of a GMS gene (e.g., bHLH142) and control pollen development in transgenic plants, eliminating the costly need to maintain MS lines.
  • Rice anthers are composed of four lobes attached to a central core by connective and vascular tissue. When anther morphogenesis is completed, microsporocytes form in the middle, surrounded by four anther wall layers: an epidermal outer layer, endothecium, middle layer, and tapetum9. The tapetum is located in the innermost cell layer of the anther walls and plays an important role in supplying nutrients such as lipids, polysaccharides, proteins, and other nutrients for pollen development10. The tapetum undergoes programmed cell death (PCD) during the late stage of pollen development11; this PCD causes tapetal degeneration and is characterized by cellular condensation, mitochondria and cytoskeleton degeneration, nuclear condensation, and internucleosomal cleavage of chromosomal DNA. Tapetal PCD must occur at a specific stage of anther development for normal tapetum function and pollen development, and premature or delayed tapetal PCD and cellular degeneration can cause male sterility3,12-14.
  • Genetic and functional genomic studies of MS in Arabidopsis have shown that many transcription factors (TFs) play an essential role in pollen development and the regulation of tapetal PCD, such as mutations in DYSFUNCTIONAL TAPETUM 1 (DYT1), Defective in Tapetal Development and Function 1 (TDF1, AtMYB35), ABORTED MICROSPORES (AMS, homolog of TDR1 in rice), and MALE STERILITY 1 (MS1); and mutations in these factors all result in MS phenotype. The genetic regulatory pathway of pollen development suggests that DYT1, TDF115 and AMS16 function at early tapetum development, while MS18817 and MS115,18,19 play important roles in late tapetum development and pollen wall formation. Whilst, in rice, several TFs, such as Undeveloped Tapetum1 (UDT1, homolog of DYT1), are known to be key regulators of early tapetum development20. In addition, mutations in TAPETUM DEGENERATION RETARDATION (TDR1)14, GAMYB21,22, ETERNAL TAPETUM 1 (EAT1)23 and DELAYED TAPETUM DEGENERATION (DTD)24 all cause MS associated with tapetal PCD. TDR1, ortholog of the Arabidopsis AMS gene, plays an essential role in tapetal PCD in rice; and tdr1 shows delayed tapetal degeneration and nuclear DNA fragmentation as well as abortion of microspores after release from the tetrad. Molecular evidences indicate that TDR1 directly binds the promoter of CP1 and C6 for their transcription14. C6 encodes a lipid transfer protein that plays a crucial role in the development of lipidic orbicules and pollen exine during anther development17. CP1 is involved in intercellular protein degradation in biological system and its mutant shows defected pollen development25. EAT1 acts downstream of TDR1 and directly regulates the expression of AP25 and AP37, which encode aspartic proteases involved in tapetal PCD23.
  • The basic helix-loop-helix (bHLH) proteins are a superfamily of TFs and one of the largest TF families in plants. There are at least 177 bHLH genes in the rice genome26,27 and more than 167 bHLH genes in Arabidopsis genome28,29. Generally, eukaryotic TFs consist of at least two discrete domains, a DNA binding domain and an activation or repression domain that operate together to modulate the rate of transcriptional initiation from the promoter of target genes30. The bHLH TFs play many different roles in plant cell and tissue development as well as plant metabolism3. The HLH domain promotes protein-protein interaction, allowing the formation of homodimeric or heterodimeric complexes31. They bind as dimers to specific DNA target sites and are important regulatory components in diverse biological processes29. So far, three of the bHLH TFs have been shown to be involved in rice pollen development—UDT1 (bHLH164), TDR1 (bHLH5), and EAT1/DTD1 (bHLH141).
  • From a screening of T-DNA tagged rice mutant pool of TNG6732, we isolated a novel MS-related gene encoding for another member of the bHLH TFs (bHLH142). In this invention, the molecular mechanism of MS in this mutant is elucidated, and it suggests that bHLH142 is specifically expressed in the anther and bHLH142 coordinates with TDR1 in regulating EAT1 promoter activity in transcription of protease genes required for PCD during pollen development. That is to say, bHLH142 plays an essential role in rice pollen development by controlling tapetal PCD. Both null mutant and overexpression transgenic plants showed a completely male sterile phenotype. Most interestingly, the overexpression plants have restored the fertility under low temperature. Homologs of SEQ ID NO: 2 with high similarity are found in other major cereal crops, and its use may increase the productivity of cereal crops by manipulating the bHLH gene for development of male sterility and production of hybrid crops.
    • SUMMARY OF THE INVENTION
  • The object of the present invention is developing a mutated nucleotide molecule, and a transformed plant cell and a male sterile mutant plant comprising the mutated nucleotide molecule; in which the male sterile mutant plant can be used as a female parent to produce F1 hybrid seeds, thereby improving yield and quality of crops.
  • The present invention provides a mutated nucleotide molecule, comprising a nucleotide sequence of the transcription factor bHLH142 and an inserted T-DNA segment. Preferably, the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • In one preferred embodiment of the mutated nucleotide molecule, the T-DNA segment has comprises a single copy of T-DNA.
  • In one preferred embodiment of the mutated nucleotide molecule, the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1. In addition, the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2. Preferably, a polypeptide sequence having at least 80% similarity to SEQ ID No: 2; more preferably, a polypeptide sequence having at least 90% similarity to SEQ ID No: 2; even more preferably, a polypeptide sequence having at least 95% similarity to SEQ ID No: 2; and most preferably, a polypeptide sequence of SEQ ID No: 2.
  • The present invention provides a transformed plant cell, which comprises the above-mentioned mutated nucleotide molecule. Preferably, the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • In one preferred embodiment of the transformed plant cell comprising the mutated nucleotide molecule, the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1. In addition, the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2. Preferably, a polypeptide sequence having at least 80% similarity to SEQ ID No: 2; more preferably, a polypeptide sequence having at least 90% similarity to SEQ ID No: 2; even more preferably, a polypeptide sequence having at least 95% similarity to SEQ ID No: 2; and most preferably, a polypeptide sequence of SEQ ID No: 2.
  • The present invention also provides a male sterile mutant plant comprising the above-mentioned mutated nucleotide molecule, and the transcription factor bHLH142 is not expressed; particularly, not expressed in anthers. Preferably, the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142; more preferably, the T-DNA segment is inserted at +1257 bp.
  • In one preferred embodiment of the male sterile mutant plant, the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1. In addition, the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2. Preferably, a polypeptide sequence having at least 80% similarity to SEQ ID No: 2; more preferably, a polypeptide sequence having at least 90% similarity to SEQ ID No: 2; even more preferably, a polypeptide sequence having at least 95% similarity to SEQ ID No: 2; and most preferably, a polypeptide sequence of SEQ ID No: 2.
  • In one preferred embodiment of the male sterile mutant plant, the male sterile mutant plant of the present invention is a homozygous mutant.
  • In one preferred embodiment of the male sterile mutant plant, the plant is a monocot; preferably, the monocot is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
  • In one preferred embodiment of the male sterile mutant plant, the plant is a dicot; preferably, the dicot is Arabidopsis or Brassica species.
  • The present invention also provides a transformed plant cell, which comprises a plasmid comprising the sequence of the transcription factor bHLH142 and a strong promoter.
  • In one preferred embodiment of the transformed plant cell comprising the sequence of the transcription factor bHLH142, the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1.
  • In one preferred embodiment of the transformed plant cell comprising the sequence of the transcription factor bHLH142, the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • The present invention also provides a reversible male sterile transgenic plant, wherein the transcription factor bHLH142 is overexpressed; particularly, overexpressed in anthers.
  • In one preferred embodiment of the reversible male sterile transgenic plant, the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1. In addition, the transcription factor bHLH142 has a polypeptide sequence of SEQ ID No: 2 or a polypeptide sequence having at least 60% similarity to SEQ ID No: 2. Preferably, a polypeptide sequence having at least 80% similarity to SEQ ID No: 2; more preferably, a polypeptide sequence having at least 90% similarity to SEQ ID No: 2; even more preferably, a polypeptide sequence having at least 95% similarity to SEQ ID No: 2; and most preferably, a polypeptide sequence of SEQ ID No: 2.
  • In one preferred embodiment of the reversible male sterile transgenic plant, the expression of the transcription factor bHLH142 is controlled by a strong promoter; preferably, by an Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • In one preferred embodiment of the reversible male sterile transgenic plant, the pollen fertility of the plant is recovered under low temperature. Particularly, the pollen fertility of the plant is recovered at 21-23° C.
  • In one preferred embodiment of the reversible male sterile transgenic plant, the plant is a monocot; preferably, the monocot is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
  • In one preferred embodiment of the reversible male sterile transgenic plant, the plant is a dicot; preferably, the dicot is Arabidopsis or Brassica species.
  • The present invention also provides a method for preparing the above-mentioned reversible male sterile transgenic plant, comprising:
      • (a) constructing a plasmid comprising the DNA sequence of bHLH142 and a strong promoter, and
      • (b) introducing the plasmid into a target plant.
  • In one preferred embodiment of the preparation method, the DNA sequence of bHLH142 is SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1. Preferably, a DNA sequence having at least 80% similarity to SEQ ID No: 1; more preferably, a DNA sequence having at least 90% similarity to SEQ ID No: 1; even more preferably, a DNA sequence having at least 95% similarity to SEQ ID No: 1; and most preferably, a DNA sequence of SEQ ID No: 1.
  • In one preferred embodiment of the preparation method, the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter; preferably, the anther tapetum-specific promoter is Osg6B or TA29, and the pollen-specific promoter is LAT52 or LAT59.
  • In one preferred embodiment of the preparation method, the plasmid is introduced into calli of the target plant via Agrobacterium tumefaciens.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1. Phenotypic Analyses of ms142 Mutant. (A) Comparison of the wild-type plant (left) and ms142 mutant (right) after bolting; (B) comparison of the wild-type panicle (left) and ms142 mutant (right) at heading stage; (C) comparison of the wild-type panicle (left) and ms142 mutant (right) at seed maturation stage; (D) phenotype of the wild-type spikelet (left) and ms142 mutant (right) one day before anthesis; (E) phenotype of the wild-type spikelet (left) and ms142 mutant (right) after anthesis; (F) comparison of the wild-type grain (left) and ms142 mutant (right) at harvest stage; (G) phenotype of the wild-type grain (left) and ms142 mutant (right) after removing rice husk; (H) phenotype of the wild-type anther (left) and ms142 mutant (right) one day before anthesis; (I) staining of anther by Sudan black in the wild-type (left) and ms142 mutant (right); (J) staining of wild-type pollen grains by I2/KI solution; and (K) staining of mutant pollen grains by I2/KI solution. Bars=20 cm in (A), 3 cm in (B) and (C), 0.5 cm in (D) to (G), 0.1 cm in (H) and (I), and 20 μm in (J) and (K).
  • FIG. 2. Evidences of T-DNA insertion in ms142 mutant. (A) Southern blotting to hptII probe confirmed single T-DNA insertion (marked with arrow) in ms142 mutant. (B) T-DNA tagged construction map of pTag4 vector. (C) Gene structure and T-DNA insertion site in the mutant at 3rd intron (+1257 bp from ATG). (D) Genotyping heterozygous T4 mutant progeny. Genotype: WT, wild-type like; He, heterozygous; and Ho, homozygous. Grain fertility: F, fertile; and S, sterile.
  • FIG. 3, Transverse anatomical comparison of the anther development in the wild type (TNG67) and ms142 mutant. E, epidermis; En, endothecium; ML, middle layer; T, tapetum; Ms, microsporocyte; Td, tetrads; Msp, microspore; MP, mature pollen; Arrow, degenerated microspore; and arrowhead, two tapetum layers. Bars=20 μm.
  • FIG. 4. TUNEL assay showed defect tapetal program cell death in ms142 mutant. DNA fragmentation signals (yellow fluorescence) started at tetrad stage and exhibited obvious positive signal at young microspore stage in wild type (TNG67). No DNA fragmentation signal was observed in ms142 anther. Red signal shows the propidium iodide (PI) staining, and yellow fluorescence is the merged signal from TUNEL (green) and PI. Scale bar=50 μm.
  • FIG. 5. Scheme of bHLH142 gene, multiple alignment, and subcellular localization of bHLH142 fused with GFP. (A) Scheme of the bHLH142 gene and T-DNA insertion position. Gray boxes represent exons and interventing lines represent introns. The ATG start codon and TGA stop codon are indicated. bHLH, basic helix-loop-helix domain (amino acids 182 to 228); NLS, two nuclear localization signals (amino acids 159 to 165 and 235 to 240, respectively). (B) Alignment of bHLH domains. The bHLH142 protein was aligned with the bHLH domains of the analogous proteins from other species. Asterisks indicate the conserved basic amino acid Arg that is important for binding DNA. Pound signs indicate conserved Leu residues important for forming the α-helix. (C) Schemes of fusion constructs. P35S, cauliflower mosaic virus 35S promoter; Trios, nopaline synthase gene terminator. The NLS domain of VirD2 fused with mRFP was used as the nuclear marker. (D) In vivo targeting of fusion protein. DIC (bright field, left column) and overlays (Merge, right column) are shown. Scale bar=20 μm.
  • FIG. 6. Phylogenetic analysis of bHLH142 related proteins. Aral, Arabidopsis lyrata; Aegt, Aegilops tauschii; At, Arabidopsis thaliana; Brad, Brachypodium distachyon; Os, Oryza sativa; Sei, Setaria italica; Sb, Sorghum bicolor; SeMa, Selaginella moellendorffii; Triu, Triticum urartu; and Zm, Zea may.
  • FIG. 7. Spatial and temporal gene expression of bHLH142 in various tissues of TNG67 (WT) by (A) RT-PCR and (B) qRT-PCR, and (C) in TNG67 spikelet at various developmental stages; and (D) ISH of bHLH142 antisense (left panel) and sense (right panel) probes in spikelet of TNG67 at meiosis stage. Error bars indicate SD (n=3), SC, sporogenous cell; MMC, meiocyte mother cell; Mei, meiosis; YM, young microspore; VP, vacuolated pollen; PM, pollen mitosis; and MP, mature pollen. Scale bar=1 mm in (C), 50 μm in (D).
