Data for: Defective kernel 66 encodes a GTPase essential for kernel development in maize
Data files
Sep 27, 2023 version files 484.45 KB
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JEXBOT2023310235.xlsx
477.99 KB
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README.md
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Abstract
Mitochondria is a semi-autonomous organelle that provides energy for cell activities through oxidative phosphorylation. In this study, we identified a defective kernel 66 (dek66)-mutant maize with defective kernels. We characterized the candidate gene DEK66, encoding a ribosomal assembly factor, located in mitochondria, and possessing GTPase activity (the GTPase belonged to ribosome biogenesis GTPase A family). In the dek66 mutant, abolishment of mitochondrial structure and function led to the accumulation of reactive oxygen species and promoted programmed cell death in endosperm cells. Furthermore, transcript levels of most of the key genes associated with nutrient storage, mitochondrial respiratory chain complex, and mitochondrial ribosomes in the dek66 mutant were significantly altered. Collectively, the results suggested that DEK66 is essential for the development of maize kernels via affecting mitochondrial function. This study provided a reference to understand the impact of mitochondrial ribosomal assembly factors in maize kernel development.
README: Data for: Defective kernel 66 encodes a GTPase essential for kernel development in maize
Primary data in experimental procedures and results.This file is intended to provide key information for understanding and reuse of the dataset “Defective kernel 66 encodes a GTPase essential for kernel development in maize”.
Description of the data and file structure
Each figure plate corresponds to a sheet in the excel file. The content marked in bright yellow and bright blue in each datasheet represent the Figure number and line headers, respectively. The contents in parentheses in the line headers is the unit of each parameter.
- Fig. 1G The statistical data of the length of per kernel of WT and dek66
- Fig. 1H The statistical data of the width of per kernel of WT and dek66
- Fig. 1I The statistical data of hundered-grain weight of WT and dek66
- Fig.2D Quantification of zein, non-zein, and total protein contents in WT and dek66 mature endosperm <br> repeat 1, repeat 2, repeat 3 technical replicates A595 absorbance value at 595nm 1/2 total The total protein diluted by twice 1/2 ZEIN The zein protein diluted by twice 1/2 Non-ZEIN The Non-zein protein diluted by twice
- Fig.2I, J The raw data of starch content per kernel <br> WT1, WT2, WT3 biological replicates dek66-1, dek66-2, dek66-3 biological replicates A510 absorbance value of sample at 510nm ODck absorbance value of the control at 510nm ODstandard absorbance value of the standard solution at 510nm
- Fig. 2K The raw data of the soluble sugars content in WT and dek66 endosperm <br> A620 absorbance value at 620nm Ack absorbance value of the control at 620nm WT1, WT2...WT6 biological replicates dek66-1, dek66-2...dek66-6 biological replicates g edosperm weight in gram (g)
- Fig. 2L The raw data of carbon/nitrogen (C/N) ratio in mature WT and dek66 endosperm
- Fig. 4B Expression pattern analysis of DEK66 <br> Ratio expression level of DEK66 Ratio Error Standard deviation (SD) of three biological replicates YL young leaves OL old leaves 5 DAP, 10 DAP, 15 DAP, 20 DAP the seeds of 5, 10, 15, and 20 days after pollination
- Fig. 4D Kinetic analysis of GTP hydrolysis rates of DEK66 proteins <br> GTP (mM) the concentration of GTP standard solution concentration of Pi (μM) the concentration of Pi in three technical replicates
- Fig. 5A, S8 Mitochondrial gene expression analysis
WT1, WT2...WT6 biological replicates
