Difference between revisions of "Os03g0411500"
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Next, researchers investigated whether the virescent yellow phenotype of the vyl mutant was associated with ultra-structural changes in the chloroplasts. Leaf samples of L3U (upper half of the third leaf), L3L (basal half of the third leaf), and L4 (fourth leaf above the shoot base) were collected from wild-type and vyl mutant seedlings and compared (Fig. 2A). Normally, when the third leaf has fully emerged from the shoot base of a rice plant, the shoot also contains the fourth to the seventh immature leaves. The leaf cells in the L3L and L3U samples contain mature chloroplasts, whereas those in the shoot base and L4 samples contain proplastids and early developing immature chloroplasts (Sugimoto et al., 2004). Similar to the wild type, the chloroplasts from the L3U green leaf sample (already turned green) of vyl mutant seedlings displayed well-developed lamellar structures and were equipped with normally stacked grana and thylakoid membranes (Fig. 2, B and C). By contrast, the chloroplasts from the L3L and L4 pale leaves (still wrapped in leaf sheath) of the vyl mutant had much reduced thylakoid membrane networks compared with wild-type plants (Fig. 2, D–G). This developmental defect is similar to the phenotype reported in the Arabidopsis CLPP6 antisense transgenic plants (Sjögren et al., 2006). | Next, researchers investigated whether the virescent yellow phenotype of the vyl mutant was associated with ultra-structural changes in the chloroplasts. Leaf samples of L3U (upper half of the third leaf), L3L (basal half of the third leaf), and L4 (fourth leaf above the shoot base) were collected from wild-type and vyl mutant seedlings and compared (Fig. 2A). Normally, when the third leaf has fully emerged from the shoot base of a rice plant, the shoot also contains the fourth to the seventh immature leaves. The leaf cells in the L3L and L3U samples contain mature chloroplasts, whereas those in the shoot base and L4 samples contain proplastids and early developing immature chloroplasts (Sugimoto et al., 2004). Similar to the wild type, the chloroplasts from the L3U green leaf sample (already turned green) of vyl mutant seedlings displayed well-developed lamellar structures and were equipped with normally stacked grana and thylakoid membranes (Fig. 2, B and C). By contrast, the chloroplasts from the L3L and L4 pale leaves (still wrapped in leaf sheath) of the vyl mutant had much reduced thylakoid membrane networks compared with wild-type plants (Fig. 2, D–G). This developmental defect is similar to the phenotype reported in the Arabidopsis CLPP6 antisense transgenic plants (Sjögren et al., 2006). | ||
Revision as of 08:00, 8 June 2014
A nuclear gene coding caseinolyse positioned in plastid or mitochondrion regulating early morphogenesis. VYL is a gene in rice.Its RAP ID is Os03g0411500 and its MSU ID is LOC_Os03g29810. The mutant of this gene produces chlorotic leaves throughout the entire growth period.
Contents
Annotated Information
Function
The protein encoded by this gene belongs to the peptidase family S14 and hydrolyzes proteins into small peptides in the presence of ATP and magnesium. The protein is transported into mitochondrial matrix and is associated with the inner mitochondrial membrane[1], or plastid inner membrane in plants[2]. The plastidic caseinolytic protease (Clp) of higher plants is an evolutionarily conserved protein degradation apparatus composed of a proteolytic core complex (the P and R rings) and a set of accessory proteins (ClpT, ClpC, and ClpS).[2] Rice yellow leaf mutant vyl, the performance of the entire growth period, new leaves chlorotic phenotype, then gradually turn green from the top down.[2] VYL Arabidopsis Clp protease subunit ClpP6 homologous protein in rice, is one of the subunits of the chloroplast Clp protease, with the Clp protease subunit interactions OsClpP3 and OsClpP4 respectively, play an important role in the biosynthesis of rice chloroplast.[2] What's more, the gene D53 product shares predicted features with the class I Clp ATPase proteins and can form a complex with the a/b hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL(Strigolactones) perception, which means, in a D14- and D3-dependentmanner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth.[3] The role and molecular composition of Clps in higher plants has just begun to be unraveled, mostly from studies with the model dicotyledonous plant Arabidopsis (Arabidopsis thaliana).Some researchers isolated a virescent yellow leaf (vyl) mutant in rice (Oryza sativa), which produces chlorotic leaves throughout the entire growth period.[2]
1.The vyl Mutant Displays Reduced Chlorophyll Accumulation
The vyl mutant was derived by transforming tissue cultures of the japonica rice variety Kita-ake. When grown under an alternating light/dark cycle (12 h of light at 30°C/12 h of darkness at 20°C) in a growth chamber, vyl mutant plants displayed a virescent yellow leaf pheno-type, and during development, leaves gradually turned green from their tips (more developed) to their bases (less developed; Fig. 1, A and B). At maturity, the vyl mutant plants also had reduced height and smaller seeds (Fig. 1, C and D). Mutant leaves also contained less chlorophyll than the wild type at various growth stages (Fig. 1E).