  • FIG. 8. In situ hybridization analysis of bHLH142 expression in the anther of WT and ms142 mutant at various developmental stages. Transverse sections of anther were hybridized with antisense or sense dig-labeled probe of bHLH142. Scale bar=20 μm.
  • FIG. 9. Analysis of alternation in expression of key regulatory genes involved in pollen development in ms142 by qRT-PCR. Error bars indicate SD (n=3). MMC, meiocyte mother cell; Mei, meiosis; and VP, vacuolated pollen.
  • FIG. 10. Gene hierarchy of bHLH142, as determined by the expression profiles of the key regulatory genes involved in pollen development in ms142 and eat1 mutants. (A) Phenotype of spikelet in TNG67 (WT) and ms142. (B) Phenotype of spikelet in Hitomebore and H0530 (eat1 mutant). (C) Real-time RT-PCR of bHLH142 in ms142 and eat1 mutants and their respective wild-types. (D) Real-time RT-PCR of EAT1 (bHLH141) in ms142 and eat1 mutants and their respective wild types. qRT-PCR value presented are means±SE (n=3). MMC, meiocyte mother cell; Mei, meiosis; YM, young microspore; and VP, vacuolated pollen.
  • FIG. 11. Coordinated Regulation of EAT1 Promoter by bHLH142 and TDR1. (A) Schematic diagrams of the reporter, effector, and internal control plasmids used in the transient transactivation assay in rice leaf protoplasts. The reporter plasmid contains the CaMV35S minimal promoter and the EAT1 promoter sequence (2 Kb) fused to the firefly luciferase gene (Luc). In the effector plasmids, bHLH142, TDR1, and EAT1 genes were driven under the control of the CaMV35S promoter. Nos and t35s denote the terminators of nopaline synthase and CaMV35S, respectively. The pBI221 vector contains a CaMV35S promoter driving the expression of GUS as the internal control. (B) Transactivation of the Luc reporter gene by bHLH142 and TDR in rice protoplasts. Different effectors were co-transfected with the reporter and internal control plasmid (pBI221). The data represent means of three independent transient transformations. Error bars indicate SD. Transient transformation without the effector plastnid (mini35p) was used as a negative control.
  • FIG. 12. Analysis of protein interaction between bHLH142, TDR1, and EAT1 by (A) Yeast two-hybrid assay and (B) BiFC in rice leaf protoplasts expressing the indicated constructs. Scale bars=20 μm.
  • FIG. 13. The Interactions between bHLH142 Protein and TDR1, and between TDR1 and EAT1. (A) Yeast two-hybrid (Y2H) assays. Constructs expressing the full length bHLH142 were cloned into the prey vector pGADT7 (AD), and truncated forms of TDR and EAT1 were prepared in the bait vector pGBKT7 (BD). (B) BiFC in rice protoplasts expressing the indicated constructs. Bars represent 10 μm. (C) Co-IP assay of HA fused TDR and bHLH142 recombinant proteins expressed in E. coli using anti-HA antibody. (D) Co-IP assay of HA fused TDR and bHLH142 recombinant proteins expressed in E. coli using bHLH142 antibody.
  • FIG. 14. RNAi Knockdown (KD) of bHLH142 Inhibited Pollen Development. (A) Construct of RNAi vector. (B) RT-PCR showed down regulation of bHLH142 in the anthers of four RNAi knock down lines. (C) Phenotype of WT and KD line #3. Scale bars=20 cm in (C), 0.5 mm (D), 1 mm (E) and 20 μm (F).
  • FIG. 15. Overexpression rice bHLH142 driven by Ubiquitin promoter in transgenic rice. (A) Construction of bHLH142 (LOC_Os01g18870) driven by Ubiquitin promoter in pCAMBIA1301 vector, (B) Genomic PCR confirmed T-DNA insertion of target gene (upper panel) and selection marker hygromycin (lower panel) in the transgenic rice.
  • FIG. 16. Phenotype of TNG67 (WT) and Ubi::bHLH142 transgenic lines. (A) Plant type of WT (left) and transgenic line (right), (13) panicles of WT (bottom) and transgenic line (top panel), (C) panicles of WT (left) and different transgenic lines, (D) spikelet of WT (left) and different transgenic lines at one day before anthesis, (E) mature seed of WT (left) and different transgenic lines, and (F) removed husk rice seed of WT (left) and different transgenic lines. Scale bars=20 cm in (A), 3 cm in (B), 7 cm in (C) and 1 cm in (F).
  • FIG. 17. Overexpression bHLH142 prematurely up-regulated Udt1 and EAT1 before meiosis stage but significantly down-regulated MS2 that associated in pollen exine development. SC=sporogenous cell, MMC=meiocyte mother cell, Mei=meiosis, YM=young microspore, PM=pollen mitosis, MP=mature pollen.
  • FIG. 18. Gene expression pattern of bHLH142 homolog in various organs of maize by using RT-PCR. Floret size by measuring the length of floret. 10G, floret length at 10 mm with green color, 1 DBA, one day before anthesis.
  • FIG. 19. Heterologus overexpressing Ubi::bHLH142 caused male sterility in transgenic maize, (A) The transgenic line has smaller angle of tassel branch (right panel) than the WT (left panel). (B) Closed up tassel during anthesis stage, WT has large and anther opened during anthesis stage (left panel), while anther of transgenic maize were significantly smaller in size and anther no dehiscence (right panel). (C) Morphology of spikelet of WT (left panel) and transgenic line (right panel), (D) Stained of pollen grains by I2/KI solution in the fertile WT, but not stainable in the transgenic line and pollen was not viable showing transparent pollen. Scale bars=3 cm in (A), 2 mm in (C) and 50 um in (D).
  • FIG. 20. The male sterility of Overexpression Ubi::bHLH142 transgenic line is sensitive to environment. The bHLH142 overexpressed lines produced no pollen grains during summer season (Left panel) but had fertile pollens during winter seasons. Pollen grains were stained by I2/KI solution.
  • FIG. 21. A proposed model for the molecular function of bHLH142 in rice anther development, relative to other key regulators. bHLH142 is in the downstream of UDT1 but upstream of TDR1, and bHLH142 interacts with TDR1 protein and coordinately regulate the promoter of EAT1. In turn, EAT1 regulates AP37 and CP1 and promotes tapetal PCD. Evidences from previous works were indicated by black arrows, while data demonstrated in the present study were indicated by red arrows.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • The following examples are presented to demonstrate the present invention. These examples are in no way to be construed as a limitation on the invention. The disclosure would enable those skilled in the art to practice the present invention without engaging in undue experimentation. All recited publications are incorporated herein by reference in their entirety.
    • Plant Materials and Growth Conditions
  • The seed of ms142 mutant was obtained from TRIM library. Seedlings of ms142 mutant and its WT (TNG67) were raised in half strength Kimura solution for 3 weeks and then transplanted into soil in AS-BCST GMO screen house located in Tainan, Taiwan.
    • Anther Anatomy
  • Spikelets and anthers of the WT and ms142 mutant were sampled at various stages of development and fixed overnight in phosphate buffer, pH 7.0, that contained 4% paraformaldehyde and 2.5% glutaraldehyde. They were then rinsed with the same buffer and post fixed for 30 min in phosphate buffer, pH 7.0, containing 1% osmium tetroxide. After dehydration, the specimens were embedded in Spurr's Resin (EMS). The processor, KOS Rapid Microwave Labstation, was chosen for post fixation, dehydration, resin infiltration, and embedding. For TEM, ultrathin sections (90 to 100 nm thick) collected on coated copper grids were stained with 6% uranyl acetated and 0.4% lead citrate and examine using transmission electron microscope.
    • Total RNA Isolation and PCR.
  • Total RNA was isolated from rice tissues using MaestroZol™ RNA PLUS (Invitrogen) as described by the supplier. Various rice organs at different developmental stages were harvested for RNA isolation: root, shoot, flag leaf, internode, panicles of 0.5 cm, 1 cm, 5 cm, 9 cm, and 20 cm length, spikelet at 1 day before anthesis (1 DBA), lemma, palea, anthers, ovary, seed at 5 days after pollination (S1), 15 days after pollination (S3), 25 days after pollination (S5), and callus. The stages of anthers were classified into the following categories according to spikelet length: microspore mother cell (MMC) with spikelet length of approximately 2 mm, meiosis (4 mm), young microspore (YM, 6 mm), vacuolated pollen (VP, 8 mm), mitosis pollen (MP, 8 mm with light green lemma), and mature pollen at one day before anthesis (1 DBA). Total RNA was treated with DNase (Promega), and 1 μg RNA was used to synthesize the oligo(dT) primed first-strand cDNA using the M-MLV reverse transcriptase cDNA synthesis kit (Promega). One μL of the reverse transcription products was used as template in PCR reactions. Ubiquitin-like 5 and 18srRNA were used as normalizer control. Each sample has three biological repeats.
  • qRT-PCR Analysis.
  • Fifteen μL of RT-PCR reaction contained 4 μL, of ¼ diluted cDNA, 3 μM of primers, and 7.5 μL of 2×KAPA SYBR FAST master mix (KAPA Biosystems, USA). Quantitative Real-Time PCR (qRT-PCR) was performed using a CFX96 Real-Time PCR detection system (Bio-Rad, USA). Quantification analysis was carried out using CFX Manager Software (Bio-Rad, USA). Primers used for qPCR are listed in Table 1.
  • TABLE 1
    Primers Used in Examples
      RAP Acces-
    Primer′s Names sion No. Sequence (5′→′) Sequence ID
    Screening of ms142 Mutant T-DNA inserted
    S80qPCR-F3 Os01g0293100 GGAGCACGTACATCCAGCGG SEQ ID No. 3
    S80-GT-R3 ACTCATCCACCACTTCAATCAGCC SEQ ID No. 4
    RB-13 AACTCATGGCGATCTCTTACC SEQ ID No. 5
    Hyg-F GATGTAGGAGGGCGTGGATA SEQ ID No. 6
    Hyg-R CGTCT GCTGC TCCAT ACAAG SEQ ID No. 7
