Open Access Research article

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles

Uma K Aryal1, Jana Stöckel2, Ravi K Krovvidi1, Marina A Gritsenko1, Matthew E Monroe1, Ronald J Moore1, David W Koppenaal1, Richard D Smith1, Himadri B Pakrasi2 and Jon M Jacobs1*

Author Affiliations

1 Pacific Northwest National Laboratory, Richland, WA 99352, USA

2 Department of Biology, Washington University, St. Louis, MO 63130, USA

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BMC Systems Biology 2011, 5:194  doi:10.1186/1752-0509-5-194

Published: 1 December 2011

Additional files

Additional file 1:

Table S2. List of all the 721 labeled proteins with their ORF, gene identifier, functional annotations, protein descriptions, and the log2 transformed RIA values across different time points. RIA was calculated as the ratio of the heavy peptide intensity (IH) to the sum of heavy and light peptides intensity (IH+IL); (RIA = IH/(IH+IL)). The consecutive diurnal cycles are labeled as D1, D2, and D3 for the dark and L1 and L2 for the light. The extensions (-1), (-5) and (-9) indicate 1, 5, 9 hrs into the dark and the light cycles. The values are given as the normalized average log2 ratios of the labeled peptides (listed in the Additional file 1, Table S1) corresponding to each proteins. ** ORFs are labeled according to the deposited genome sequence in GenBank (accession nos. CP000806 - CP000811).

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Additional file 2:

Table S1. List of all the 2837 labeled peptides with their ORF, functional annotations, protein descriptions, and the actual RIA values across different time points. RIA was calculated as mentioned before, and are the actual values which were used for given log2 transformation and rollup into proteins as listed in the Additional file 2, Table S2. ** ORFs are labeled according to the deposited genome sequence in GenBank (accession nos. CP000806 - CP000811).

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Additional file 3:

Figure S1. (A), Distribution of the labeled peptides/proteins at different time points. (B), Venn diagram showing the comparison of the current labeled proteomic data with the previous transcriptomic data [12] and the label-free quantitative proteomic data [16].

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Additional file 4:

Figure S2. Heatmaps showing light-dark induced changes in protein abundances of different functional groups over time. The complete lists of all the proteins with their RIA values are shown in Additional file 2, Table S2. Psaf, photosystem II stability/assembly factor; D-X5P/D-F6P, putative D-xylose-5-phosphate/D-fructose 6-phosphate phosphoketolase; Trx, thioredoxin.

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