<div><p>The following are excerpts from Walworth et al. 2016a. Please refer to this reference for more details of the methodology used to generate these data.</p>
<p>"Protein spectral counts are generated by extracting proteins from cells, digesting into smaller peptides, separating them on HPLC (high-performance liquid chromatography), and measuring peptide masses on a mass spectrometer to ascertain mass-to-charge ratio. Peptide fragment ratios are then compared to a reference genome and spectral counts per protein are enumerated."</p>
<p>"Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean."</p>
<p>"Spectral counts compare a specific protein’s abundance between treatments, rather than against other proteins, because the sensitivity of spectral counts can vary between proteins depending on the number of tryptic peptides within the sequence and their chemical characteristics." </p></div>
Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2
<div><p><em>Trichodesmium erythraeum</em> was grown in biological triplicate under two CO2 regimes (380 and 750 uatm pCO2) and four different nutrient regimes (replete, phosphorus-limited,iron-limited, iron/phosphorus colimited). </p>
<p>Raw sequence reads from the <em>Trichodesmium </em><em>erythraeum</em><em> </em>used in this experiment can be accessed at The National Center for Biotechnology Information (NCBI) under the BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA312342" target="_blank">PRJNA312342</a>. </p>
<p>Protein sequences can be accessed through NCBI BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA318/" target="_blank">PRJNA318</a>.</p>
<p>The fasta file <a href="https://datadocs.bco-dmo.org/docs/302/HiCO2_AdaptCyano/data_docs/IMG_Trichodesmium_IMS101_genes.fasta">IMG_Trichodesmium_IMS101_genes.fasta</a> (5.4 MB) contains all of the Integrated Microbial Genomes (IMG)-annotated genes in the Trichodesmium erythraeum IMS101 genome. More information can be found at the IMG Trichodesmium genome portal, "<a href="https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=proteinCodingGenes&taxon_oid=637000329" target="_blank">genes page</a>" and <a href="https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000329" target="_blank">IMG Genome ID 637000329</a> page.</p>
<p>Raw spectra are available as dataset PXD010515 in the PRIDE proteome-exchange repository (doi: 10.6019/PXD010515).</p>
<p>These results were published in:<br />
* Walworth et al., 2016a<br />
* Walworth et al., 2016b<br />
* Walworth et al., 2018</p>
<p><strong>Related dataset: </strong><a href="https://www.bco-dmo.org/dataset/649904" target="_blank">Trichodesmium physiology and cell growth</a></p></div>
Trichodesmium proteomes and Hi CO2 adaptation
<div><p>BCO-DMO data manager notes:<br />
* Data version 2: 2018-03-15 replaces version 1: 2016-06-22. Data version 2 removed column "accession_numbers" containing protein sequence accession numbers at NCBI which were no loger valid due to an annotation remapping effort. The appropriate protein accessions can instead be found through the NCBI BioProject page: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA318/" target="_blank">PRJNA318</a>. The data parameter "Gene ID" was changed to name "Locus Tag" to be consistent with terminology at IMG and NCBI.</p></div>
649873
Trichodesmium proteomes and Hi CO2 adaptation
2016-06-22T14:51:35-04:00
2016-06-22T14:51:35-04:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:649873
Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project)
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Hutchins, D. A., Webb, E. A., Saito, M. A. (2018) Trichodesmium nutrient-limited proteomes in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2018-03-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/649873 [access date]
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