    Quantitative Real-time PCR
    S80qPCR-F3 Os01g0293100 GGAGCACGTACATCCAGCGG SEQ ID No. 8
    S80-GT-R3 ACTCATCCACCACTTCAATCAGCC SEQ ID No. 9
    OsMS2-qRT-F Os03g0167600 TGGAGCAGTTCGCCAGCTACG SEQ ID No. 10
    OsMS2-qRT-R CTTCTCCTCCTCCGACATCTCCC SEQ ID No. 11
    OsTDR-F Os02g0120500 CGCTCGCTCGTCCCAAACAT SEQ ID No. 12
    OsTDR-R CGGTCATTGCTGGGTCCTTGT SEQ ID No. 13
    Os C6-F Os11g0582500 TCCTCCTCGTCCTGCTCGTC SEQ ID No. 14
    Os C6-R GGTTCACGATGTGGCACAGG SEQ ID No. 15
    18SrRNA-F2 TTAGG CCACG GAAGT TTGAG G SEQ ID No. 16
    18SrRNA-R2 ACACT TCACC GGACC ATTCA A SEQ ID No. 17
    Udt1-F Os07g0549600 GATCTTCTGGACCAAGAGGGCAG SEQ ID No. 18
    Udt1-R GTCAGGAGTGTCTCAGATGCTTGG SEQ ID No. 19
    OsCP1-F Os09g0381400 GGACCACCTGCTGCTGCAACT SEQ ID No. 20
    OsCP1-R GAACACTTCGTGCCATCGCC SEQ ID No. 21
    bHLH141-F Os04g0599300 TGGTGGAACAGAAGAGGCATGG SEQ ID No. 22
    bHLH141-R GCATGAAGCAGAGAGTTGGCCTT SEQ ID No. 23
    OsUBQ5-F Os01g0328400 GCGGAAGTAAGGAAGGAGGAGG SEQ ID No. 24
    OsUBQ5-R GGCATCACAATCTTCACAGAGGTG SEQ ID No. 25
    MSP1-F Os01g0917500 GAGAACTTCGAGCCGAGGGTCT SEQ ID No. 26
    MSP1-R CCAGCCGACGAGGTTTCCAC SEQ ID No. 27
    AP37-F Os04g0448500 AGGCGGGCAGCGTCTCCAT SEQ ID No. 28
    AP37-R CCATAAGCCAGCCACGATGATGA SEQ ID No. 29
    GAMyb-F Os01g0812000 CATCCTGGTCCATTCCTCAATGAC SEQ ID No. 30
    GAMyb-R TTCAGGATGAGGTGAAGTGTCCC SEQ ID No. 31
    Subcellular localization analysis
    S80cDNA-XbaI-F TATCTAGAGTGGTAGAGTGCGAGGAAG SEQ ID No. 32
    KpnI-S80-nonstop-R GAGGTACCAGGTACTCATCCACCACTTCAA SEQ ID No. 33
    In situ hybridization analysis
    S80qPCR-F2 CATGTTCAACACCAAGATTCATTCG SEQ ID No. 34
    S80FLcds-R2 TGCAAACCATGACATACCAAAGATC SEQ ID No. 35
    BiFC construction
    BiFC-TDR-BamHI-F AGGGATCCCACCACATGGGAAGAGGAGACC SEQ ID No. 36
    BiFC-TDR-SalI-R ATGTCGACTCAAACGCGAGGTAATGCAGG SEQ ID No. 37
    BiFC-UDT-BamHI-F GTGGATCCATGCCGCGGCGCGCGAGGGCGA SEQ ID No. 38
    BiFC-UDT-Xho-R TGCTCGAGATGCTTGGAACCTCCACAATGCTGG SEQ ID No. 39
    BiFC-bHLH141-Pst-F AGCTGCAGTTTGCCAAAATGATTGTTGGG SEQ ID No. 40
    BiFC-bHLH141-Sal-R GCGTCGACTTGAATATGTCGAGGGCCTGG SEQ ID No. 41
    S80-Y2H-AD-BamH-F GTGGATCCCGAGGAAGATGTATCACC SEQ ID No. 42
    S80-Y2H-AD-Xho-R AGCTCGAGCTAGTTAGTACTCATCCACCAC SEQ ID No. 43
    Yeast Two Hybrid
    S80-Y2H-AD-BamH-F GTGGATCCCGAGGAAGATGTATCACC SEQ ID No. 44
    S80-Y2H-AD-Xho-R AGCTCGAGCTAGTTAGTACTCATCCACCAC SEQ ID No. 45
    S80-Y2H-BD-Pst-R CGCTGCAGTTAGTACTCATCCACCACTT SEQ ID No. 46
    141-Y2H-BD-Eco-F AGGAATTCTTTGCCAAAATGATTGTTGGG SEQ ID No. 47
    141-Y2H-BD-Pst-R GCCTGCAGTTAGTTGAATATGTCGAGGGCCTG SEQ ID No. 48
    TDR-Y2H-EcoR-F AAGAATTCATGGGAAGAGGAGACCACCTGC SEQ ID No. 49
    TDR-Y2H-BamH-R CTGGATCCTCAATCAAACGCGAGGTAATGCA SEQ ID No. 50
    Y2H-Deletion141-N-BD TAGAATTCATGAAGGGTGAGTTCGGAAAGGGC SEQ ID No. 51
    Y2H-Deletion141-C-BD AGGTCGACTTACCCTCTCCTGCATTCAAGTACA SEQ ID No. 52
    Y2H-DeletionTDR-N-BD ACGAATTCATGCATGTCCACCATAAGCCGC SEQ ID No. 53
    Co-Immunoprecipitation
    CO-IP-HA-SacII-F AACCGCGGAAATGAGTTACCCATACGATGTTCCTG SEQ ID No. 54
    CO-IP-HA-Not-R CAGCGGCCGCAGCGTAATCTGGAACGTCATAT SEQ ID No. 55
    CO-IP-TDR-HA-Xba-F AATCTAGACATGGGAAGAGGAGACCACCTGC SEQ ID No. 56
    TDR-cDNA-SalI-R CAGTCGACTCAATCAAACGCGAGGTAATGCA SEQ ID No. 57
    CO-IP-S80-Flag-Xba-F CGTCTAGAGATGTATCACCCGCAGTG SEQ ID No. 58
    S80-Y2H-AD-Xho-R AGCTCGAGCTAGTTAGTACTCATCCACCAC SEQ ID No. 59
    Promoter transience assay
    BiFC-TDR-BamHI-F AGGGATCCCACCACATGGGAAGAGGAGACC SEQ ID No. 60
    TDR-cDNA-SaII-R CAGTCGACTCAATCAAACGCGAGGTAATGCA SEQ ID No. 61
    BiFC-bHLH141-Pst-F AGCTGCAGTTTGCCAAAATGATTGTTGGG SEQ ID No. 62
    bHLH141-cDNA-Sal-R GCGTCGACTTAGTTGAATATGTCGAGGGCCT SEQ ID No. 63
    141-2kb-P-Spe-F CCACTAGTTGCTTTGGTTTTGATTCCTGGAAG SEQ ID No. 64
    141-2kb-P-Sal-R AAGTCGACAACAGTGCTAGGCACCTTCGC SEQ ID No. 65
    S80-Y2H-AD-BamH-F GTGGATCCCGAGGAAGATGTATCACC SEQ ID No. 66
    S80-Y2H-AD-Xho-R AGCTCGAGCTAGTTAGTACTCATCCACCAC SEQ ID No. 67
    RNAi transgenic line
    PANDA-GUS-F-Spe acactagtATCTACCCGCTTCGCGTCGG SEQ ID No. 68
    PANDA-GUS-R-Pst atctgcagCGAGTGAAGATCCCTTTCTTGTTACC SEQ ID No. 69
    142RNAi-5′-F-Pst gcctgcagCAACAAACCTAGTTAATT SEQ ID No. 70
    TAGCTCTAGTTGG
    142RNAi-5′-R-Sal gcgtcgacAGGCTCTCAAGCGGCATCAG SEQ ID No. 71
    142RNAi-5′-F-Spe gcactagtCAACAAACCTAGTTAATT SEQ ID No. 72
    TAGCTCTAGTTGG
    142RNAi-5′-R-Not tagcggccgcAGGCTCTCAAGCGGCATCAG SEQ ID No. 73
    Overexpression bHLH142 in transgenic rice
    Hyg-F GATGTAGGAGGGCGTGGATA SEQ ID No. 74
    Hyg-R CGTCT GCTGC TCCAT ACAAG SEQ ID No. 75
    S80qPCR-GT-F GGAGCACGTACATCCAGCGG SEQ ID No. 76
    Pzp200-NOS-R ATCGCAAGACCGGCAACAGGA SEQ ID No. 77
    Overexpression bHLH142 in transgenic maize
    Zm142-F TGACCTCGTCCACCTCTCCG SEQ ID No 117
    Zm142-R CAGTCTGTAACGAGCAAGCGGA SEQ ID No. 118
    • In-Situ Hybridization
  • Spikelets of TNG67 and ms142 at various developmental stages were fixed in PFA [4% paraformaldehyde, 4% dimethylsulfoxide 0.25% glutaraldehyde, 0.1% Tween 20, 0.1% Triton X-100 in diethyl pyrocarbonate (DEPC)-treated H2O] at 4° C. overnight immediately after collection, and the tissue processor, KOS Rapid Microwave Lab station, was used for dehydration and wax infiltration. After embedding, sections of 10 μm thickness were prepared by a rotary microtome (MICROM, 315R) and mounted on APS adhesive microscope slides (FINE FROST). Tissue sections were deparaffinized with xylene, rehydrated through an ethanol series, and pre-treated with proteinase K (2 mg/mL) in 1-phosphate buffered saline (PBS) at 37° C. for 30 min. Pre-hybridization (additionally including 25% RNAmate, BioChain) and hybridization were performed according to the previous protocols39. Hybridization was performed at 59° C. in hybridization solution: 50% formamide, 4×SSPE, 1×Denhardt's (Fluka), 250 μg/mL fish sperm DNA (Genemarker), 250 μg/mL yeast tRNA (Sigma), 10% dextran sulfate, 40 U/mL RNasin (Promega) and 40 ng of DIG-labeled RNA probe/per slide. RNA probes were synthesized by in vitro transcription of the RT-PCR fragment in pGEM-T easy vector using the DIG RNA labeling kit (SP6/T7, Roche). Antisense RNA probes were synthesized by SP6 RNA polymerase, while sense RNA probes were synthesized by T7 RNA polymerase and used as control. Sequence of fragment to synthesize RNA probe (SEQ ID No. 119):
  • 5′-catgttcaacaccaagattcattcgggatctccagtgtttgcaa
    gtgcagtggccagcaggctgattgaagtggtggatgagtactaacta
    gatcgagctagctaattagccgaccgaccgatcgatatgatgaaagt
    ttctatgttgctagctagctagggttcttggatgcatgagtactgag
    tagctctttaattaatttccttttaattttagactgtttaatttgga
    ttggtaaagactcgtgttagcttttgggagatctttggtatgtcatg
    gtttgca-3′
    • Gene Hierarchy Analysis Using Knockout Mutants
  • We have some T-DNA/Tos17 knock out mutant lines in hands such as: in udt1 (TRIM), bHLH142 (ms142, TRIM), and eat1 (bHLH141) Tos17 mutant line H0530 (background of Hitomebore) was obtained from Rice Tos17 Insertion Mutant Database (http://tos.nias.affrc.go.jp/). Flanking sequences were confirmed by genotyping PCR amplification with specific primers (Table 1). We will verify their gene hierarchy using these mutants. Spikelet samples at various developmental stages were collected, isolated RNA, and performed qRT-PCR analysis.
    • TUNEL Assay
  • PCD is characterized by cellular condensation, mitochondria and cytoskeleton degeneration, nuclear condensation, and internucleosomal cleavage of chromosomal DNA33. To investigate the nature of the tapetal breakdown in ms142, the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay was performed using DeadEnd Fluorometric TUNEL system (Promega). This assay detects in situ DNA cleavage, a hallmark feature of apoptosis-like PCD, by enzymatically incorporating fluorescein-12-dUTP into the 3′-OH ends of fragmented DNA. Stage of anther development was based primarily on spikelet size and developmental stages.
  • Subcellular Localization of bHLH142
  • For subcellular localization of bHLH142, the coding sequences of the gene were subcloned into p2FGW7 (Invitrogen) to generate bHLH142-GFP fusion genes driven by the CaMV 35S promoter. Rice protoplasts were isolated and transformed using the polyethylene glycol (PEG) method following procedures described previously34. After incubation at room temperature for 16 h in light, protoplasts were observed with a Zeiss LSM 780 laser scanning confocal microscope.
  • Phylogenetic Analysis of the bHLH142 Subfamily
  • The bHLH142 protein sequence was used to search for the closest homologues from their plant species using BLASTP programs. Multiple sequence alignment of full-length protein sequences was performed using ClustalW online (http://www.ch.embnet.org/software/ClustalW.html), and the alignment was used to perform neighbor-joining analysis using Mega 5.0535. The numbers at the nodes represent percentage bootstrap values based on 1000 replications. The length of the branches is proportional to the expected numbers of amino acid substitutions per site. Gene identification numbers used to generate the phylogenetic trees and the alignment are listed in Table 2.
  • TABLE 2
    Peptide Sequences Used for Phylogenetic Analysis
    Seq-
    uence
    Peptide ID. Peptide sequence (N′ → C′) ID
    BradXP_003567568 myhpqcellmphesldmdavvgqshlaasgvsaipaelnfhllhhsfvdtaaspqpptvdyffpgtdpppaa SEQ ID 
    vqfeqlaatnhhamsmlrdyygqqypaetylrggprtttagssslvfgvahddesaaynmvgpfvesspttr No. 78
    aagggrkrnrgsraaggpahggvekkekqrrlrltekytalmllipnrtkedratvisdaieyiqelgrtve
    eltllvgkkrrrngagehhlhqgdvvdaapavgaagelvlaaessegevqaplaalqpirstyiqrksket
    fvdvrivedevnikltkrrrdgclaaasralddlrldlvhlsggkigdchiymfntkihqgspvfasavas
