Post-transcriptional program governing the proteome of the green alga Micromonas pusilla
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Velos
ORGANISM(S): Micromonas Pusilla Ccmp1545 (ncbitaxon:564608)
SUBMITTER: Alexandra Z. Worden
PROVIDER: MSV000079604 | MassIVE | Wed Mar 23 17:44:00 GMT 2016
SECONDARY ACCESSION(S): PXD004136
REPOSITORIES: MassIVE
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Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies.
2014-01-08 | GSE53409 | GEO
Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies. A total of 12 samples were analyzed representing three berry developmental stages (two after the onset of ripening, one during green growth). At each stage, heat stress was applied at day and night. Controls and treated berry samples were drawn in triplicates (two in duplicates) at day and at night on the microvine dwarf (Dwarf Rapid Cycling and Continous Flowering; DRCF) gibberellin-insensitive (GAI) mutant.
2014-01-08 | E-GEOD-53409 | biostudies-arrayexpress
Project description:Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3' UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.
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Project description:This a model from the article:
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model.
Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ.
Mol Syst Biol.2010 Sep 21;6:416.
20865009,
Abstract:
Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation.
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Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Experiment Overall Design: Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºCâ¢h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.
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