Abstract
BACKGROUND: Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis. Since the energy-generating electron transport chains in chloroplasts and mitochondria are encoded by both nuclear and organellar genomes, sequencing total RNA after removal of ribosomal RNAs provides essential information on transcription of organellar genomes. The changes in the levels of ADP, ATP, NADP(+), NADPH and 41 metabolites upon illumination were also quantified. RESULTS: Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly, the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated whereas members of the same complex are co-regulated with each other. The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated. One such example is the negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology. CONCLUSION: This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination and to determine whether there are any correlations between changes in transcript and protein abundances of a particular gene or pathway upon illumination. The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date.
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Claims 8
Claim · model-written summary
Illumination did not significantly change transcription of plastid encoded genes.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianat0 - Organ / stage
- leavest0
- Treatment
- illuminatione0
- Outcome
- transcription of the genes encoded by the plastid genomee0
- Direction
- did not changee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
Illumination differentially regulated nuclear genes encoding photosystem complexes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Treatment
- illuminatione1
- Outcome
- transcription of nuclear genes encoding different functional complexes in the photosysteme0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated”
e1“Upon illumination”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
Members of the same photosystem complex were co-regulated.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Outcome
- co-regulated with each othere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“members of the same complex are co-regulated with each other”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
mRNA and protein abundances encoded by the three genomes did not always correlate positively.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Gene
- all three genomese0
- Outcome
- abundance of mRNAs and proteinse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
Photosystem component mRNA and protein abundances were negatively correlated.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Gene
- photosystem componentse0
- Outcome
- mRNA and protein abundances of the photosystem componentse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“negative correlation between mRNA and protein abundances of the photosystem components”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
The negative mRNA–protein correlation was interpreted as evidence of post-transcriptional regulation.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Outcome
- negative correlation between mRNA and protein abundancese0
- Qualifier
- post-transcriptional regulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
The study provides systems-wide leaf transcriptome, proteome and metabolite datasets after illumination.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- leavest0
- Outcome
- systems-wide datasetse0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination”
t0“Arabidopsis thaliana leaves”
Claim · model-written summary
Integrated organelle and metabolic pathway data provided a more complete picture of illumination responses than previously attained.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- more complete picture to the changes in plant physiology upon illuminatione0
- Comparator
- than has been attained to datee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date”
t0“Arabidopsis thaliana leaves”
The same questions in other papers
light · molecular: expression · Arabidopsis thaliana (thale cress)Positive and negative results
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- positive
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See all 47 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.