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Parallel comparison of mutant proteomes with altered carbon metabolism reveals Hik8 regulates PII phosphorylation and the basal level glycogen accumulation in a cyanobacterium

ABSTRACT: To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all the five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Synechocystis Sp. Pcc 6803

SUBMITTER: Chengcheng Huang

LAB HEAD: Yingchun Wang

PROVIDER: PXD035864 | Pride | 2023-07-20

REPOSITORIES: Pride

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Parallel Proteomic Comparison of Mutants With Altered Carbon Metabolism Reveals Hik8 Regulation of P<sub>II</sub> Phosphorylation and Glycogen Accumulation in a Cyanobacterium.

Huang Chengcheng C Duan Xiaoxiao X Ge Haitao H Xiao Zhen Z Zheng Limin L Wang Gaojie G Dong Jinghui J Wang Yan Y Zhang Yuanya Y Huang Xiahe X An Hongyu H Xu Wu W Wang Yingchun Y

Molecular & cellular proteomics : MCP 20230522 7

Carbon metabolism is central to photosynthetic organisms and involves the coordinated operation and regulation of numerous proteins. In cyanobacteria, proteins involved in carbon metabolism are regulated by multiple regulators including the RNA polymerase sigma factor SigE, the histidine kinases Hik8, Hik31 and its plasmid-borne paralog Slr6041, and the response regulator Rre37. To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared th ...[more]

PMID: 37225018

Similar Datasets

Parallel comparison of mutant proteomes with altered carbon metabolism reveals Hik8 regulates PII phosphorylation and the basal level glycogen accumulation in a cyanobacterium

Project description:To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all the five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism.

2023-07-20 | PXD035898 | Pride

Proximity labeling facilitates defining neighborhood proteome of photosystem II oxygen evolution complex in a model cyanobacterium

Project description:APEX2-based proximity labeling coupled with mass spectrometry have great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach it is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis, and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO.

2023-02-17 | PXD036113 | Pride

A systematic survey of the light-dependent protein quality control in a model cyanobacterium

Project description:We conducted a large-scale identification of protein degradation under light or dark condition in the model cyanobacterium Synechocystis PCC 6803 (Hereafter referred as Synechocystis) using the isobaric labeling based quantitative proteomics technique. This is the first discovery about redox-regulated protein degradation in cyanobacteria. Our results provide the first comprehensive catalog of the light-dependent protein degradation events, and would act as an important resource in future study toward understanding light-regulated processes and protein quality control mechanism in cyanobacteria.

2021-11-10 | PXD023181 | Pride

Synechocystis spatial proteome LC-MS/MS

Project description:We treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803, with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble compartments using a quantitative proteomics approach.

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Synechocystis 6803 LC-MS/MS - Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins

Project description:Identification of the membrane and the soluble proteins in Synechocystis sp. PCC6803

2015-01-16 | PXD001246 | Pride

Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation

Project description:Cyanobacteria have shaped the earth’s biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signalling, adaptation and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry towards the unbiased detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labelling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2,382 proteins and 183 phosphorylation events and quantifying 2,111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 hours. Among the proteins with increased phosphorylation, the PII signalling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.

2016-05-09 | PXD001831 | Pride

The signal transduction protein PII controls ammonium, nitrate and urea uptake in cyanobacteria

Project description:PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homologue GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.

2019-07-10 | PXD013411 | Pride

Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803

Project description:We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify 97 cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. One quantification method was calibrated with artificial 15N-labelled proteins comprising concatenated proteotypic tryptic peptides and the other three methods were label-free (DDA-iBAQ, DDA-Top3, DIA-Top3) calibrated with the Sigma UPS2 standard protein mixture. As expected, the quantification methods gave individual distributions of abundance levels for each target protein that, for statistical validity, were not combined into single central tendency and variation metrics. Instead, overlapping distributions were merged to provide consensus abundance ranges. Quantification, expressed as copy numbers per cell (cpc), spanned four orders of magnitude, representing the complete abundance range from <1000 to >100,000 cpc of the proteins representing the complexes and pathways that were the focus of this study.

2023-01-04 | PXD035632 | Pride

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Project description:In this study, by using shotgun LC-MS/MS approach with the Tandem Mass Tag (TMTs) isobaric labelling technique we show that proteins in photosystem, inorganic carbon uptake and CO2 fixation systems are significantly changed in Δhik33 cells compared with WT cells.This is the normal culture condition proteomic data.

2017-05-19 | PXD005085 | Pride

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Project description:Cyanobacteria are photoautotrophs that profoundly impact the biogeochemical cycles on Earth. Due to their photosynthetic lifestyle that includes the fixation of atmospheric CO2, they are of increasing interest for a sustainable economy. Knowledge of protein expression and regulation is key for understanding of the cyanobacterial metabolism; however, proteome studies in cyanobacteria are still limited and cover only a fraction of the theoretical proteome. Here, we performed a proteogenomic analysis of 628 LC-MS/MS measurements for the unicellular model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover potential novel open reading frames (ORFs). By mapping extensive shotgun MS proteomics data generated by the SCyCode consortium onto a six-frame translation of the Synechocystis genome, we re-annotated 96 start sites and discovered 103 novel open reading frames (ORFs). Through re-analysis of previously published multi-omics datasets, we confirmed 48 re-annotated or novel ORFs with high confidence. Our study resulted in the largest reported proteome and phosphoproteome dataset for Synechocystis, covering expression of about 80% of the theoretical proteome and 642 O-phosphorylation events under various cultivation conditions, such as nitrogen or carbon limitation. This dataset will serve as a resource providing dedicated information on condition-dependent protein expression and phosphorylation.

2024-01-05 | PXD033243 | Pride

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