Lysine acetylome analysis of rice under drought
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza Sativa
SUBMITTER: 
Xumin Zhang
PROVIDER: PXD042247 | iProX | Mon May 15 00:00:00 BST 2023
REPOSITORIES: iProX
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Project description:Drought stress significantly reduces rice productivity, necessitating efforts to understand resistance mechanisms. This study utilizes quantitative proteomic and lysine acetylomic analyses to elucidate the complex drought responses in three rice cultivars with distinct drought resistance strategies. Proteomic analysis reveals that Hanyou73, an integrated drought avoidance and drought tolerance cultivar, exhibits exceptional resistance to water deprivation compared to other cultivars. Critically, lysine acetylomic analysis underscores the pivotal role of histone acetylation, particularly H4K5ac, in modulating water management efficiency, which underpins Hanyou73's drought resilience. Leveraging this enhanced water management, Hanyou73 exhibits superior photosynthetic efficiency under drought conditions, primarily attributed to the deacetylation of ATP synthase beta subunit (AtpB) at K100, thereby augmenting ATPase catalytic activity. Additionally, deacetylation of phosphoglucomutase (PGM) at K155 indicated an adaptive metabolic response across all drought-resistant cultivars, ensuring sustained energy and metabolic intermediate supply crucial for broad adaptation mechanisms. Collectively, these findings elucidate the intricate regulatory networks in Hanyou73, highlighting its sophisticated balance between drought avoidance and tolerance strategies. This research offers valuable insights into the proteomic and lysine acetylomic dynamics underlying rice drought resistance, providing potential biomarkers for breeding towards genetic enhancement.
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Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
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Project description:Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. In this study, we identified H3K9ac as an efficient histone mark that response dynamically to drought stress in rice and re-constructed high-resolution 3D genome contact maps based on these sites under the normal, drought, and recovery conditions. We discovered significant decondensation of chromatin contacts with over 10000 chromatin loops lost upon drought stress treatment while the recovery of 3D genome was limited after 4-day’s re-watering. We identified dominate promoter-promoter interacting (PPI) loops under each condition and identified their significant correlations to altered gene expressions in response to the corresponding condition. Based on the relative contact intensities of the PPI connections, we characterized super-promoter regions that integrate closer connections of genes with more vigorous inductions to condition shifts. Especially, about 75% of the drought stress-dominate PPI loops were associated to the binding by a well-defined drought stress-responsive transcription factor, OsbZIP23. The mutation of OsbZIP23 led to the diffuse of over 80% DS-dominate PPI loops and impaired the expression of the connected genes. As a case study, we showed how OsbZIP23 binding to a super-promoter region can integrate the PPI loop formation and transcriptional activation of four function-vital dehydrin genes upon drought stress. Our results shed light on the mechanisms of 3D genome dynamic in response to water supply variations in rice and highlight the role of OsbZIP23 in the regulation of chromatin loop formation under drought stress.
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Project description:Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. In this study, we identified H3K9ac as an efficient histone mark that response dynamically to drought stress in rice and re-constructed high-resolution 3D genome contact maps based on these sites under the normal, drought, and recovery conditions. We discovered significant decondensation of chromatin contacts with over 10000 chromatin loops lost upon drought stress treatment while the recovery of 3D genome was limited after 4-day’s re-watering. We identified dominate promoter-promoter interacting (PPI) loops under each condition and identified their significant correlations to altered gene expressions in response to the corresponding condition. Based on the relative contact intensities of the PPI connections, we characterized super-promoter regions that integrate closer connections of genes with more vigorous inductions to condition shifts. Especially, about 75% of the drought stress-dominate PPI loops were associated to the binding by a well-defined drought stress-responsive transcription factor, OsbZIP23. The mutation of OsbZIP23 led to the diffuse of over 80% DS-dominate PPI loops and impaired the expression of the connected genes. As a case study, we showed how OsbZIP23 binding to a super-promoter region can integrate the PPI loop formation and transcriptional activation of four function-vital dehydrin genes upon drought stress. Our results shed light on the mechanisms of 3D genome dynamic in response to water supply variations in rice and highlight the role of OsbZIP23 in the regulation of chromatin loop formation under drought stress.
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Project description:Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. In this study, we identified H3K9ac as an efficient histone mark that response dynamically to drought stress in rice and re-constructed high-resolution 3D genome contact maps based on these sites under the normal, drought, and recovery conditions. We discovered significant decondensation of chromatin contacts with over 10000 chromatin loops lost upon drought stress treatment while the recovery of 3D genome was limited after 4-day’s re-watering. We identified dominate promoter-promoter interacting (PPI) loops under each condition and identified their significant correlations to altered gene expressions in response to the corresponding condition. Based on the relative contact intensities of the PPI connections, we characterized super-promoter regions that integrate closer connections of genes with more vigorous inductions to condition shifts. Especially, about 75% of the drought stress-dominate PPI loops were associated to the binding by a well-defined drought stress-responsive transcription factor, OsbZIP23. The mutation of OsbZIP23 led to the diffuse of over 80% DS-dominate PPI loops and impaired the expression of the connected genes. As a case study, we showed how OsbZIP23 binding to a super-promoter region can integrate the PPI loop formation and transcriptional activation of four function-vital dehydrin genes upon drought stress. Our results shed light on the mechanisms of 3D genome dynamic in response to water supply variations in rice and highlight the role of OsbZIP23 in the regulation of chromatin loop formation under drought stress.
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