SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations

SummaryMeasuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently‐used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower‐abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).

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“…Proteome sizes were estimated previously by Hooper et al . (). Marker collections are detailed in Table S3.…”

Section: Resultsmentioning

confidence: 97%

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples

et al. 2017

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“…Close examination of other up‐regulated DEGs identified that nine of them (g22426.t2 , g23216 .t1, g28049.t1 , g3557.t1 , g850.t1 , g9424.t1 , g20853.t1 , g9939.t1 , and g16955.t1 ) encode proteins that are predicted to be targeted to plastids in T. subterraneum (TargetP) or are homologs of genes that encode plastid‐localized proteins in Arabidopsis ( SUBA4 ; Hooper, Castleden, Tanz, Aryamanesh, & Millar, ; logFC > 2, FDR < 0.05, Table S1). These include IMMUTANS (plastid alternative oxidase, g28049.t1 ), two enzymes in thiamine synthesis ( g3557.t1 , g9424.t1 ), an alkenal/one oxidoreductase ( g20853.t1 ), and a plastid ABC transporter ( g22426.t2 ) (Table S1).…”

Section: Resultsmentioning

confidence: 99%

Globular structures in roots accumulate phosphorus to extremely high concentrations following phosphorus addition

Ryan

Kaur

Nazeri

et al. 2019

Plant Cell & Environment

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Crops with improved uptake of fertilizer phosphorus (P) would reduce P losses and confer environmental benefits. We examined how P‐sufficient 6‐week‐old soil‐grown Trifolium subterraneum plants, and 2‐week‐old seedlings in solution culture, accumulated P in roots after inorganic P (Pi) addition. In contrast to our expectation that vacuoles would accumulate excess P, after 7 days, X‐ray microanalysis showed that vacuolar [P] remained low (<12 mmol kg−1). However, in the plants after P addition, some cortex cells contained globular structures extraordinarily rich in P (often >3,000 mmol kg−1), potassium, magnesium, and sodium. Similar structures were evident in seedlings, both before and after P addition, with their [P] increasing threefold after P addition. Nuclear magnetic resonance (NMR) spectroscopy showed seedling roots accumulated Pi following P addition, and transmission electron microscopy (TEM) revealed large plastids. For seedlings, we demonstrated that roots differentially expressed genes after P addition using RNAseq mapped to the T. subterraneum reference genome assembly and transcriptome profiles. Among the most up‐regulated genes after 4 hr was TSub_g9430.t1, which is similar to plastid envelope Pi transporters (PHT4;1, PHT4;4): expression of vacuolar Pi‐transporter homologs did not change. We suggest that subcellular P accumulation in globular structures, which may include plastids, aids cytosolic Pi homeostasis under high‐P availability.

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“…To specifically assess the extent of how much SnRK1 anterograde signaling could affect plastidial and mitochondrial proteins, we focused on nuclear-encoded targets of those TFs with a known or clearly predicted localization in plastids or mitochondria according to SUBA 4.0 (http://suba.live; Hooper et al, 2017). This analysis uncovered a remarkable list of nuclearencoded organellar proteins with important functions in mitochondria and chloroplasts (Supplemental Table S1).…”

Section: Anterograde Signals To Organelles Via Phosphorylation Of Tramentioning

confidence: 99%

The SnRK1 Kinase as Central Mediator of Energy Signaling between Different Organelles

et al. 2018

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The evolutionarily conserved SNF1-related protein kinase 1 (SnRK1) kinase complex is a key regulator in adjusting cellular metabolism during starvation, stress conditions, and growth-promoting conditions. Over the last two decades, extensive genetic evidence for a widespread SnRK1 signaling network has accumulated. It is now well established that SnRK1 is a central integrator of energy signaling. However, little is known about the connections between the cytoplasmic and nuclear-localized SnRK1 and plastids and mitochondria as the main energy-producing compartments in the cell. Here, we review recent findings indicating how SnRK1 affects metabolic adaptation, including plastidial and mitochondrial functions. Special emphasis is put on identified direct targets of SnRK1, which would eventually enable cross talk with organelles. In this context, a number of transcription factors (TFs) are emerging as mediators of SnRK1 signaling, potentially linking SnRK1 activity to organellar functions. Furthermore, many SnRK1 targets act in various hormonal signaling pathways, which are at least partly localized in plastids. With this review, we summarize the current knowledge on SnRK1 organelle interaction and provide ideas on the potential molecular mechanisms governing these interactions. METABOLIC REPROGRAMMING BY SNRK1 KINASE ACTIVITY UNDER DIFFERENT GROWTH AND STRESS CONDITIONSAlready under optimal growth conditions, plants need to continuously adjust their metabolic balance between autotrophic growth based on photosynthesis during the day and respiration during the night. At daytime, sugars and other metabolites are produced by photosynthesis in chloroplasts and further distributed to be used in other metabolic pathways at different cellular compartments or transported to nonphotosynthetic sink tissues. During the night, starch and sugars supply carbon equivalents for respiration, providing the necessary energy for further growth and metabolic activities. Additionally, metabolic reprogramming is required for plants to adjust their metabolism to diverse biotic and abiotic environmental stimuli. This often leads to a stop of plant growth involving a reduction in ribosomal protein synthesis, and in parallel, accumulation of protective metabolites or defense compounds. This switching of cellular energy metabolism is mediated by the activity of the evolutionarily conserved AMPK/ SNF1/SnRK1 kinase complex (Box 1; Crozet et al.,

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SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations

Cited by 392 publications

References 37 publications

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples

Globular structures in roots accumulate phosphorus to extremely high concentrations following phosphorus addition

The SnRK1 Kinase as Central Mediator of Energy Signaling between Different Organelles

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