Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes
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ABSTRACT:
PROVIDER: PRJNA236081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1138410.fastq.gz | Fastqsanger.gz | |||
| SRR1138420.fastq.gz | Fastqsanger.gz | |||
| SRR1138430.fastq.gz | Fastqsanger.gz | |||
| SRR1138440.fastq.gz | Fastqsanger.gz | |||
| SRR1138450.fastq.gz | Fastqsanger.gz |
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Project description:Maize and rice are the two most economically important grass crops and utilize distinct forms of photosynthesis to fix carbon: C4 and C3 respectively. Relative to C3 photosynthesis, C4 photosynthesis reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses. [Maize] Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates. [Rice] 14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.
2014-10-12 | E-GEOD-54274 | biostudies-arrayexpress
Project description:Maize and rice are the two most economically important grass crops and utilize distinct forms of photosynthesis to fix carbon: C4 and C3 respectively. Relative to C3 photosynthesis, C4 photosynthesis reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses.
2014-10-12 | GSE54274 | GEO
Project description:Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes - maize dataset
2020-04-03 | E-CURD-27 | ExpressionAtlas
Project description:Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes - rice dataset
2020-04-03 | E-CURD-26 | ExpressionAtlas
Project description:C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.
2021-08-01 | GSE178320 | GEO
Project description:During Zea mays (maize) C4 differentiation, mesophyll (M) and bundle sheath (BS) cells accumulate distinct sets of photosynthetic enzymes, with very low photosystem II (PSII) content in BS chloroplasts. Consequently, there is little linear electron transport in the BS and ATP is generated by cyclic electron flow. In contrast, M thylakoids are very similar to those of C3 plants and produce the ATP and NADPH that drive metabolic activities. Regulation of this differentiation process is poorly understood but involves expression and coordination of nuclear and plastid genomes. Here, we identify a recessive allele of the maize Hcf136 homologue that in Arabidopsis thaliana functions as a PSII stability or assembly factor located in the thylakoid lumen. Proteome analysis of the thylakoids and electron microscopy reveal that Zm hcf136 lacks PSII complexes and grana thylakoids in M chloroplasts, consistent with the previously defined Arabidopsis function. Interestingly, hcf136 is also defective in processing the full-length psbB-psbT-psbH-petB-petD polycistron specifically in M chloroplasts. To determine whether the loss of PSII in M cells affects C4 differentiation, we performed cell-type specific transcript analysis of hcf136 and wild-type seedlings. The results indicate that M and BS cells respond uniquely to the loss of PSII, with little overlap in gene expression changes between data sets. These results are discussed in the context of signals that may drive differential gene expression in C4 photosynthesis. Keywords: cell type comparison
2008-02-01 | GSE9698 | GEO
Project description:During Zea mays (maize) C4 differentiation, mesophyll (M) and bundle sheath (BS) cells accumulate distinct sets of photosynthetic enzymes, with very low photosystem II (PSII) content in BS chloroplasts. Consequently, there is little linear electron transport in the BS and ATP is generated by cyclic electron flow. In contrast, M thylakoids are very similar to those of C3 plants and produce the ATP and NADPH that drive metabolic activities. Regulation of this differentiation process is poorly understood but involves expression and coordination of nuclear and plastid genomes. Here, we identify a recessive allele of the maize Hcf136 homologue that in Arabidopsis thaliana functions as a PSII stability or assembly factor located in the thylakoid lumen. Proteome analysis of the thylakoids and electron microscopy reveal that Zm hcf136 lacks PSII complexes and grana thylakoids in M chloroplasts, consistent with the previously defined Arabidopsis function. Interestingly, hcf136 is also defective in processing the full-length psbB-psbT-psbH-petB-petD polycistron specifically in M chloroplasts. To determine whether the loss of PSII in M cells affects C4 differentiation, we performed cell-type specific transcript analysis of hcf136 and wild-type seedlings. The results indicate that M and BS cells respond uniquely to the loss of PSII, with little overlap in gene expression changes between data sets. These results are discussed in the context of signals that may drive differential gene expression in C4 photosynthesis. To explore the disruption of PSII activity on gene expression, transcript profiles from separated M and BS cells were examined using two-label microarray analysis. Total RNA was isolated from the second leaves of mutant and wild-type silbings. Six biological replicates were used to compare wild-type and mutant transcript profiles in separate M and BS