    klievvdey
    TriuEMS50437 myhqqcellmphegldmdagqshhlaagsavpaelnfhllsyvdtavspqqptveyffggadqphaqfeqla SEQ ID
    anhqamtvlrdyygqyhpatadaylpgggprtgssslvfgaaeeesaymvggfqcspkprasgsrkrgrgag No. 79
    ssfhgfpanggvekkekqrrqrlsekftalmllipnrtkedratviydaieyiqelgrtveeltllvekkrg 
    rrehqgdvvdpaptlvagdgecsagevaaavmpampappqpirstyiqrrsketfvdvrivedevnikltkr
    rrdgclaaasralddlhldlvhlsggkigdchiymfntkihpgspvfasavasklievvdey
    SbXP_002457706 myhpqcellmaheaqdldaagqphhlavsgvagsipaelsfhllhsldataavnnsvtpqstidyflgvggad SEQ ID 
    phqpaalqyeplpppgghhqhtmnmlrdycsnggggghyptaepylrgtrtgalvfgatdddesaaaympggp No. 80
    fvetspppratggrkrgralgggfhaglangvekkekqrrqrltekytalmhlipnvtkpdratvisdaieyi 
    qelgrtveeltllvekkrrrrelqgdvvdaaptavvvaaaatggeaessegevappppppaavqrqpirstyi
    qrrskdtsvdvriveedvnikltkrrrdgclaaasralddlrldlvhlsggkigdchiymfntkihkgssvfa
    savasrlmevvdey
    ZmLOC100283549 Myhpqcelltmahetpdldagqphltvsgvasipaelsfhllhsldaaaavnpvtappqstidyfiggadphqq SEQ ID 
    amqyeplppaagghhqytmdmfrdycdghyptaepyirgtmtgalvfgatddddsaaaympgghfetsppppratg No. 81
    rgrkrgralgggfhavlangvekkekqrrirltekytalmhlipnvtktdratvisdaieyiqelgrtveelti
    lveklelqgdvvdaapaavvaaageaessegevappppavprqpirstyiqrrskdtsvdvri
    veedvnikltkrrrdgclaaasraldcllrldlvhlsggkigdcqiymfntkihkgssvfasavagrlmevvdey
    AegtEMT16792 myhqqcellmphedldmdagqshhlaaasavpaelnfhllsyvdaavspqqptveyffggadqphahsfhgfpang SEQ ID 
    gvekkekqrrqrlsekftalmllipnrtkedratviydaieyiqelgrtveeltllvekkrgrrehqgdvvdp No. 82
    aplvvagegecsagelrappppppqpirstyiqrrsketfvdvrivedevnikltkrrrdgclaaasra
    lddlhldlvhlsggkigdchiymfntkihpgspvfasavasklievvdey
    ZmEU974003 mvfskiqykvvsskiqtptlvrvetthetnmekkrrrrelqgdvvdaapaavvaaageaessegevapppp SEQ ID 
    avprqpirstyiqrrskdtsvdvriveedvnikltkrrrdgclaaasralddlrldlvhlsggkigdcqiy  No. 83
    mfntkihkgssvfasavagrlmevvdey
    VitvCBI38213 mcrkitrprrmyvyeenacfdgtksvaegddegfsqsvappptnnsfedstnmrvsmedasatmeielhqq SEQ ID 
    lafdmdqqcynsnndgndsnqvfsyemqemgfnhhqqqqedplllqqhqaemqnahqnfsaaypptpdllnlfhlpr No. 84
    ctpssllpnssisftnpdssataasgilydplfhlnlppqppvgggygdgddhrqfdngvlkftrdmacigkgregk
    gtksfatekqrrehlndkynalrslvpnptksdrasvvgdaieyirellrtvnelkllvekkrcgrerskrhktede
    stgdvkssssikpepdqsyneslrsswlqrkskdtevdvriiddevtiklvqrkkincllfvskildelq
    ldlhhvagghvgdyysflfntkiyegssvyasaianklievvdrqyaaipipipipptssf
    VitvCAN77001 Mymyeenacfdgtksvaegddegfsqsvappptnnsfedstnmrvsmedasatmeielhqqlafdmdqqcynsnn SEQ ID 
    dgndsnqvfsyemqemgfnhhhqqqddplllqqhqaemqnaqqnfsaaypptpdllnlfhlprctpssllpnss No. 85
    isftnpdssataasgilydplfhlnlppqppvfrelfqslphgynlpasrvgslfgggmdereasgggygdgddhrq 
    fdngvlkftrdmaciggregkgtksfatekqrrehlndkynalrslvpnptksdrasvvgdaieyirellrtvnelkl
    lvekkrcgrerskrhktedestgdvkssssikpepdqsyneslrsswlqrkskdtevdvriiddevtiklvqrkkin
    cllfvskildelqldlhhvagghvgdyysflfntkiyegssvyasaianklievvdrqyaaipipipipptssf
    VitvXP_002265098.2 mgrgfshllgfcksenplndlsrlksrysgpnlrlvhsesnrnnienmvdafpvqidlnfsdsrndkatqt SEQ ID 
    ishprvkhshqgarrrimrstnhaeqcqnkrgyrkitrprrmyvyeenacfdgtksvaegddegfsqsvappptnns No. 86
    fedstnmrvsmedasatmeielhqqlafdmdqqcynsnndgndsnqvfsyemqemgfnhhqqqqedplllqqhqae
    mqnahqnfsaaypptpdllnlfhlprctpssllpnssisftnpdssataasgilydplfhlnlppqppvfrelfqslp
    hgynlpasrvgslfgggmdereasgggygdgddhrqfdngvlkftrdmacigkgregkgtksfatekqrrehlndkyn
    alrslvpnptksdrasvvgdaieyirellrtvnelkllvekkrcgrerskrhktedestgdvkssssikpepdqs
    yneslrsswlqrkskdtevdvriiddevtiklvqrkkincllfvskildelqldlhhvagg
    hvgdyysflfntkiyegssvyasaianklievvdrqyaaipipipipptssf
    RiccXP_002534354.1 myeetgcfdpnsmvegaddglcqvlqippqpqplmagsttnshnsyeenlklsadqelsyhhsnnphhhhqeddas SEQ ID 
    asaaaametqlqnhqmgfdthlmqdssnqmafnsstslqdatfaqtpdllnlfhlprgstssllpnssisft No. 87
    npshtaplgfvgdlpmadtasassilydplfhlnlppqpplfrdlfqsIpphgyslpgsmvnslfgagvggddh
    vegsgdgggiyqdgdgeqqfdngvldftwdmpcmgkgrdagkktkpfaterqrrqhlndkykalqnlvpnp
    tkadrtsvvgdaidyikellrtvnelkllvekkrcarerskrqkteedsignghdsscitkplgdpdqsfnng
    slrsswierkskdtevdvriiddevtiklvqrkkincllfvskvldeIqIdlhhvagghi
    gdyysflfntkifegssvyasaianklievvdrhyastpstn
    PoptXP_002323376 myvetacfepnnsmvedvtddgfchaiplmagnsttnsfeehlklsmeefsshypqeesaaaasmeeiqlqhhmafs SEQ ID 
    nnntnhhlmqqyptqllsydhssnwdpniiqfqemhqvldqnssfdatantqsslppdllnlfnlprctststllpn No. 88
    ssisftnpahkaplgfmgvdntsarfdpytlapqphlfrelvqslpphgytlptplfgggqgddhvdgqsggglsyq
    dgdhgdgvfeftdemacigkgikktgkvtkhfaterqrrehlngkytalrnlvpnpskndrasvvgeaidyikellr
    tvqelkllvekkrcgrerskwrkteddggvevldnsdikvepdqsaysngslrsswlqrkskdtevdvrliedevti
    klvqrkrvncllyvskvldelqldlhhaaggligdyysflfntkinegscvyasaianrlievvdrqyasstttvpa
    agscy
    Zm_HLH_ miagggyfdgshdhilmegsmihdssqssiydntdveqqnfrfapfiiedhsnpanltseaarvidqiqhqIgidie SEQ ID 
    containing_ qdhsdhmmqevppaetenlvpavygvqdhilshqiegphnitveqqvlgydpasyrngtyaaahdllnslhiqrcsl No. 89
    protein ipefpstehifsdpaqnmvnrlditndlpgvanhesgmmfsdstvplgyhatqshmlkdlyhslpqnyglftsdde
    rdgmvgvpgvsgnifgeidgrqfdspilgsrkqkggfgkgkgkanfatererrxqfnvkygalrslfpnptkndra
    sivgdaieyinelnrtvkelkillekkrnsadrrkilkldeeaaddgesssmqpvsddqxnqmngtirsswvqrrs
    kecdvdvrivddeinikftekkransllcaakvleefhlelihvvggiigdhhifmfntkipkgssvyacavakkl
    leaveikkqaynifn
    PoptXP_002308327 myeetacfetnnsiveggnddgfcqvspfmtgssttssfeesfklsmeelsnhyhqeesaaaasmeeiqlq SEQ ID 
    hhmafnnnchhlmeqyptnhhqvlsydhpsnwdpntiqfqemhqvldqngnfnatantpssllpdllnlfn No. 90
    lprctststllpnssisftnpahktpsgfmgvdstsvlfdsnplapqfrelvhslpphgyglpaplfgggq
    ggdhvdglsggglsyqdgghgdgvfeftaemacigkgirksgkvitkhfaterqrrehlngkytalnlvpn
    pskndrasvvgdainyikellrtveelkllvekkrngrerikrrkpeedggvdvlensntkveqdqstynn
    gslrsswlqrkskhtevdvrliedevtiklvqrkkvncllsvskvldelqIdlhhaaggligdyysflfnt
    kinegscvyasgiankllevvdrqyasstsvpaasc
    SbXP_002452697 miagggyfdgshdhilmegsmihdssqssiydntdveqqnfrlapfiiedhsnpanltseparvidgihh SEQ ID 
    qlgidmeqdhsdhmiqgvppaetanlvpvvygvqdrilshqiegphnitveqqvldydpasygngtyaaa No. 91
    hdllnslqiqrcslipefpstehifgdpaqnmvnplditndlqgvathesgmmfsdstlplgyhatqshm
    lkdlyhslpqnygiftsdderdgmvgvagvsgnifqeidgrqfdspvlgtrrqkggfgkgkgkanfater
    erreqlnvkygalrslfpnptkndrasivgdaidyinelnrtvkelkillekkrnstdrrkilklddeaa
    ddgesssmqpvsddqnnqmngairsswvqrrskecdvdvrivddeinikftekkransllca
    akvleefrlelihvvggiigdhhifmfntkipkgssvyacavakklleaveikkgalnifn
    MedtXP_003638306 mssgsgdkqnmheqngcfdpntkdegvenspndnntnnnnsleenfkpsveelpyhnhqnsqhlddvstytngftp SEQ ID 
    ssvdieqlqnlglnigntynnmdnhlvqevyqnstwdpsvqdmdyvnhqehrqlseqqyqqfieaqnhnqsynpst No. 92
    ildphypspdvlnllnlprcssslltnssticmtnptqnppnfhnsmtflgdlpigssdntsgssvlydplyplnlp
    pqppalrelfqslprgysmptnsrngslfgggdemegdgdmgvlefnrvtasvgkgrggkatkhfatekqrreqlng
    kykilrdlipsptktdrasvvgdaieyirelirtvnelkllvekkrhgremckrlkteddaaescnikpfgdpdgsi
    rtswlqrkskdsevdvriidddvtiklfqrkkvncllfvskvldelqlelhhvagghvgeycsflfnskvnegssvy
    asaianrvidvmdtqyaaglphisrl
    MedtXP_003638303 mssgsgdnqnmheqtgcfdpdtmaegvenspednnspqtmpnqvvagnsnnsieenfrpsveefsyhnhhspqhl SEQ ID 
    edvstytngftpsseniaqqnlglnignyyynnmdnlleqevyqnsswdpsaqdmdyanhqeyhqlhnhkqsynps No. 93
    ttqaphypspdvlnlhfprssasslltnpsticitnptqkppnfhysmsflgdlpigsdnssgssvlydplfplnl
    paqspalrelpqslprvysmptnsrngspfgggdemegdggmgvsqfnkvtafvgkgkgkatehlttekqrreglk
    grykilrslipnstkddrasvvgdaieylrelirtvnelkllvekkrheieickrhktedyaaeschmkpfgdpdg
    sirtswlqrkskdsevdvriidddvtiklfqrkkvncllfvskvldelqlelnhvagghvgeycsflfnskviegs
    svhasaianrvidvldtqyaavvphnrm
    CucsXP_004173553 meldfqqaaaaptpgfdgeltsdsnpmlcldqsnwvgtqiqemgfnhnhvqsqfsdsaipptpytqppdllnflnmp SEQ ID 
    ptarcsnnssisfsnlhtpamgaflgdlppgdapnssstslsilydplfhlnlppqpplfrelfhsIphgygmpaa  No. 94
    ssrgrggslfpegseiveregtagvyedgdgsgvlefsrdmadcigkrrdgkmtkhfaterqrrvqlndkykalrslv
    piptkndrasivgdainyiqellrevkelkllvekkrssrerskrvrtaeeieqgggsessnakggegvvedqrynlr
    sswlqrktkdtevdvrivddevtvklvqrklnclllvsklledlqldlhhvagghigdyysflfntkiyegss
    vyasaiankvmeavdrqynntsispltnty
    BradXP_003580474 Miiggdyfegshdhslmagslihdssqapkcngntdielqkfkvpsfsseiltnstnlsseaarainhlqhqlg SEQ ID 
    idleqdmqpvetatwdasicsiqdhiinnqisedpqnilveqqiqqydaaiypnssytpapdllnllhctvapa No. 95
    fptttsvfgdtslsstnyldlngeftgvaatpesglmftsdsalqlgyhatqshplkdichslpqnyglfpgede
    revmigvgsvggdifqdiddrqfdtvlecrrgkgefgkgkgkanfatererreqlnvkyktlkdlfpnptksdra
    svvgdaieyidelnrtvkelkilveqkwhgnkrtkiikldeevaadgesssmkpmrddqdnqfdgtirsswvqr
    rskechidvrivenevnikltekkkvnsllhaarvldefglelihavggiigdhhifmfntkv
    segssvyacavakrllqavdaqhqainifh
    CucsXP_004139000 myeetecsdpnsispetmphisafpnsfpppliaqqthpnfhhnnnlnlsidhisyhhhstalqpadameld SEQ ID 
    fqqaaaaptpgfdqeltsdsnpmlcldqsnwvgtqiqemgfnhnhvqsqfsdsaipptpytqppdllnflnm No. 96
    pptarcsnnssisfsnlhtpamgaflgdlppgdapnssstslsilydplfhlnlppqpplfrelfhslphgyg 
    mpaassrgrggslfpegseiveregtagvyedgdgsgvlefsrdmadcigkrrdgkmtkhfaterqrrvqlndky
    kalrslvpiptkndrasivgdainyiqellrevkelkllvekkrssrerskrvrtaeeieqgggsessnakggegv
    vedqrynlrsswlqrktkdtevdvrivddevtvklvqrklnclllvsklledlqldlhhvagghigdyysflfntki
    yegssvyasaiankvmeavdrqynntsispltnty
    AegtEMT05766 miaeggyfdgsrdailmagslihdsldsicdnteieqgnfhgpsffiedicnptnltsesartinhiqhraefdmdq SEQ ID 
    dlhghmiqetqvetsnwvpamfgtqnhiisqqsieqqmddydaasypdgahtaapdllnllqiprysmttafpstehi No. 97
    fgdpgqnagnqldinndvlgraihdsgmmlgdstlplqyndnqshlfkdlyhslpqsfglfssdderdramgvvgaa
    gnilqeidgrqfgspklgrskkggfgkakanfatekerreqinvkygalrsllpsptkndrasivgdaieyinelnr
    tlkeltslvegdtkhrmkrlkldddaacdngessslqqvkddqdsqlngairsswiqrrskechvdvrivgnein
    ikftekkktnsllcaakvidefrlelihvvggvigdqrifmfntkisegssvyasalaskllramemehlavdifs
    FravXP_004308623 myvdsstaaagacnfdpntdtnpmsesapevvlhhqnnpttfasthdenlrslsmeeelsnyhhnhnaameieq SEQ ID 
    qlqtemgfgtmdqntnntnphlinpfdthqatnwdnndemqqqqqlppvaptpdllslfhlpnssvlphssitft No. 98
    npktpggcfpgsfgyetlpetpsgavasnsvmydpmfhlnqlppqpqpplfrellqslphgykrngsslfsnggde