dek66-1, dek66-2...dek66-6 biological replicates
n/a invalid data
- Fig. 6C Alternate oxidase gene (ZmAOX1, ZmAOX2, ZmAOX3) expression analysis
Mean the average value of three/six biological replicates
SD Standard deviation (SD) of three/six biological replicates
N the numbers of biological replicates
- Fig. 7C Concentration of H2O2 in 15 DAP endosperm of WT and dek66
standard solution (μM) the concentration of GTP standard solution
A560 absorbance value at 560nm
WT1, WT2...WT6 biological replicates
dek66-1, dek66-2...dek66-6 biological replicates
repeat 1, repeat 2, repeat 3 absorbance value at 560nm of three technical replicates
- Fig. 7D Expression analysis of NADPH oxidase family genes in 15 DAP endosperm of WT and dek66
WT1, WT2, WT3 biological replicates
dek66-1, dek66-2, dek66-3 biological replicates
Ratio expression level of DEK66
Ratio Error Standard deviation (SD) of three biological replicates
- Fig. 7E Expression analysis of antioxidant-related genes in 15 DAP endosperm of WT and dek66
AOX2 alternative oxidase 2
APX4 ascorbate peroxidase 4
CAT1 catalase 1
GST4 glutathione-S-transferase 4
POX1 guaiacol peroxidase 1
POX3 guaiacol peroxidase 3
SOD3 superoxide dismutase 3
SOD4A superoxide dismutase 4A
Ratio expression level of DEK66
Ratio Error Standard deviation (SD) of three biological replicates
- Fig. S6B qPCR assay of DEK66 mRNA level of transgenic lines
CK non-transgenic control
OE-1, OE-2, OE-3 three independent overexpression transgenic lines
Ratio expression level of DEK66
Ratio Error Standard deviation (SD) of three biological replicates
- Fig. S6K The statistical data of the length of per kernel
CK non-transgenic control
OE-1, OE-2, OE-3 three independent overexpression transgenic lines
- Fig. S6L The statistical data of the width of per kernel
CK non-transgenic control
OE-1, OE-2, OE-3 three independent overexpression transgenic lines
- Fig. S6M The statistical data of hundered-grain weight
CK non-transgenic control
OE-1, OE-2, OE-3 three independent overexpression transgenic lines
- Fig. S9 raw data of RNAseq for differentially expressed genes <br> MT_1, MT_2, MT_3 Three biological repeats of dek66 WT_1, WT_2, WT_3 Three biological repeats of WT log2FoldChange It represents the log2-transformed fold change, indicating the difference in gene expression levels lfcSE Log2 Fold Change Standard Error stat Statistic pvalue a statistical test that represents the probability of observing a difference under the assumption of no difference padj Adjusted P-Value baseMean It serves as the foundation for calculating differential expression
- Fig. S10 raw data of RNAseq for genes of interest (DEGs related to mitochondria) <br> MT_1, MT_2, MT_3 Three biological repeats of dek66 WT_1, WT_2, WT_3 Three biological repeats of WT log2FoldChange It represents the log2-transformed fold change, indicating the difference in gene expression levels lfcSE Log2 Fold Change Standard Error stat Statistic pvalue a statistical test that represents the probability of observing a difference under the assumption of no difference padj Adjusted P-Value baseMean It serves as the foundation for calculating differential expression
- Fig. S11 Polysome profiling assay with sucrose density gradient <br> A254 absorbance value at 254nm 10-1, 10-2, 10-3, 10-4, 10-5 The sample from 10% sucrose solution 15-1, 15-2, 15-3, 15-4, 15-5 The sample from 15% sucrose solution 20-1, 20-2, 20-3, 20-4, 20-5 The sample from 20% sucrose solution 25-1, 25-2, 25-3, 25-4, 25-5 The sample from 25% sucrose solution 30-1, 30-2, 30-3, 30-4, 30-5 The sample from 30% sucrose solution 35-1, 35-2, 35-3, 35-4, 35-5 The sample from 35% sucrose solution 40-1, 40-2, 40-3, 40-4, 40-5 The sample from 40% sucrose solution 45-1, 45-2, 45-3, 45-4, 45-5 The sample from 45% sucrose solution