experiments. To maximize biological replication, different seedling pools were used for each of the 12 hybridizations. Microarray experiments and analyses were performed using the Genisphere MPX900 kit and the Maize Array Consortium oligonucleotide platform (GPL5439; GPL5440). Feature intensity values were log-transformed and corrected for local background signal, and a LOWESS procedure (Dudoit et al., 2002) was used to normalize between channels. Features with either low or saturating signal intensity were discarded from further analysis. High expression filtering was less stringent to avoid elimination of previously characterized, high abundance, C4 cell-specific transcripts. After filtering, features that were not assigned an MZ number by the Maize Array Consortium were discarded from further analysis. The moderated t-test (Smyth, 2004) using the R package limma was applied to identify differentially expressed genes. The p-values for each test (gene) were converted to q-values for false discovery rate analysis as described by Storey et al. (2004). To avoid confounding treatment effects associated with direct comparisons of M and BS transcriptomes (Sawers et al., 2007), comparisons were only made using the same cell type across the hcf136 and wild-type sibling genotypes. Bundle sheath (BS) Samples: GSM245063-GSM245164 Mesophyll (M) Samples: GSM245165 - GSM245206
2008-01-31 | E-GEOD-9698 | biostudies-arrayexpress
Project description:In Cleomaceae species, NAD-malic enzyme (NAD-ME) was independently co-opted to participate in C4 photosynthesis. In C4 Cleome species, all NAD-ME genes (NAD-MEα, -ß1 and -ß2) were affected by C4 evolution and are expressed at higher levels than their C3 orthologs in Tarenaya hassleriana. In C3 Cleome, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/ß1 and NAD-MEα/ß2, with similar biochemical properties and tissue occurrence. In the C4 species, Gynandropsis gynandra and Cleome angustifolia, this role is performed only by the NAD-MEα/ß2 heteromer. In these C4 species NAD-MEα/ß1 is preferentially present in leaves of the C4 species where is the predominant isoform. GgNAD-MEα/ß1 exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate. In C4 Cleome NAD-MEα/ß1 represents thus the C4-decarboxylase. GgNAD-MEß1and CaNAD-MEß1 are non-catalytic subunits but impart a stabilizing effect on the associated α-subunit. We conclude that in C4 Cleome the functions of NAD-ME as a TCA cycle associated enzyme and as a C4 photosynthetic decarboxylase coexist in BSC mitochondria and are performed by isoforms originated through associations of differentially adapted subunits.
2021-11-30 | PXD026547 | Pride
Project description:The comparison of the cell-specific transcriptomes of bundle sheath (BS) and mesophyll (M) cells from successive developmental stages of maize leafs reveals that the number of genes preferentially transcribed in one cell type or the other varies considerably from the sink-source transition to mature photosynthetic stages. The number of differentially expressed (DE) genes is maximal at a stage well prior to full maturity, including those that encode key functions for C4 photosynthesis. The developmental dynamics of BS/M differential expression can be used to identify candidates for other C4-related functions and to simplify the identification of specific pathways members from otherwise complex gene families. The candidates for C4-related transcription factors identified with this developmental DE strategy overlap with those identified in studies using alternative strategies.
2014-05-18 | GSE54272 | GEO
Project description:The C4 pathway is a highly complex trait that increases photosynthetic efficiency in over sixty plant lineages. Although the majority of C4 plants occupy disturbed, arid and nutrient-poor habitats, some grow in high-nutrient, waterlogged conditions. One such example is Echinochloa glabrescens, which is an aggressive weed of rice paddies. We generated comprehensive transcriptome datasets for C4 E. glabrescens and C3 rice to identify genes associated with adaption to waterlogged, nutrient-replete conditions, but also used the data to better understand how C4 photosynthesis operates in these conditions. Similar to arid C4 species, leaves of E. glabrescens exhibited classical Kranz anatomy with lightly lobed mesophyll cells. As with rice and other hygrophytic C3 species, leaves of E. glabrescens accumulated a chloroplastic phosphoenolpyruvate carboxylase protein, albeit at reduced levels relative to rice. We identified a molecular signature associated with C4 photosynthesis in nutrient-replete, waterlogged conditions that is highly similar to those previously reported from C4 plants that grow in more arid conditions. We also identified a cohort of genes that have been subjected to a selective sweep associated with growth in paddy conditions. Overall, this approach highlights the value of using wild species such as weeds to identify adaptions to specific conditions associated with high-yielding crops in agriculture.
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