    vddgsrqlfengvlefskemkpfgrgrggnkgtkhfaterqrrvqlndkfsalrelvpnptkpdrasvvgdaidyi
    qelkrtvselkllvekkrcgrerskrhkteqdigardddescnmkplgdpdhdhsynngslrsswlqrksk
    dtevdvriiddevtiklvqrkkinlllsvsklldelqlelhhaagghignsysflfntkmyegsslyas
    aianklidtvdrqyaaaipptnsy
    AegtEMT07628 miwiegarhcfvkmivggdyfegshdhnlmtgslthdsslapkcndntnielgrfkvqsfsadilsdstnlsseaar SEQ ID 
    ainhlqhqlgigleqdmppvetatwdtsictiqdqiinhqlsedpqnilvqqqiqqydaalypnsgytpapdllnllh No. 99
    ctvapvfpatasvfgdtalsggtnyldlngeftgvaaipdsglmytsdpalqlgyhaapshalkdichslpqnyglfp
    sederdvmlgvgsvggdlfqdmddrqfetvlegrrgkgefgkgkgkanfatererreqlnvkyktlrmlfpnptkndr
    asvvgdaieyidelnrtvkelkilveqkwhgtnrrrirkldeeaaadgesssmrpmrdeqdnqldgairsswvqrrsr
    echvdvriveneinikltekkkanssllhvakvldefhleiihvvggiigdhyifmfntkvtegssvyacavakri
    lqavdaqhqaldifn
    AralXP_002879311 Myeesscfdpnpmvdnngsfcaaettfpvshqfqppvgsttnsfnddlklptmeefsafpsvislpnsetqn SEQ ID 
    qnisnnnhlinqmiqepnwgvsedntgffmntshpnttttpipdllsllhlprcsmalpssnlsdimagscf No. 100
    tydplchlnlppqpplipsndysgyllgidtntttqgdesnvgdennnaqfdsgiiefskeirrkgrgkrkn
    kpfttererrchlneryealkllipnpskgdrasilqdgidyinelrrrvselkylverkreggrhknneld
    nninnnnsndhdndeddiddenmekkpesdvvdqcssnnslrcswlqrkskvtevdvrivddevtikvvqkk
    kinclllvskvldqlqldlyhvaggqigehysflfntkiyegstiyasaianrvievvdkhymaalpiny
    AralXP_002892324 megggmfeeigcfdpnapaemtaessfspaeppptitvigsnsnsncsledlsefhlspqdsslpasasay SEQ ID
    vhqlhvnatpncdhqfqssmhqtlqgpsypqqsnnwdngyqdfvnlvpnhttpdllsllqlprsslppfan No. 101
    pslqdiimttsssvaaydplfhlnfplqppngtfigvdqdqteienqgvnlmydeennnldnglnrkgrgs
    rkrkvfptererrvhfkdrfgdlknlipnptkndrasivgeaidyikellrtidefkllvekkrtkqrnre
    gddvidenfkaqsevveqclinkkrtnahtswlkrkskftevdvriidddvtikivqkkkinclvfvskvv
    dqlqldlhhvagaqigehhsflfnakicegssvyasaiadrvmevlekqymealstnngyhcyssd
    AtbNP_180679 myeesscfdpnsmvdnnggfcaaettvshqfqpplgsttnsfdddlklptmdefsvfpsvislpnsetqnqnisn SEQ ID 
    nnhlinqmiqesnwgvsednsnffmntshpnttttpipdllsllhlprcsmslpssdimagscftydplfhlnlp No. 102
    pqpplipsndysgyllgidtntttqrdesnvgdennnaqfdsgiiefskeirrkgrgkrknkpfttererrchlner 
    yealkllipspskpskgdrasilqdgidyinelrrrvselkylverkrcggrhknnevddnnnnknlddhgneddd
    dddenmekkpesdvidqcssnnslrcswlqrkskvtevdvrivddevtikvvqkkkinclllvskvldqlqldlhh
    vaggqigehysflfntkiyegstiyasaianrvievvdkhymaslpnsny
    AtbCAD58593 myeesscfdpnsmvdnnggfcaaettvshqfqpplgsttnsfdddlklptmdefsvfpsvislpnsetqnqnisnn SEQ ID 
    nhlinqmiqesnwgvsednsnffmntshpnttttpipdllsllhlprcsmslpssdimagscftydplfhlnlppq No. 103
    pplipsndysgyllgidtntttqrdesnvgdennnaqfdsgiiefskeirrkgrgkrknkpfttererrchlnery 
    ealkllipspskpskgdrasilqdgidyinelrrrvselkylverkrcggrhknnevddnnnnknlddhgnedddd
    ddenmekkpesdvidqcssnnslrcswlqrkskvtevdvrivddevtikvvqkkkinclllvskvldqlqldlhhv
    aggqigehysflfntkiyegstiyasaianrvievvdkhymaslpnsny
    AtbNP_172107 mggggmfeeigcfdpnapaemtaessfspaeppptitvigsnsnsncsledlsafhlspqdsslpasasaya SEQ ID 
    hqlhinatpncdhqfqssmhqtlqgpsypqqsnhwdngyqdfvnlgpnhttpdllsllqlprsslppfanpsi No. 104
    qdiimttsssvaaydplfhlnfplqppngsfmgvdqdqtetnqgvnlmydeennnlddglnrkgrgskkrki
    fptererrvhfkdrfgdlknlipnptkndrasivgeaidyikellrtidefkllvekkrvkqrnregddvvde
    nfkaqsevveqclinkknnalrcswlkrkskftdvdvriiddevtikivqkkkincllfvskvvdqleldlh
    hvagaqigehhsflfnakisegssvyasaiadrvmevlkkgymealsanngyhcyssd
    GlymXP_003548659 myeesscydpdammaegaedcfpqmvseseavmsatptqththntfaysyscgedaanangpiamehpqqnpyn SEQ ID 
    ysntqfveelysnqqftyhtptpdlldllhlpnpipgdnrtnvssysydpylhlnlqqqqqptlrellphmpalrn No. 105
    dfpfggaaggddiqdfgnglvdftlqqevgkrrggkrtkqftsttterqrrvdlsskfdalkelipnpsksdrasv
    vgdainyirelkrtveelkllvelkkrlekqrvmmrhkvetegessnldpaeyseslrsswiqrktkdtevdvri
    vdnevtiklvqrkkidclvhvshlldqlnldlqhvagghigdfcsylfntkicegssiyasaiankliqvmdts
    laaasla
    GlymXP_003524131 Mheqtgefdpntmgesvpflkdnfpqtlppspivvgnttnsnnnmdnhlvqevidaypyqlstwdpatvqelqdiay SEQ ID 
    anhteqqqqqqqneqqfqqietqncsqsynnpssildppypspdllnllhmprcsasslltnpsicltnptqntpn No. 106
    fqnpmaflgdltigsentsassvlydplfhlnlppqppalrelfqslprgyslptnsrngslfaggdemegdgsq
    ldmgvlefnrvtpsvgkgrggkatkhfatekqrreqlngkykilrnlipsptkligwvwfntddrasvvgdaidyi
    relirtvnelkllvekkryakerykrpkteedaaescnikpfgdpdggirtswlqrkskdsevdvriidddvtikl
    fqrkkincllfvskvldelqlelhhvagghvgeycsflfnskglvslrximegssvyasaianrvidvldsqyta
    avphtnsy
    GlymXP_003532668 mstgdrpkmhdqtgcfdpnttgesvpslkdnfpqtlppsspmvvgntttnsnnnmdnhlvqevidafpyqqstwdpti SEQ ID
    vqelqdmayanhteqtqqqqqneqqfqqfetqncsqsynnpssildppypspdllnllhmprcsasslltnpsicltn No. 107
    ptqntpnfqnpmaflgdlpigsentsassvlydplfhlnlppqppalrelfqslprgyslptnsrngslfgggdemeg
    dgsqldmgvlefnrvtltpsvgkgrrgkatkhfatekqrreqlngkykilrnlipsptklvgfvltqtdrasvvgda
    idyirelirtvnelkllvekkryakdrckrpkteedaaescnikpfgdpdggirtswlqrkskdsevdvriidddvt
    iklfqrkkincllfvskvldelqlelhhvagghvgeycsflfnskglvslrximegssvyasaian
    rvidvldsqyaaavphtnsy
    LotjACN21644 maegvssqkdsfpqtlldpqpqslmvtenttnsnnimdnhlvqevidaplyqqstwdpnvqevqdmsyanhpeqqf SEQ ID 
    qhidaqnycqsytpsildpsypspdllnflhlptcsasslltnppnicisnptqrtpnfqnsmtflgdlpmgpdnts No. 108
    assvlydplfhlnlppqppalrelfqslprgyrlptssrddslfgggdemegdgsqldmgvldfnrdtasvgkgre
    gkgakpfatekdrreqlngkykilrslipnptkligwvlfkpdrasvvgdaieyirelirtvnelkllvekkrher
    erckrpkneedaeescnikpfgdpdgyirtswlqrkskdsevdvriidddvtikffqrkkincllfvskvldelq
    lelhhlagghvgeywsflfnskrpvsltqviegssvyasaianrvidvldsqyaaavpqtssy
    AtbAAL55717 mgcfdpntpaevtvessfsqaeppppppqvlvagstsnsncsveveelsefhlspqdcpqasstplqfhinpppp SEQ ID
    ppppcdqlhnnlihqmashqqqhsnwdngyqdfvnlgpnsattpdllsllhlprcslppnhhpssmlptsfsdim No. 109
    ssssaaavmydplfhlnfpmqprdqnqlrngscllgvedqiqmdanggmnvlyfegannnnggfeneilefnngv
    trkgrgsrksrtsptererrvhfndrffdlknlipnptkidrasivgeaidyikellrtieefkmlvekkrcgrf
    rskkrarvgeggggedqeeeedtvnykpqsevdqscfnknnnnslrcswlkrkskvtevdvriiddevtiklvqk
    kkincllfttkvldqlqldlhhvaggqigehysflfntkicegscvyasgiadtlmevvekqymeavpsngy
    AtbNP_180680 meeereslyeemgcfdpntpaevtvessfsqaeppppppqvlvagstsnsncsveveelsefhlspqdepqasstp SEQ ID 
    lqfhinppppppppcdqlhnnlihqmashqqqhsnwdngyqdfvnlgpnsattpdllsllhlprcslppnhhpssm No. 110
    lptsfsdimssssaaavmydplfhlnfpmqprdqnqlrngscllgvedqiqmdanggmnvlyfegannnnggfene
    ilefnngvtrkgrgsrksrtsptererrvhfndrffdlknlipnptkidrasivgeaidyikellrtieefkmlve
    kkrcgrfrskkrarvgeggggedqeeeedtvnykpqsevdqscfnkunnnslrcswlkrkskvtevdvriiddevt
    iklvqkkkincllfttkvldqlqldlhhvaggqigehysflfntkicegscvyasgiadtlmevvekqymeavpsngy
    OsBAD67851 Mdeqrgrggfdelvllhqqqeqrrrreqqqeeeeeevrrqmfgavvgglaafpaaaaalgcqqqvdcggelggfcdse SEQ ID 
    aggssepeaaagarprggsgskrsaaevhnlsekrrrskinekmkalqslipnsnktdkasmldeaieylkqlqlqvq No. 111
    mlsmrngvylnpsylsgalepaqasgmfaalggnnvtvvhpgtvmppvnqssgahhlfdlnsppqnqpqslilpsv
    pstaipeppfhlessqshlrqfqlpgssefhkilflhvllsvkdgvswrdnakappiitsrksarkrde
    lhqeriihvehq
    OsbHLH141_LOC_ mivgagyfedshdqslmagslihdsnqapassentsidlqkfkvhpystealsntanlaeaarainhlqhqlei SEQ ID 
    Os04g51070 dleqevppvetanwdpaictipdhiinhqfsedpqnilveqqiqqydsalypngvytpapdllnlmqctmapafpa No. 112
    ttsvfgdttlngtnyldlngeltgvaavpdsgsglmfasdsalqlgyhgtqshlikdichslpqnyglfpseder
    dviigvgsgdlfqpiddrqfdsvlecrrgkgefgkgkgkanfatererreqlnvkfrtlrmlfpnptkndrasi
    vgdaieyidelnrtvkelkilveqkrhgnnrrkvlkldqeaaadgesssmrpvrddqdnqlhgairsswvqrr
    skechvdvrivddevnikltekkkansllhaakvldefqlelihvvggiigdhhifmfntkvsegsavyaca
    vakkllqavdvqhqaldifn
    OsbHLH142_LOC_ myhpqcellmpleslemdvgqshlaaavaaampgelnfhllhsldaaaaaasstaasassqptvdyffggadqqpppp SEQ ID 
    Os01g18870 aamqydqlaaphhhqtvamlrdyygghyppaaaaaaateayfrggprtagssslvfgpaddesafmvgpfessptprs No. 113
    gggrkrsratagfhgggpangvekkekqrrlrltekynalmllipnrtkedratvisdaieyiqelgrtveeltllv 
    ekkrrrremqgdvvdaatssvvagmdqaaessegevmaaaamgavappprqapirstyiqrrsketfvdvrivedd
    vnikltkrrrdgclaaasralddlrldlvhlsggkigdchiymfntkihsgspvfasavasrlievvdey
    OsUDT_LOC_ mprrarargggggggeevkveddfidsvlnfggggggeedgddgeeeqqqqqaaaaamgkefksknleaerrrrg SEQ ID 
    Os07g36460 rlngnifalravvpkitkmskeatlsdaiehiknlqnevlelqrqlgdspgeawekqcsascsesfvptenahyq No. 114
    gqvelislgsckynlkifwtkraglftkvlealcsykvqvlslntisfygyaesfftievkgeqdvvmvelrsll
    ssivevpsi
    OsTDR_LOC_ mgrgdhllmknsnaaaaaaavngggtsldaalrplvgsdgwdyciywrlspdqrflemtgfccsseleaqvsal SEQ ID 
    Os02g02820 ldlpssipldsssigmhaqallsnqpiwqssseeeeadggggaktrllvpvagglvelfasrymaeeqqmaelv No. 115
    maqcggggagddgggqawpppetpsfqwdggadaqrlmyggsslnlfdaaaadddpflgggggdavgdeaaaag
    awpyagmavsepsvavaqeqmqhaagggvaesgsegrklhggdpeddgdgegrsggakrqqcknleaerkrrkk
    lnghlyklrslvpnitkmdrasilgdaidyivglqkqvkelqdelednhvhhkppdvlidhpppaslvgldndd
    asppnshqqqpplavsgsssrrsnkdpamtddkvggggggghrmepqlevrqvqgnelfvqvlwehkpggfvrl
    mdamnalglevinvnvttyktlvlnvfrvmvrdsevavgadrvrdsllevtretypgvwpspqeeddakfdggd
    ggqaaaaaaaaggehyhdevgggyhqhlhylafd
    • Yeast Two Hybrid (Y2H) Assay
  • The MATCHMAKER GAL4 Two-Hybrid System (Clontech, USA) was used for Y2H assays. Since both full-length EAT1 and TDR1 proteins were reported having self-activation (Ji et al., 2013), we made a truncated EAT1 (EAT1Δ, amino acids 1-254) and a truncated TDR1 (TDRΔ, amino acids 1-344) to reduce self activation. The full length cDNA of bHLH142 was cloned into pGAD-T7 (Clontech, USA), and full length bHLH142, EAT1, TDR, EAT1Δ, and TDRΔ were cloned into pGBK-T7 (Clontech, USA), respectively. The pairs of constructs to be tested were co-transformed into AH109 yeast cells and selected on plates containing Leu (for pGADT7 plasmid) and Trp (for pGBKT7 plasmid) dropout medium for 3-4 days at 30° C. Transformants were tested for specific protein interactions by growing on SD/-Leu/-Trp/-His plates with 30 mM 3-amino-1,2,4 triazole (3AT), and tested after X-α-Gal induction to confirm positive interaction. This system provides a transcriptional assay for detecting and confirming protein interactions in vivo in yeast.
