THERMO-SENSITIVE BARREN PANICLE (TAP) is required for rice panicle and spikelet development at high temperature
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE212443 | GEO | 2022/12/01
REPOSITORIES: GEO
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Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 80% (2.6 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops.
2016-08-01 | GSE42467 | GEO
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding3. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 70% (2.4 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40). TMS5 encodes an evolutionarily conserved endonuclease, RNase ZS1. RNase ZS1 can process tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Furthermore, over-expression of UbL401 and UbL404 in wild-type plants causes male sterility, while knockdown of UbL401 and UbL404 in tms5 partially restores its fertility. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications in hybrid breeding not only of rice but also of other crops.
2014-09-11 | GSE42314 | GEO
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 80% (2.6 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops. To address whether RNase ZS1 involves in mRNA metabolism, degradome sequencing was performed using RNA from young panicles of wild type (ZH11) and tms5 (Os02g12290iL1) plants grown at restrictive temperatures.
2016-08-01 | E-GEOD-42467 | biostudies-arrayexpress
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding3. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 70% (2.4 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40). TMS5 encodes an evolutionarily conserved endonuclease, RNase ZS1. RNase ZS1 can process tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Furthermore, over-expression of UbL401 and UbL404 in wild-type plants causes male sterility, while knockdown of UbL401 and UbL404 in tms5 partially restores its fertility. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications in hybrid breeding not only of rice but also of other crops. Examination of differences in mRNA accumulation between 93-11, NIL5 and NIL8.
2014-09-11 | E-GEOD-42314 | biostudies-arrayexpress
Project description:We developed a Transcriptomic Analysis Pipeline (TAP) as a flexible workflow for comprehensive transcriptome analysis from any species with a reference genome. We tested TAP in a case study to compare polyA+ and rRNA-depletion RNA-seq library protocols using Drosophila melanogaster following different thermal stress temperatures. TAP provides a flexible and complete pipeline to enable researchers to extract more biologically relevant interpretations by integrated and interactive transcriptome analysis.
2023-11-09 | GSE229448 | GEO
Project description:For immunotherapy, there is an urgent need to restore presentation-competence of cancer cells with defects in MHC-I processing/presentation. We identified two tumor-specific antigens expressed in the ER of pancreatic ductal adenocarcinoma cells (PDACCs) that induced effector CD8 T cells either independent (Cripto-1-Kb/Cr16-24) or dependent (gp70-Kb/p15E) on TAP-mediated antigen processing/presentation by DNA immunization. In systematic analyses, we showed that transplantation into syngeneic C57BL/6J mice or IFNγ-treatment in vitro upregulated MHC-I but also co-inhibitory PD-L1 molecules on PDACCs. IFNγ-treated PDACCs efficiently formed solid tumors in transplanted C57BL/6J and PD-L1-/- but were rejected in PD-1-/- mice. PDACCs induced a prophylactic immunity against tumor transplants in C57BL/6J mice when irradiated at day 2-3 post IFNγ-treatment, thereby silencing the tumor-initiated immune-suppressive PD-L1/PD-1-signaling axis. Immune-protection correlated with a significant enhanced induction of CD8 T cells against the TAP- but not the TAP-dependent antigen/epitope.
2020-08-06 | GSE140397 | GEO
Project description:The study was aimed to investigate by differential proteomics heat stress response mechanisms in tomato anthers collected from flowers of Solanum lycopersicum cv Saladette (SAL), already annotated as a thermo-tolerant tomato genotype and flowers from Solanum lycopersicum cv M82, reported as a thermo-sensitive genotype. Proteins constitutively present at higher or lower level in the tolerant genotype and/or proteins whose abundance was modulated by growth under high temperature in both genotypes were identified, thus leading to define processes involved in the heat stress response and responsible for efficient reduction of the adverse effects of HS. Results showed differences in the abundance of ninety-six proteins and their functional classification highlighted that heat stress mainly affected metabolic pathways, such as energy metabolism (glycolysis and sucrose degradation), nitrogen assimilation and amino acid biosynthesis and modulated the expression of proteins involved in the folding and degradation machinery and ROS detoxification systems
2018-07-25 | PXD010156 | Pride
Project description:Data for replicate Drn1-TAP and Dbr1-TAP CLIP-seq experiments to identify RNA-protein interactions
2013-06-28 | GSE44959 | GEO
Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein We purified TAP::ALG-1 complexes from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2, serving as a mock control) animals and hybridized the associated mRNAs to two-color microarrays
2012-03-01 | GSE32941 | GEO
Project description:Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants. Monocots generate 21- and 24-nt phasiRNAs by miR2118 and miR2275 respectively from noncoding RNAs with spatial-temporal specificity during anther development. However, which ARGONAUTES (AGOs) associate with these two miRNAs remains elusive. Here we show that rice AGO1d, specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. Furthermore, AGO1d also binds to miR2118-triggered 21-nt phasiRNAs preferentially with a 5’-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes reduction of 21- and 24-nt phasiRNAs and temperature-sensitive sterility. Anthers of the ago1d mutants at lower temperatures mainly display defects in tapetal cells and vacuolation during pollen formation. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function
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