Additionally, vyl mutants developed chlorotic leaves under different temperature conditions and light/dark cycles, suggesting that the virescent yellow phenotype of the vyl mutant was developmentally regulated but independent of external cues (such as temperature and light)
2.The vyl Mutant Has Impaired Chloroplast Development
Next, researchers investigated whether the virescent yellow phenotype of the vyl mutant was associated with ultra-structural changes in the chloroplasts. Leaf samples of L3U (upper half of the third leaf), L3L (basal half of the third leaf), and L4 (fourth leaf above the shoot base) were collected from wild-type and vyl mutant seedlings and compared (Fig. 2A). Normally, when the third leaf has fully emerged from the shoot base of a rice plant, the shoot also contains the fourth to the seventh immature leaves. The leaf cells in the L3L and L3U samples contain mature chloroplasts, whereas those in the shoot base and L4 samples contain proplastids and early developing immature chloroplasts (Sugimoto et al., 2004). Similar to the wild type, the chloroplasts from the L3U green leaf sample (already turned green) of vyl mutant seedlings displayed well-developed lamellar structures and were equipped with normally stacked grana and thylakoid membranes (Fig. 2, B and C). By contrast, the chloroplasts from the L3L and L4 pale leaves (still wrapped in leaf sheath) of the vyl mutant had much reduced thylakoid membrane networks compared with wild-type plants (Fig. 2, D–G). This developmental defect is similar to the phenotype reported in the Arabidopsis CLPP6 antisense transgenic plants (Sjögren et al., 2006).
3.The vyl Mutant Has Impaired Photosynthesis
Chloroplasts are the organelles in plant cells that perform photosynthesis; therefore, they play an essential role in plant growth. To test whether the photosynthetic apparatus was affected in vyl mutants, we compared some key parameters of PSI and PSII between vyl and wild-type plants. Distinct differences in photochemical efficiency of PSII (FPSII), electron transport rate (ETR), nonphotochemical quenching (NPQ), and photochemical quenching (Qp) were detected between vyl mutants and the wild type. In contrast, the maximal efficiency of PSII photochemistry (F v /F m ) values was almost comparable between vyl and wild-type plants (Table I). These observations indicate that vyl mutants absorbed much less light energy, as shown by the lower NPQ values. PSII photochemistry was reduced at both the donor and acceptor sites, as indicated by the greatly decreased Qp and ETR in vyl mutants. Notably, the PSII structure appeared intact in the mutant plants (indicated by the equivalent F v /F m values), but the actual FPSII was much lower in the mutants. These differences may underlie the defects in chloroplast biogenesis and retarded growth in the vyl mutant (Fig. 1, C and D)
Expression
Expression is constitutive in most tissues examined (roots, stems, leaves, leaf sheath, panicle)but most abundant in leaf sections containing chloroplasts in early stages of development,which can be light-mediated.[2] The young chlorotic leaves turn green in later developmental stages, accompanied by alterations in chlorophyll accumulation, chloroplast ultrastructure, and the expression of chloroplast development- and photosynthesis-related genes. Positional cloning revealed that the VYL gene encodes a protein homologous to the Arabidopsis ClpP6 subunit and that it is targeted to the chloroplast. VYL expression is constitutive in most tissues examined but most abundant in leaf sections containing chloroplasts in early stages of development. The mutation in vyl causes premature termination of the predicted gene product and loss of the conserved catalytic triad (serine-histidine-aspartate) and the polypeptide-binding site of VYL. Using a tandem affinity purification approach and mass spectrometry analysis, we identified OsClpP4 as a VYL-associated protein in vivo. In addition, yeast two-hybrid assays demonstrated that VYL directly interacts with OsClpP3 and OsClpP4. Furthermore, we found that OsClpP3 directly interacts with OsClpT, that OsClpP4 directly interacts with OsClpP5 and OsClpT, and that both OsClpP4 and OsClpT can homodimerize. Together, our data provide new insights into the function, assembly, and regulation of Clps in higher plants.[2]
Evolution
ATP-dependent Clp protease proteolytic subunit is an enzyme that in humans is encoded by the CLPP gene.[4][1] It is found in mitochondria and is widely distributed in bacterial species. In several bacteria, such as E. coli, proteins tagged with the SsrA peptide (ANDENYALAA) encoded by tmRNA are digested by Clp proteases.[5]
Labs working on this gene
National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
References
- ↑ 1.0 1.1 a b "Entrez Gene: CLPP ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)".