    • Bimolecular Fluorescence Complementation (BiFC) Assay
  • BiFC assay allows visualization of protein-protein interactions in living cells and the direct detection of the protein complexes in subcellular compartments, providing insights into their functions. Full-length cDNAs of bHLH142, UDT1, TDR1, and EAT1 were independently introduced into pJET1.2 (Thermo Scientific). The sequence for the N-terminal amino acid residues 1-174 of YFP was then in-frame fused to the sequence of the C-terminal region of the tested proteins, while the sequence of the C-terminal amino acid residues 175-239 of YIP was in-frame fused to the sequence of the N-terminal end of the proteins. Next, the tested genes were introduced into pSAT5-DEST_CYN1 and pSAT4(A)-DEST_NYN1. Ballistic bombardment-mediated transient transformation in rice protoplasts was carried out following a previously published protocol36. Florescence images were photographed on a LSM 780 Plus ELYRA S.1 confocal microscope with Plan-Apochromat 40×/1.4 oil objective lens (Zeiss, Germany).
    • Co-Immunoprecipitation Assay
  • Recombinant proteins of bHLH142 and TDR1 fused with hemagglutinin (HA) tag were expressed in bacteria harboring pET-53-DEST (HIS-tag), and cell extracts after lysis were cleared by centrifugation at 12,000 rpm for 15 min, suspended in binding buffer (20 mM Tris-HCl, pH 7.9, 500 mM NaCl), and sonicated on ice for 30 s using an ultrasonic homogenizer (Misonix XL Sonicator Ultrasonic Cell Processor). The supernatants were purified using Ni2+ resin. For immunoprecipitation, extracts were pre-cleared by 30 min incubation with 20 μl of Pure Proteome Protein G Magnetic Beads (Millipore Co., Billerica, Mass.) at 4° C. with rotation. The antibodies (anti-bHLH142 or anti-HA) were then added to the pre-cleared extracts. After incubation for 4 h at 4° C., 40 μL of PureProteome Protein G Magnetic Beads was added, and the extracts were further incubated for 10 min at room temperature with rotation. After extensive washing, bound proteins were analyzed by western blotting. Rabbit antiserum against rice bHLH142 was produced using a synthetic peptide (CSPTPRSGGGRKRSR, SEQ ID No. 116) as antigen (GenScript Co).
  • RNAi-Mediated Gene Silencing of bHLH142
  • To generate an RNA intereference (RNAi) construct for suppressing the expression of bHLH142, a 149 bp fragment from 5′UTR region of bHLH142 was amplified by PCR with specific primers (Table 1) and cloned into pENTR (Invitrogen) to yield an entry vector pPZP200 hph-Ubi-bHLHI42 RNAi-NOS (12,483 bp). The RNAi construct was transformed into WT (TNG67) rice calli via Agrobacterium tumefaciens-mediated transformation system37. Transgenic plants were regenerated from transformed calli by selection on hygromycin-containing medium.
    • Examples Identification of a New Male Sterility Rice Mutant
  • From the T2 population of Taiwan Rice Insertional Mutants (TRIM) (http://trim.sinica.edu.tw) lines we identified a T-DNA-tagged rice mutant (denoted ms142) with a completely MS phenotype. In the field, this mutant produced no viable seeds but maintained a normal vegetative growth (FIG. 1A), with panicles and spikelet developing similarly to those of the wild-type (WT) (FIGS. 1B to 1E). The ms142 mutant exhibits normal opening of spikelets and elongation of anther filaments, and its anthers are exerted completely in the husk (FIG. 1E). However, the anthers of ms142 were significantly smaller in size and appeared yellowish white (FIG. 1H), and there were no pollen dehiscence (FIGS. 1B and 1E) and pollen grain filling (FIGS. 1F and 1G). The anthers of the ms142 mutant could not be stained by Sudan black due to the lack of lipid accumulation (FIG. 1I) and showed no pollen grain development (FIG. 1K). As revealed later, ms142 with a full MS is a null mutant.
  • Sequence Analysis of the T-DNA-Tagged Gene in ms142 Mutant
  • To determine T-DNA insertion copy number, Southern blot analysis of T2 mutant lines using hptII as a probe was conducted, and only a single band was detected in the mutant lines (FIG. 2A). Thus, the mutation in ms142 is due to a single T-DNA insertion. Analysis of flanking sequence tag (FST) in the TRIM database suggests that ms142 is a putative mutant with T-DNA inserted at 1257 bp from the ATG start codon in the 3rd intron of bHLH142 (RAP Locus Os01g0293100, MSU Locus Os01g18870). The protein encoded by the gene is annotated as a basic helix-loop-helix dimerization region bHLH domain containing protein (RiceXPro Version 3.0). The bHLH142 gene comprises of four exons and three introns. Furthermore, genotyping by PCR using specific primers acrossing the T-DNA insertion site verified its FST (FIG. 2). The primers are designed for the mutant allele (R+RB, amplicon=340 bp) and wild-type allele (F+R, amplicon=458 bp). Three primers sets were incorporated in one PCR reaction for genotyping.
  • Agronomic Traits of ms142 Mutant and Genetic Study
  • The agronomic traits of the mutant were examined in the selfed progenies of heterozygous mutant grown in the outdoor GMO net house. Heterozygous plants behaved similarly to WT in terms of vegetative and reproductive growth and produced fertile seeds. However, homozygous ms142 mutant plants exhibited similar plant height, panicle number, and panicle length to the WT, but produced no viable seeds.
  • To understand whether the sterility in ms142 is due to male sterility or female sterility, homozygous mutant was backcrossed with WT pollen; and all F1 plants displayed WT-like phenotype in growth and fertility (data not shown). These results imply that the female organs of ms142 develop normally. When the ms142 BCF1 was selfed, the BCF2 progenies segregated into fertile and sterile plants in a ratio of 3:1 (Table 3), suggesting the MS trait is controlled by a recessive gene. Consistent with mutant phenotype, backcross segregants showed MS only in the homozygous plants, indicating that the MS phenotype co-segregated with the genotype. Moreover, when the selfed seeds derived from heterozygous plants of T2, T3, T4, and BCF2 generations were planted in different years and different cropping seasons, the scoring of phenotype indicated that MS in ms142 is stable and not affected by cropping season or year. Again, the fertile and sterile plants segregated approximately in a 3:1 ratio, supported by Chi-square analysis (data for T4 and BCF2 shown in Table 4). Taken together, these genetic analyses validate that the MS in ms142 is controlled by a single recessive locus.
  • TABLE 3
    Genotype
    Trait WT like Heterozygote Homozygote
    Plant height (cm) 118.4 ± 7.9  116.7 ± 8   118.4 ± 7   
    Tiller number   8 ± 2.7   9 ± 2.4 13.8 ± 3.8 
    Panicle number  7.8 ± 2.7  8.7 ± 2.5 8.7 ± 2.1
    Ave. panicle length (cm) 20.1 ± 1.4 20.1 ± 1.5 20.2 ± 1.6 
    Panicle Fwt (g)  30.8 ± 12.6   34 ± 12.5 8.8 ± 3 
    Grain No./panicle 168.3 ± 28.1 164.3 ± 30.2  180 ± 31.2
    Fertile grain number 1137 ± 466 1248 ± 464  6 ± 4.2
    Grain fertility (%) 84.9 ± 7.5 86.6 ± 6  0.4 ± 0.2
    Grain yield/plant (g)  28.3 ± 11.3  31.3 ± 11.3 0.2 ± 0.1
    1000 grain wt. (g)  25 ± 0.8 25.2 ± 1  6.8 ± 1.2
    n = 27 62 22
  • TABLE 4
    Cropping season Wild type Heterozygous Homozygous X2
    BCF2 (n = 111)
    1st Crop
    No. of plant 28 61 22 1.59
    Grain fertility Fertile Fertile Sterile
    ms142 T4 (n = 119)a
    1st Crop
    No. of plant 30 58 31 0.07
    Grain fertility Fertile Fertile Sterile
    ms142 T4 (n = 120)a
    2nd Crop
    No. of plant 29 57 34 0.71
    Grain fertility Fertile Fertile Sterile

    Defects in Anther Wall and Pollen Development in the ms142 Mutant
  • To determine the defects in the anthers of ms142, we examined the anatomy of anther in WT and homozygous mutant. At the microspore mother cell (MMC) stage, the WT anther walls contained epidermal cell layer, endothecial cell layer, middle layer and tapetal cell layer (FIG. 3A). During the early meiosis stage, the microspore mother cells underwent meiosis to form tetrads of haploid microspores; the tapetal cells differentiated to form large vacuole; and the middle layer cells began to degenerate (FIG. 3B). At tetrad stage, the meiocytes formed tetrads (FIG. 3C). During the young microspore stage, free microspores were released into the anther locule, and the microspores developed and exine was deposited on pollen grain wall. The middle layers shrinked and the tapetal cell layers became very dense (FIG. 3D). At the mature pollen stage, the uninucleate pollen developed to trinucleate pollen with starch, protein, lipid, and other nutrients enriched in the pollen cytoplasm. At maturity, the tapetal cells were completely degenerated and the endothecial cell layers were thickening, ready for anther dehiscence (FIG. 3E).
  • At the MMC stage, there were no visible differences in the anthers between WT and ms142. The ms142 anther consisted of normal epidermis, endothecium, middle layer and tapetum (FIG. 3F). During early meiosis stage, however, ms142 microspore mother cells did not enter meiosis and formed abnormal organelles (FIG. 3G, indicated by arrows). Abnormal endoplasmic reticulum structure and apoptosis was also observed by transmission electron microscopy. The ms142 tapetal cells continuously became vacuolated and elongated, with some cells divided into two tapetum layers (FIG. 3G). The mid-layers of the mutant tapetum maintained their initial shapes, but failed to divide into four cells at tetrad stage (FIG. 3H). The ms142 mutant's microspores finally degenerated during the vacuolated pollen stage. The tapetal and middle layer cells contained a large vacuole, and the middle layer cells did not degenerate (FIG. 3I). Consequently, there were no mature pollen grains formed in the locules at the mature stage. The mutant anther wall still retained four to five layers of cells, i.e. epidermis, endothecium, middle layer, and one or two layers of tapetum cells. By contrast, the endothecial cell layer did not become thickened in the mutant even at the latter stage of anther development (FIG. 3J).
  • Mutated bHLH142 Causes Defects in Tapetal PCD
  • Histological analysis indicated that ms142 has abnormal anther morphology and aborted degradation of tapetal cells (FIG. 3). Thus, we suspect that mutation of bHLH142 might have altered tapetal PCD, which is responsible for tapetal degeneration3,12-14. Tapetal PCD is characterized by cellular condensation, mitochondria and cytoskeleton degeneration, nuclear condensation, and internucleosomal cleavage of chromosomal DNA33. Therefore, we performed the TUNEL assay to detect DNA fragmentation in the anthers of WT and ms142. A TUNEL positive signal began to appear in the tapetal cells of WT during meiosis and a strong TUNEL signal was detected during the young microspore stages (FIG. 4). In contrast, no DNA fragmentation was observed in the tapetal layer in ms142 throughout anther development (FIG. 4).
  • bHLH142 is a Nuclear Protein
  • The gene structure of bHLH142, shown in FIG. 5A, indicates that bHLH domain contains bipartite nuclear localization signal (NLS), and the gene is predicted to encode a protein of 379 amino acids with a theoretical molecular mass of 40.7 kDa and pI of 6.2.
