Dataset Information

Phototropin-Mediated Signaling Kinase regulation in Chlamydomonas reinhardtii

ABSTRACT: Green algae, such as Chlamydomonas reinhardtii, use light as an energy source, as well as a source of information. Light is processed by photoreceptors, such as phototropin, which subsequently send signals throughout the organism. Herein, a phosphoproteomic workflow is employed to charachterize signaling pathways of phototropin. For phosphopeptide enrichment, tryptic digests were diluted with 100 µL of acetonitrile. A Fe-IMAC column was equilibrated, and each sample was injected separately onto the column.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Chlamydomonas Reinhardtii

SUBMITTER: Leslie Hicks

LAB HEAD: Leslie Hicks

PROVIDER: PXD045599 | Pride | 2025-02-03

REPOSITORIES: Pride

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			Action	DRS
	20230508_PWS_DIMITRIS_CR_WT_B_4.timeseries.data	Other
	20230508_PWS_DIMITRIS_CR_WT_B_4.wiff	Wiff
	20230508_PWS_DIMITRIS_CR_WT_B_4.wiff.scan	Wiff
	20230508_PWS_DIMITRIS_CR_WT_B_4.wiff2	Wiff
	20230512_PWS_DIMITRIS_CR_PHOT_B_1.timeseries.data	Other

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Project description:Pelagic aggregates function as hotspots for microbial activity and biological carbon pumps for exporting OM fixed by photoautotrophs to sediments in lakes and oceans. In iron-rich (ferruginous) lakes, photoferrotrophic or chemolithoautotrophic bacteria appear to contribute to CO2 fixation by oxidizing reduced iron which leads to the formation of iron-rich pelagic aggregates called iron-snow. In acidic lakes, iron snow is colonized mainly by acidophilic iron-cycling microbes that can trigger interspecies aggregation mechanisms. However, the significance of iron oxidizers in carbon fixation, their general role in iron snow functioning, and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis with a 13CO2 metabolic labeling approach to determine general metabolic activities. Protein-based stable isotope probing (protein-SIP) was used to trace the 13CO2 incorporation in iron snow microcosms over time under both oxic and anoxic conditions. Analysis of our mRNA-derived metatranscriptome data identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6%-85.7%) in iron snow encoding a variety of ecologically relevant pathways, including carbon fixation, polysaccharide biosynthesis, and flagellar-based motility. We did not detect transcriptional activity for carbon fixation from archaea or eukaryotes. The largest numbers of expressed genes (3008, 2991, 2936) matched to the genomes of our previously obtained iron snow isolates (Acidithrix sp. C25, Acidiphilium sp. C61, Acidocella sp. C78) separately. 13CO2 incorporation studies identified Leptospirillum and Ferrovum, as the main active chemolithoautotrophs under oxic conditions, and Ferrovum was the main active organism under anoxic conditions as well. Small amounts of labeled 13C (Relative isotope abundance: 1.0%-5.3%) were found in the heterotrophic Acidiphilium and Acidocella. Overall, our data show that iron oxidizers play an important role in the formation of iron minerals and CO2 fixation, but the majority of fixed C apparently did not reach other iron snow microbes. This finding suggests that most of the fixed C will be directly exported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h) Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1 Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1 Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1 Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1 Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Keywords = phorbol ester Keywords = macrophage Keywords = polysome Keywords = post-transcriptional regulation Keywords: parallel sample

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Phototropin-Mediated Signaling Kinase regulation in Chlamydomonas reinhardtii

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