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Hui Dong et al. A Rice Virescent-Yellow Leaf Mutant Reveals New Insights into the Role and Assembly of Plastid Caseinolytic Protease in Higher Plants. Plant Physiology, 2013, 162(4): 1867-1880
- ↑ Zhou Feng et al.D14–SCFD3-dependent degradation of D53 regulates strigolactone signaling. Nature,2013. doi:10.1038/nature12878
- ↑ Bross P, Andresen BS, Knudsen I, Kruse TA, Gregersen N (Feb 1996). "Human ClpP protease: cDNA sequence, tissue-specific expression and chromosomal assignment of the gene". FEBS Lett 377 (2): 249–52. doi:10.1016/0014-5793(95)01353-9. PMID 8543061.
- ↑ Gottesman S, Roche E, Zhou Y, Sauer RT (1998). "The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system". Genes Dev 12 (9): 1338–47. doi:10.1101/gad.12.9.1338. PMC 316764. PMID 9573050
Structured Information
| Gene Name |
Os03g0411500 |
|---|---|
| Description |
Peptidase S14, ClpP family protein |
| Version |
NM_001056884.1 GI:115453496 GeneID:4333096 |
| Length |
3448 bp |
| Definition |
Oryza sativa Japonica Group Os03g0411500, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 3:17630235..17633682 |
| Sequence Coding Region |
17630290..17630357,17630478..17630512,17631200..17631269,17631410..17631614,17631776..17631841 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008396:17630235..17633682 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008396:17630235..17633682 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcgcctatggccatctccaccccgctcgccctccgcgcctccccgacccgcctcctctcccgcaggcggagcggagccaaatcaggcgtggctctcccaggtccacaatttgtaccacctggtatttcttcaaagttggacgagaggatacattgtcattcttctctgaggaaaaatacaattgtagcatcagagaatgaaaatccacctttaatgcctgccataatgactcctgctggtgctcttgatctggcaactgtattgttggggaaccgcattatcttcattggtcaatatattaactcgcaagtagcacagcgtgtaatatcacagcttgtcacacttgctgctgttgatgaagaggctgatattctgatctacctgaactgccccggcggaagtctctactccatcttagcaatttatgattgcatgtcctggatcaagcccaaagttggaacagtgtgctttggtgttgttgctagccaggcagcaattatacttgctggcggtgagaagggaatgcgttatgccatgccaaatgctagagtaatgattcatcaacctcaaggtgtatcagagggtaatgtggaggaggtgaggcgacaggttggggaaaccatttatgctcgtgataaagttgataagatgtttgctgcttttactgggcaaaccttggatatggtacaacagtggacagagagggatcgtttcatgtcttcatctgaagccatggactttggactagttgatgccctgctggaaacaagatactaa</cdnaseq> |
| Protein Sequence |
<aaseq>MAPMAISTPLALRASPTRLLSRRRSGAKSGVALPGPQFVPPGIS SKLDERIHCHSSLRKNTIVASENENPPLMPAIMTPAGALDLATVLLGNRIIFIGQYIN SQVAQRVISQLVTLAAVDEEADILIYLNCPGGSLYSILAIYDCMSWIKPKVGTVCFGV VASQAAIILAGGEKGMRYAMPNARVMIHQPQGVSEGNVEEVRRQVGETIYARDKVDKM FAAFTGQTLDMVQQWTERDRFMSSSEAMDFGLVDALLETRY</aaseq> |
| Gene Sequence |
<dnaseqindica>56..123#244..278#966..1035#1176..1380#1542..1607#2217..2357#2569..2622#2758..2850#2949..2996#actcctcagtcctcgcctcggctcggctccctcccacgctccagctccgcctccaatggcgcctatggccatctccaccccgctcgccctccgcgcctccccgacccgcctcctctcccgcaggtgagctccacggaactacaacttccacctccttcgctcgctcgctcgccccgcgcttctctcttcatggattcccccgttcttgtcccctcaccctctgtctggtccttctttcttcaggcggagcggagccaaatcaggcgtggctctcccaggtgagatttcctaacccttggtttagcaaaccatttcccttggtcagctcgttaggccaggactgtttggtggaatttgatcgttgatttgataagctttactgagatgttgtccatggtggtgcacatattagaacatgaccatttgggcagccgtcccatcagctcctagttgtctttctctgtgccaattttttatggagtcgtcattggtaggttttgcaaagcatatagaacctctgaatgtcggcattatccaagagtatgccgacctggggttatctgaaccagtgtcaactccttcctgggccaatgtctggtatgcatcagcattagctcactaagtacacgaaaaatggatgtgcttggttgaacggatatgtataaaaacgataacctgcatataacatatcacctcagtttggtctgattctgaaattagtttagggccttttagcaaactgctgaatgagatttccagactgtatatgtgttattgtgtttgtcagtaactcagtatggtgtattagcacaactcaacatgccataatgacaggatatgcggagcacaaacttttctttggacatgttttttggattcctttactgtttagtccatctgtctttcacatgatatattgctgcaaatgtgctgagttgcattctcactcaaatttccacacctaggtccacaatttgtaccacctggtatttcttcaaagttggacgagaggatacattgtcattcttctctgaggtgatatatttgaaactgtcatgcctgatatacaatgaggatacattgcctgatttgaaactgctcatctaggttttatttgtgctgtgtatcagaatcctgttttattcattcgtaatattgtaaatattttttcacaggaaaaatacaattgtagcatcagagaatgaaaatccacctttaatgcctgccataatgactcctgctggtgctcttgatctggcaactgtattgttggggaaccgcattatcttcattggtcaatatattaactcgcaagtagcacagcgtgtaatatcacagcttgtcacacttgctgctgttgatgaagaggctgatattctggttagtgtttatttttgtgtttttcagatcataacagttaccctattgttcactgcagcagctcttgattgctcaacttcactcccttggcttgctcctttagctcacaggtgtgttgctctatatcttataactccttttgtataattctgttttgccagatctacctgaactgccccggcggaagtctctactccatcttagcaatttatgattgcatgtcctgggtatgccatctatgttgagctactttttccatgtccttcatgcattcaaatttcagagattgtattcacctatatttattcttgtggatgctttctgagttattctcatctaatttaatatttacattgttggatgagaacacattatagatgcatctcaacattttgtatcttccacattatgcatgcccctagctagtgaatttatatttataatatagcacagatatagcatttacaggaaagcctaatgtaatttaggcaaaaattatatctcatatcaatggtagtgcttgcaacatttgtattcttatatttttattgtagtacatactagacatgagcatttgccatgctgagactgtgctaattgggtttggtctggtactgcagacaacagatctcatttcctgaaatcatgcctgtctctaaaactggctttgagctggaccagccttgttagttgttagatttggctgtgtttttacttgttatgccagttttccataaccaaatactttatctacaatttcgcctactgataaataaatcccagaatattaatctttttttgttgttctgcactaacacatgaaccatttattgcagatcaagcccaaagttggaacagtgtgctttggtgttgttgctagccaggcagcaattatacttgctggcggtgagaagggaatgcgttatgccatgccaaatgctagagtaatgattcatcaacctcaaggtgtatcagaggtatgattctggggctttctgcctttctgagttactgcagcgggtgcattatgattttctaacattgtgactacagtaaataataatcatcatcattttagctggccacatgaaacttacaatatacagtcttgctaggacatacttgcttgcctttgtgtttgttgtacttgaagtttgttttttattctaaaaattggatgatttgcagggtaatgtggaggaggtgaggcgacaggttggggaaaccatttatgctcgtgatgtaagtgttttgtgatagataacaagttctatattttcttcagtgtacatttgaattagatgtttgatgagggtaaggaatttctcttgattctgctctctaagcgattaaagcttctgaaaaatctggatgcagaaagttgataagatgtttgctgcttttactgggcaaaccttggatatggtacaacagtggacagagagggatcgtttcatgtcttcatctgaagtaactttcatctcttaaatgtatcagaagaaagtaaatcatcatttgccatgtgaattataacttatttcccccttctttttttggttttaccctaggccatggactttggactagttgatgccctgctggaaacaagatactaacaaacaaacacttaggcacagtttgattagcagaggctggtacaaggattgtgaaactggagctgaagttgagattttcgccgtccttctagttcaaggactccaatgacaggaggctggatctgcgagacttgaatgcatcgccatcgctcctatgagcaaaacatctctgcgttgagtgtgattttttgctcttcttttttggatctggttttacatgccgccagcctatggtctcaatgcattggtcctgctaatgtttagtgtagaccagatgatcctttagacagcaaaacatcagttattactccgtagattttcccatgagctgattccagactgtgtgcaacttttgtgttccaattgcaaagtttgcaacccaacccaacccaacacatgggctgatgggctgttgacaaaggagagattttacacttcacatatgtcaaact</dnaseqindica> |
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