  • The nucleotide sequence of bHLH142 is shown below:
  • SEQ ID NO: 1
    AAGAAACCAACTGCTTTCTCCTACCCAATATCACCCTTGCCCCTTTTAT
    ATACTCTTCCTCTCATCACCTTCTCGATCGGCCTCTCTCCTCTCCTCTC
    ATCAGCTCACACCCCCAACCAACAAACCTAGTTAATTTAGCTCTAGTTG
    GTTCATCCCTGCTGCACTGCGAGCTCAAGTAATCGATCTGAGCTCTGAA
    GAAAAAGGTGGTAGAGTGCGAGGAAGATGTATCACCCGCAGTGCGAGCT
    CCTGATGCCGCTTGAGAGCCTGGAGATGGACGTCGGCCAGTCGCACCTC
    GCCGCCGCCGTCGCAGCAGCCATGCCGGGGGAGCTCAACTTCCACCTCC
    TCCACTCGCTCGACGCCGCCGCGGCGGCTGCCTCCTCCACCGCCGCCTC
    GGCCTCCTCCCAGCCCACCGTCGACTACTTCTTCGGCGGCGCCGACCAG
    CAGCCGCCGCCGCCGGCGGCGATGCAGTACGACCAGCTGGCGGCGCCGC
    ACCACCACCAGACGGTGGCCATGCTGCGCGACTACTACGGCGGCCACTA
    CCCGCCGGCGGCGGCGGCGGCGGCGGCCACGGAGGCCTACTTCCGCGGC
    GGGCCAAGGACGGCCGGGTCGTCGTCGCTCGTGTTGGGGCCGGCCGACG
    ACGAGTCGGCCTTCATGGTCGGACCCTTCGAGAGCTCCCCGACGCCGCG
    GTCCGGCGGCGGCAGGAAGCGTAGCCGCGCCACCGCCGGCTTCCACGGC
    GGCGGGCCGGCCAACGGCGTCGAGAAGAAGGAGAAGCAGCGCCGCCTGC
    GGCTCACCGAGAAGTACAACGCCCTCATGCTCCTCATCCCCAACCGCAC
    CAAGGAGGATAGAGCGACGGTGATCTCAGACGCGATCGAGTACATCCAG
    GAGCTAGGGAGGACGGTGGAGGAGCTGACGCTGCTGGTGGAGAAGAAGC
    GGCGGCGGAGGGAGATGCAGGGGGACGTGGTGGACGCGGCGACCTCGTC
    GGTGGTGGCGGGGATGGATCAGGCGGCGGAGAGCTCGGAGGGCGAGGTG
    ATGGCGGCGGCGGCGATGGGCGCGGTGGCACCGCCGCCGCGGCAGGCGC
    CGATCCGGAGCACGTACATCCAGCGGCGGAGCAAGGAGACGTTCGTGGA
    CGTGCGGATCGTGGAGGACGACGTGAACATCAAGCTCACCAAGCGCCGC
    CGCGACGGCTGTCTCGCCGCCGCGTCGCGCGCGCTGGACGACCTCCGCC
    TCGACCTCGTCCACCTCTCCGGCGGCAAGATCGGCGACTGCCACATCTA
    CATGTTCAACACCAAGATTCATTCGGGATCTCCAGTGTTTGCAAGTGCA
    GTGGCCAGCAGGCTGATTGAAGTGGTGGATGAGTACTAACTAGCTCGAG
    CTAGCTAATTAGCCGACCGACCGATCGATATGATGAAAGTTTCTATGTT
    GCTAGCTAGCTAGGGTTCTTGGATGCATGAGTACTGAGTAGCTCTTTAA
    TTAATTTCCTTTTAATTTTAGACTGTTTAATTTGGATTGGTAAAGACTC
    GTGTTAGCTTTTGGGAGATCTTTGGTATGTCATGGTTTGCATGTATTAT
    TTTGGTCTACTTGGATAAATAATTGATGCTCTTTGAGACGTTAATTAAT.
  • The amino acid sequence of bHLH142 is shown below:
  • SEQ ID No: 2
    MYHPQCELLMPLESLEMDVGQSHLAAAVAAAMPGELNFHLLHSL
    DAAAAAASSTAASASSQPTVDYFFGGADQQPPPPAAMQYDQLAA
    PHHHQTVAMLRDYYGGHYPPAAAAAAATEAYFRGGPRTAGSSSL
    VFGPADDESAFMVGPFESSPTPRSGGGRKRSRATAGFHGGGPAN
    GVEKKEKQRRLRLTEKYNALMLLIPNRTKEDRATVISDAIEYIQ
    ELGRTVEELTLLVEKKRRRREMQGDVVDAATSSVVAGMDQAAES
    SGEVMAAAAMGAVAPPPRQAPIRSTYIQRRSKETFVDVRIVEDD
    VNIKLTKRRRDGCLAAASRALDDLRLDLVHLSGGKIGDCHIYMF
    NTKIHSGSPVFASAVASRLIEVVDEY
  • Since the bHLH proteins are characterized as TFs, we assumed that bHLH142 is localized in the nucleus. To verify its subcellular localization, we constructed a fusion gene of the green fluorescent protein gene (GFP) and bHLH142 under the control of the 35S promoter and the nos terminator for transient expression in rice leaf mesophyll protoplasts (FIG. 5C). As a positive control, NLS sequence was also fused to red fluorescent protein (RFP) gene using the same regulatory elements. These constructs were introduced into rice protoplasts by particle bombardment. As expected, with the GFP construct alone, free GFP was found in the nucleoplasm as well as in the cytoplasm. However, bHLH142:GFP fusion protein and the positive control of NLS:RFP were exclusively located in the nucleus (FIG. 5D). These results confirm that, as a TF, bHLH142 protein is localized in the nucleus.
    • Phylogenetic Analysis
  • To understand the evolutionary relationship of bHLH142 among various organisms, we used full-length bHLH142 protein sequence to NOM BLAST database and retrieved 21 homologs containing bHLH domain from 10 diverse terrestrial plants. The phylogenetic tree shows that UDT1 (bHLH164) and TDR1 (bHLH5) are in the same cluster, while bHLH142 and EAT1 (bHLH141) evolved and diversified into two separate clades. Phylogenetic analysis also suggests that bHLH142 is descended from a common ancestor of monocots. Rice bHLH142 shares a high similarity with the related proteins from Brachypodium distachyon, millet (Setaria italica), Triticum urartu, maize (Zea may), Sorghum (Sorghum bicolor) and Aegilops tauschii (FIG. 6). The conserved homologs of bHLH142 from the important cereal crops, such as maize, millet, sorghum and wheat, share 84.1%, 79.2%, 72.2%, and 78% similarity in amino acid sequence to the rice counterpart (Table 5). The maize homolog, GRMZM2G021276, is highly expressed in immature tassel and meiotic tassel and anther. In accordance, our RT-PCR data also verified that maize homolog is tissue specifically expressed in meiotic anther (FIG. 14). This result implies that the maize bHLH142 homolog may also play a similar role in anther and pollen development.
  • TABLE 5
    Crop Accession No. Amino acid similarity
    Sorghum XP 002457706 72.2%
    Maize ZmLOC100283549 84.1%
    Wheat EMS50437 78.0%
    Millet XP_004967599 79.2%
    Brachypodium XP_003567568 80.7%

    Expression Pattern of bHLH142
  • Both RT-PCR and qRT-PCR analyses with WT showed that the bHLH142 mRNA is accumulated in young rice panicle and anther only, but not in other tissues (e.g. root, shoot, leaf, lemma, palea, ovary, and seed). In particular, high levels of transcripts were found in developing panicles (FIGS. 7A and 7B). Specifically, bHLH142 transcripts were highly expressed in meiocyte mother cells (MMC) and extremely highly expressed in the anther at meiosis stage (FIG. 7C). Also, in-situ hybridization (ISH) clearly demonstrated the specific expression of bHLH142 in the anther but not in lemma and palea of WT spikelet at early meiosis stage (FIG. 7D). ISH with the cross sections of WT anther at various developmental stages showed positive signals in the tapetal layers at early meiosis stage and in the tapetal layers and meiocytes during meiosis stage, with decreasing signals at young microspore stage and negligible signals after vacuolated pollen stage. Interestingly, ISH signal was also detected in the vascular cells (FIG. 8), suggesting that the target genes of bHLH142 might also be associated with nutrient acquisition in the anther. On the contrary, there was no ISH signal detected in the anthers of the null mutant of ms142 (FIG. 8).
  • In addition, the expression patterns of various known pollen regulatory genes in the anther of WT versus ms142, as examined by qRT-PCR, confirmed the knockout of bHLH142 transcript in the ms142 null mutant (FIG. 9A). Also, expression of TDR1, bHLH141 (EAT1), AP37, AP25, CP1, CYP703A3, CYP704B2, MS2 and C6 was significantly down-regulated in the ms142 anther, relative to the WT anthers (FIG. 9E, 9G-9M). However, MSP1 and UDT1 transcripts were up-regulated in the mutant at MMC and meiosis stages (FIG. 9B-9C). There was no significant change in the GAMYB transcripts in ms142 (FIG. 9D). Interestingly, the suppression of TDR1 expression in ms142 was less, compared to other downstream genes (FIG. 9E-9M). In WT anther, bHLH142 transcript was more abundant during meiosis stage, but it was negligible in the ms142 null mutant. Interestingly, EAT1 mutant also showed a lower amount of bHLH142 mRNA during meiosis stage (FIG. 10). We also compared EAT1 mRNA expression in these mutants to gain more insights into the regulatory interplay of these TFs in pollen development. In WT, EAT1 was expressed slightly later (at young microspore stage) than bHLH142 (at meiosis stage) (FIG. 10). Interestingly, ms142 anther exhibited a similar amount of EAT1 mRNA to WT anthers at MMC, but tended to decline after young microspore stage (FIG. 10). Taken together, these data suggest that bHLH142 plays a role in the downstream of UDT1, but upstream of EAT1.
  • bHLH142 and TDR1 Coordinately Regulate EAT1 Promoter Activity
  • Based on the alternations in expression of known pollen regulatory genes in the different mutants (FIG. 9 and FIG. 10), we assumed that bHLH142 might regulate EAT1 promoter activity and carried out transient promoter assays with EAT1pro-Luc construct. Our results demonstrated that bHLH142 or TDR1 protein alone cannot drive the expression of EAT1pro-Luc independently. However, when combined, these two TF proteins together significantly increased Luc expression from the EAT1 promoter by up to 30 fold. However, additional expression of EAT1 in the same cells reduced Luc expression from a 30-fold down to an 18-fold increase, presumably due to the competition between EAT1 and bHLH142 in binding to TDR1 (FIG. 11). Apparently, TDR1 and bHLH142 co-regulate the activity of EAT1 promoter.
  • Protein Interactions Among bHLH142, TDR1 (bHLH5) and EAT1 (bHLH141)
  • We performed yeast two-hybrid analysis to determine whether bHLH142, as bait, interacts with the prey, TDR1 or EAT1. As previously reported that full-length EAT1 and TDR1 proteins possess self-activation activity in nature23,24, our Y2H study also confirmed this phenomenon (FIG. 12A). Therefore, we also constructed a truncated EAT1Δan(1-254) (truncated EAT1 at amino acids 1-254) and TDRΔna(1-344) (truncated TDR amino acids at 1-344) to eliminate self activation (FIG. 12A). Our results showed bHLH142 is not self-activated (FIG. 12A); only the yeast strains co-expressing both bHLH142 and TDRΔan(1-344) grew normally on stringent selection media (FIG. 13A) and there was no direct interaction between bHLH142 and EAT1Δaa(1-254). Thus, bHLH142 was not directly interacting with EAT1 as demonstrated in the yeast cells (FIG. 10A), and the retention of the C-terminal sequences of TDR1 is sufficient to confer the interaction of the two proteins. Clearly, the amino acid sequences in TDRΔaa(1-344) and EAT1Δaa(1-254) contain the interacting sites, consistent with the previous study24. These results are further supported by our results of EAT1 promoter assays in that both bHLH142 and TDR1 are required for the transcription of EAT1 (FIG. 11). Moreover, bimolecular fluorescent complementation (BiFC) assay showed that yellow fluorescent protein (YFP) signals are detected only in the nucleus of the rice cells co-expressing both NYN1-bHLH142 and CYN1-TDR1 and in the cells co-expressing both NYN1-TDR1 and CYN1-EAT1, but not in the cells co-expressing both NYN1-bHLH142 and CYN1-EAT1 (FIG. 13B). In vitro interaction of bHLH142 and TDR1 proteins was further validated by co-immunopreciptation (Co-IP) experiment, where interaction between HA fused TDR1 and bHLH142 was confirmed (FIGS. 13C and 13D). Taken together, all of these molecular data provide solid evidences of the physical interaction between TDR1 and bHLH142.
  • RNAi Transgenic Rice Lines Validate the Role of bHLH142 in Pollen Development
  • To further validate the biological function of bHLH142, we generated an RNA interference (RNAi) construct to suppress the expression of bHLH142 in rice. The gene specific region from the 5′UTR of bHLH142 was, amplified, fused with β-glucuronidase (GUS) intron and introduced into WT calli via Agrobacterium tumefaciens. All 16 TO RNAi transgenic lines obtained had a MS phenotype similar to the T-DNA mutant ms142. These RNAi lines showed reduced expression of bHLH142, as examined by RT-PCR, and produced poorly developed anthers without pollen grains (FIG. 14). This result further supports the notion that bHLH142 plays a key role in rice anther and pollen development. The RNAi fragment (SEQ ID No. 120):
  • caacaaacctagttaatttagctctagttggttcatccctgctgca
    ctgcgagctcaagtaatcgatctgagctctgaagaaaaaggtggta
    gagtgcgaggaagatgtatcacccgcagtgcgagctcctgatgccg
    cttgagagcct

    Overexpression bHLH142 Caused Male Sterility
  • For functional genomic study, we constructed overexpressing bHLH142 driven by constitutively express Ubiquitin promoter (FIG. 15A) and introduced into wild-type (TNG67 background) calli via Agrobacterium tumefaciens 38 Genomic PCR confirmed T-DNA insertion of target gene and selection marker hygromycin (lower panel) PCR has band in the 23 tested TO transgenic lines (FIG. 15B).
  • Interesting to observe that overexpressing bHLH142 TO transgenic plants all showed grain sterility (FIG. 16). Ubi::bHLH142 transgenic lines have similar plant type and panicle length (FIGS. 168 and 16C) with the WT except no grain filling after anthesis stage (FIG. 16A). It was observed anthers of overexpression transgenic lines were shorter and showed light yellow color than the WT (FIG. 16D). After seed maturation stage, grain of WT was filled with starch but there was no viable seed in those overexpressing lines (FIGS. 16E and 16F).
