Abstract
Regulation of mRNA abundance revealed a genetic program for plant leaf acclimation to iron (Fe) limitation. The transcript for SUFB, a key component of the plastid iron-sulfur (Fe-S) assembly pathway is down-regulated early after Fe deficiency, and prior to down-regulation of mRNAs encoding abundant chloroplast Fe containing proteins, which should economize the use of Fe. What controls this system is unclear. We utilized RNA-seq. aimed to identify differentially expressed transcripts that are co-regulated with SUFB after Fe deficiency in leaves. To distinguish if lack of Fe or lack of Fe-S cofactors and associated loss of enzymatic and photosynthetic activity trigger transcriptome reprogramming, WT plants on low Fe were compared with an inducible sufb-RNAi knockdown. Fe deficiency targeted a limited set of genes and predominantly affected transcripts for chloroplast localized proteins. A set of glutaredoxin transcripts was concertedly down-regulated early after Fe deficiency, however when these same genes were down-regulated by RNAi the effect on known chloroplast Fe deficiency marker proteins was minimal. In promoters of differentially expressed genes, binding motifs for AP2/ERF transcription factors were most abundant and three AP2/ERF transcription factors were also differentially expressed early after low Fe treatment. Surprisingly, Fe deficiency in a WT on low Fe and a sufb-RNAi knockdown presented very little overlap in differentially expressed genes. sufb-RNAi produced expression patterns expected for Fe excess and up-regulation of a transcript for another Fe-S assembly component not affected by low Fe. These findings indicate that Fe scarcity, not Fe utilization, triggers reprogramming of the transcriptome in leaves.
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Claims 9
Claim · model-written summary
Iron deficiency affected a limited set of Arabidopsis genes, mainly those encoding chloroplast localized proteins.
- Taxon
- Arabidopsis
Arabidopsist0 - Treatment
- Fe deficiencye0
- Outcome
- transcripts for chloroplast localized proteinse0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Fe deficiency targeted a limited set of genes and predominantly affected transcripts for chloroplast localized proteins”
t0“Arabidopsis”
Claim · model-written summary
A set of glutaredoxin transcripts was down-regulated early after iron deficiency.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- Fe deficiencye0
- Outcome
- glutaredoxin transcriptse0
- Direction
- down-regulatede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A set of glutaredoxin transcripts was concertedly down-regulated early after Fe deficiency”
t0“Arabidopsis”
Claim · model-written summary
RNAi down-regulation of glutaredoxin genes had minimal effect on chloroplast iron-deficiency marker proteins.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- down-regulated by RNAie0
- Outcome
- effect on known chloroplast Fe deficiency marker proteinse0
- Direction
- minimale0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“when these same genes were down-regulated by RNAi the effect on known chloroplast Fe deficiency marker proteins was minimal”
t0“Arabidopsis”
Claim · model-written summary
AP2/ERF transcription factor binding motifs were the most abundant in promoters of differentially expressed genes.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AP2/ERF transcription factorse0
- Outcome
- binding motifs for AP2/ERF transcription factorse0
- Direction
- most abundante0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In promoters of differentially expressed genes, binding motifs for AP2/ERF transcription factors were most abundant”
t0“Arabidopsis”
Claim · model-written summary
Three AP2/ERF transcription factors were differentially expressed early after low iron treatment.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- low Fe treatmente0
- Outcome
- AP2/ERF transcription factorse0
- Value
- threee0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“three AP2/ERF transcription factors were also differentially expressed early after low Fe treatment”
t0“Arabidopsis”
Claim · model-written summary
Low iron wild type and sufb-RNAi knockdown had little overlap in differentially expressed genes.
- Taxon
- ArabidopsisArabidopsist0
- Material
- sufb-RNAi knockdowne0
- Outcome
- overlap in differentially expressed genese0
- Direction
- very littlee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Fe deficiency in a WT on low Fe and a sufb-RNAi knockdown presented very little overlap in differentially expressed genes”
t0“Arabidopsis”
Claim · model-written summary
sufb-RNAi produced gene expression patterns expected for iron excess.
- Taxon
- ArabidopsisArabidopsist0
- Material
- sufb-RNAie0
- Outcome
- expression patterns expected for Fe excesse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“sufb-RNAi produced expression patterns expected for Fe excess”
t0“Arabidopsis”
Claim · model-written summary
sufb-RNAi up-regulated a transcript for an iron-sulfur assembly component unaffected by low iron.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- sufb-RNAit1
- Outcome
- transcript for another Fe-S assembly componente0
- Direction
- up-regulatione0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“up-regulation of a transcript for another Fe-S assembly component not affected by low Fe”
t0“Arabidopsis”
t1“sufb-RNAi produced expression patterns expected for Fe excess”
Claim · model-written summary
The findings indicate iron scarcity triggers leaf transcriptome reprogramming.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- reprogramming of the transcriptome in leavese0
- Qualifier
- Fe scarcity, not Fe utilizatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Fe scarcity, not Fe utilization, triggers reprogramming of the transcriptome in leaves”
t0“Arabidopsis”