  • By using RT-PCR, we detected some regulatory genes associated with pollen development in rice. As expected, overexpression line constitutively express abundant of bHLH142 transcripts during various stages of anther development. Interestingly, Udt1 was simultaneously upregulated in the overexpression line. EAT1 mRNA also prematurely upregulated before meiosis stage but decrease its expression at latter stage of anther development. However, MS2 was significantly downregulated in the overexpressing line (FIG. 17). Defect of grain fertility in overexpressing line presumably due to prematurely upregulation of tapetal program cell death genes such as UDT120 and EAT123. Moreover, downregulation of MS2 that reported contribution to pollen exine development might associate with the defect of pollen development in the overexpression line.
  • Heterologuos Overexpression bHLH142 Confers Male Sterility in Maize
  • Since bHLH142 shares high identity with maize38, and gene specific primer sets were designed from homolog of maize ZmLOC100283549 (denoted Zm-142). RT-PCR indicated that Zm-142 was not expressed in vegetative organs of maize such as leaf, root, shoot, and stamen. Interestingly, Zm-142 specifically expressed in floret of 1 mm to 7 mm length but not detectable at later stage and in the mature pollen (FIG. 18). The expression pattern of Zm-142 was similar to bHLH14238.
  • Therefore, we use the similar construct of overexpression bHLH142 in FIG. 15A was transformed into maize (in cultivar Crystal White background) using agrobacterium-mediated pollen transformation method. One transgenic maize showed obvious male sterility phenotype with smaller angle of tassel branch (FIG. 19A, right panel) than the WT (FIG. 19A, left panel). Closed up tassel during anthesis stage, WT has larger anther than transgenic line and it has normal opening of spikelets and elongation of anther filaments during anthesis stage (FIG. 19B, left panel). Whilst, anther of transgenic maize were significantly smaller in size and anther was completely no elongation of anther filaments (FIG. 19B, right panel). Morphology of spikelet of WT at one day before anthesis was shown in FIG. 19C (left panel) with long and fat anther, but anther of transgenic line was short and shrinkage (FIG. 19C, right panel). Stained of maize mature pollen grains with I2/KI solution, and the fertile WT pollen grains stained with dark red color. However, pollens of transgenic line could not be stained and transparent due to no starch accumulation. That implied transgenic line was male sterile (FIG. 19D).
  • Overexpression bHLH142 Induces Reversible Male Sterility in Low Temperature
  • bHLH142-overexpressed plants also showed a completely male sterile phenotype during summer season (FIG. 20, left panel). By contrast, during winter low temperature conditions, anthers of overexpression transgenic line produce many pollen grains inside the locules and their pollen grains can be stained by I2/KI solution, indicating that the plants have restored the fertility (FIG. 20, right panel). Therefore, this novel functionality nature of our target bHLH142 has a big advantage over other genetic MS (GMS) genes for hybrid crop production. This reversible pollen fertility trait makes it more desirable in producing hybrid crop seeds just in one cross without the need to maintain the seed stocks of the MS lines as with cytoplasmic MS (CMS). In addition, biotech companies are known to prefer adopting overexpression over suppression approach in generating transgenic lines because overexpression lines are more stable than RNAi or antisense knock-down lines.
  • Rice bHLH142 have homologous in maize, sorghum and wheat, and they share more than 70% similarity in amino acid sequence to the rice counterpart (Table 3). This will benefit to genetic engineering male sterile for F1 hybrid seed production and generating hybrid vigor (heterosis) in terms of growth and grain yield in cereal crops.
  • bHLH142 is a New Major Regulator of Rice Anther Development
  • So far, three of the bHLH TFs have been shown to be involved in pollen development in rice and mutations of these TF genes all lead to complete MS, including UDT1 (bHLH164)20, TDR1 (bHLH514, and EAT1/DTD1 (bHLH141)23,24. They all play an important role in pollen development by regulating tapetal PCD. In this invention, we identified a novel rice MS mutant, ms142 (FIG. 1), with T-DNA inserted in the intron of bHLH142, which encodes another basic helix-loop-helix dimerization region bHLH domain containing TF protein. The phenotype is characterized by having small anthers without pollen grain development (FIG. 1). Genetic analyses suggest that the mutation is due to a single T-DNA insertion event. We further show that this TF is located in the nuclei (FIG. 5) and plays an essential role in regulating rice pollen development. Close anatomical examination of anther development, in parallel with TUNEL assay of DNA degradation and ISH of key gene transcripts, in the null mutant demonstrate that defects in microspore development is associated with defects in tapetal PCD. Timely degradation of tapetum cells is essential for viable pollen development. Furthermore, suppressed expression of bHLH142 in WT rice by RNAi confers the MS phenotype (FIG. 21). Thus, this invention identifies the involvement of another bHLH TF in the dynamic regulation of pollen development in rice and likely in other plants as well.
  • Our analysis of expression profile of known regulatory genes involved in pollen development demonstrates the down-regulation of several genes, such as TDR1, EAT1, AP37, CP1, C6, MS2, etc. in ms142 during pollen development (FIG. 9). Therefore, we suggest that bHLH142 participates in the same regulatory pathway of anther development, with a higher gene hierarchy (FIG. 10). An earlier study reports that TDR1 positively regulates CP1 and C614, while a recent study suggests that EAT1 interacts with TDR1 in regulating the expression of two aspartic protease genes, AP25 and AP3723. Another study also reported that mutation in DTD (same as EAT1, bHLH141) in rice results in severe MS24. In consistent with this report, we also find that the NIAS Tos17 mutant H0530, a knockout of EAT1 (bHLH141) gene, also fails to produce pollens (FIG. 10B). However, the eat1/dtd mutant exhibits normal meiosis process, but ms142 cannot exceed beyond meiosis cell division, which may be due to the extra role played by bHLH142. Consistent with this notion, our ISH analysis revealed that, besides tapetal layer, bHLH142 is also expressed in meiocytes as well as in the vascular bundle (FIG. 8). This result suggests that bHLH142 might also play an additional role in nutrient acquisition for cell plate formation during microspore development.
  • This invention uncovers bHLH142 as another critical factor in the bHLH TF family for pollen development, besides UDT1 (bLHL164), TDR1 (bLHL5) and EAT1 (bHLH141). Our mutagenesis analysis suggests that the gene hierarchy of bHLH142 is in the downstream of UDT1 (bHLH164) but upstream of TDR1 (bHLH5) and EAT1 (bHLH141) (FIG. 10 and FIG. 9). Interestingly, all these 4 bHLH TFs are tissue specifically expressed in the anther and participate in the important process of sequential pollen development events, particularly in tapetal PCD. Thus, it is rather unique in that several of the bHLH TFs coordinate in regulating the anther development; and it is likely that more TFs might be involved in controlling the regulatory network to ensure normal pollen development.
  • Also, we noticed a lower suppression in expression of TDR1 in ms142, compared to other downstream genes in the regulatory network, which may be attributed to the fact that TDR1 is also known to be regulated by another TF GAMYB22. In agreement, we also found that the expression of GAMYB is not altered in ms142 (FIG. 9). Taken together, these results suggest that two parallel pathways may exist in the regulatory circuit leading to TDR1 during pollen development.
  • bHLH142 Functions Coordinately with TDR1 to Regulate EAT1 Promoter
  • Since TDR1 and EAT1 mRNA are both down-regulated in ms142, we hypothesize that TDR1 interacts with bHLH142 and positively regulate EAT1 promoter for transcriptional activities of AP25 and AP37, encoding aspartate proteases for tapetal PCD. Our promoter transient assay provides solid evidence that bHLH142 and TDR1 work coordinately in regulating EAT1 promoter (FIG. 11). We also demonstrates that additional expression of EAT1 protein significantly reduced EAT1-Luc promoter strength from a 30 fold down to 18 fold increase (FIG. 11), which may be attributed to the competition between bHLH142 and EAT to interact with TDR1. Presumably, more EAT1 favors TDR1-EAT1 interaction and might consequently reduce the interaction between bHLH142 and TDR1, therefore reducing EAT1 transcriptional activation (FIG. 11). It is likely that bHLH142 interacts with TDR1 and TDR1 in turn interacts with EAT1 and bHLH142 does not directly interact with EAT1 (FIG. 13). Whether some other TFs may be required to regulate the transcription of bHLH142 is worth further investigation to unravel the entire regulatory gene hierarchy.
  • Our molecular studies provide solid in vivo (Y2H, BiFC) and in vitro (co-IP) evidences that both bHLH142 and TDR1 can form protein interaction (FIG. 13). The co-IP provides the most convincing evidence that the two proteins physically interact in vitro. Subcellular localization also demonstrates that bHLH142 protein is localized in the nucleus (FIGS. 5D and 13B) and its protein is not self activated (FIG. 13 and FIG. 12). Since we also found self activation of full length TDR1 and EAT1 in our Y2H experiment (FIG. 12), N-terminal truncated forms of TDRΔaa(1-344) and EAT1Δaa(1-254), were used in our experiment to reduce self activation. These two N-terminal truncated protein forms did not exhibit self activation in yeast cells (FIG. 12A). Therefore, we are confident that bHLH142 interacts with TDR1 by using these truncated proteins to eliminate the bias (FIG. 13). Our data indicate that bHLH142 interacts with TDR1 in the C-terminal (FIG. 13), and support the conclusion of the previous study in that DTD/EAT1 (bHLH141) interacts with TDR1 in the C-terminal region24. In other words, both bHLH142 and EAT1 (bHLH141) can interact with TDR1 in the C′ terminal of TDR1. This finding also supports the result of our EAT1 promoter assay, where additional EAT1 protein reduces EAT1 promoter activity, presumably due to the competition between bHLH142 and EAT1 proteins in the C′ terminal of TDR1. Based on this and previous works, the current regulatory network for rice pollen development is presented in FIG. 21. Previous works with various rice MS mutants suggest that UDT1 and GAMYB may positively regulate the transcription of TDR122 and TDR1 in turn controls the transcription of C6 and CP114. A recent study presents evidence that TDR1 interacts with EAT1 for its direct regulation of the expression of two aspartate proteinase genes for initiation of tapetal PCD23. In this invention, we demonstrate that bHLH142 acts downstream of UDT1 but upstream of TDR1 and EAT1, and then bHLH142 interact with TDR1 in activating EAT1 transcription (indicated by red arrows in FIG. 21). Furthermore, we showed that EAT1 also positively regulate the transcription of AP37 and CP1 directly, two proteins involved in tapetal PCD at late pollen development stage.
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Claims (32)

What is claimed is:
1. A mutated nucleotide molecule, comprising a nucleotide sequence of the transcription factor bHLH142 and an inserted T-DNA segment.
2. The mutated nucleotide molecule according to claim 1, wherein the nucleotide sequence of the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
3. The mutated nucleotide molecule according to claim 1, wherein the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142.
4. The mutated nucleotide molecule according to claim 2, wherein the T-DNA segment is inserted at +1257 bp of the nucleotide sequence of the transcription factor bHLH142.
5. A transformed plant cell, which comprises the mutated nucleotide molecule according to claim 1.
6. The transformed plant cell according to claim 5, wherein the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
7. The transformed plant cell according to claim 5, wherein the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142.
8. The transformed plant cell according to claim 6, wherein the T-DNA segment is inserted at +1257 bp of the nucleotide sequence of the transcription factor bHLH142.
9. A male sterile mutant plant, which comprises the mutated nucleotide molecule according to claim 1, and the transcription factor bHLH142 is not expressed.
10. The male sterile mutant plant according to claim 9, wherein the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
11. The male sterile mutant plant according to claim 9, wherein the T-DNA segment is inserted in the third intron of the nucleotide sequence of the transcription factor bHLH142.
12. The male sterile mutant plant according to claim 10, wherein the T-DNA segment is inserted at +1257 bp of the nucleotide sequence of the transcription factor bHLH142.
13. The male sterile mutant plant according to claim 9, which is a homozygous mutant.
14. The male sterile mutant plant according to claim 9, wherein the plant is a monocot plant.
15. The male sterile mutant plant according to claim 14, wherein the monocot plant is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
16. The male sterile mutant plant according to claim 9, wherein the plant is a dicot plant.
17. The male sterile mutant plant according to claim 16, wherein the dicot plant is Arabidopsis or Brassica species.
18. A transformed plant cell, which comprises a plasmid comprising the sequence of the transcription factor bHLH142 and a strong promoter.
19. The transformed plant cell according to claim 18, wherein the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
20. The transformed plant cell according to claim 18, wherein the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter.
21. A reversible male sterile mutant plant, wherein the transcription factor bHLH142 is overexpressed.
22. The reversible male sterile transgenic plant according to claim 21, wherein the transcription factor bHLH142 has a DNA sequence of SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
23. The reversible male sterile transgenic plant according to claim 21, wherein the expression of the transcription factor bHLH142 is controlled by a strong promoter.
24. The reversible male sterile transgenic plant according to claim 21, wherein the fertility of the plant is recovered under low temperature.
25. The reversible male sterile transgenic plant according to claim 21, wherein the plant is a monocot plant.
26. The reversible male sterile transgenic plant according to claim 25, wherein the monocot plant is rice, maize, wheat, millet, sorghum or Brachypodium distachyon.
27. The reversible male sterile transgenic plant according to claim 21, wherein the plant is a dicot plant.
28. The reversible male sterile transgenic plant according to claim 27, wherein the dicot plant is Arabidopsis or Brassica species.
29. A method for preparing the reversible male sterile transgenic plant according to claim 21, comprising:
(a) constructing a plasmid comprising the sequence of the transcription factor bHLH142 and a strong promoter; and
(b) introducing the plasmid into a target plant.
30. The method according to claim 29, wherein the DNA sequence of bHLH142 is SEQ ID No: 1 or a DNA sequence having at least 60% similarity to SEQ ID No: 1.
31. The method according to claim 29, wherein the strong promoter is Ubiquitin promoter, CaMV 35S promoter, Actin promoter, an anther tapetum-specific promoter or a pollen-specific promoter.
32. The method according to claim 29, wherein the plasmid is introduced into calli of the target plant via Agrobacterium tumefaciens.
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