Lars Wöhlbrand

Cell biological and proteogenomic study of the chloroplast of the marine, bloom-forming dinoflagellate P. cordatum

Cells of P. cordatum adapted to growth at 20 °C and constant light:dark conditions were shifted to growth at 26 °C and 30 °C, respectively, with similar illumination conditions. During exponential and stationary growth, cells were collected for transcriptomic, proteomic and metabolomic analyses.

The family of Desulfobacteraceae comprises mtabolically versatile, completely oxidizing, sulfate-reducing bacteria that play an important role in the global carbon- and sulfor-cycles, mainly in the marine realm. In this study, six different species of Desulfobacteraceae were studied by comparative proteogenomics, i.e. Desulfobacula toluolica Tol2, Desulfococcus multivorans 1be1, Desulfonema limicola, Desulfonema magnum, Desulfosarcina variabilis 3be13 and Desulfobacterium autotrophicum ...

The soluble protein fraction was subjected to shotgun proteomics (i..e. in-solution digest) applying nanoLC ESI-Iontrap MS/MS and only detections in at least two replicates per condition and bacterium were considered for subsequent analyses. Correspondingly peptide count data was compiled per condition and strain studied.

Tryptic peptides of P. cordatum were separated by 2D SCX-/RP nanoLC coupled to ESI-Iontrap MS/MS.

The membrane fraction of Prorcentrum cordatum was prepared and proteins solubilized using SDS. Subsequently, proteins were separated by SDS-PAGE, subjected to tryptic in-gel digest and nanoLC ESI-iontrap MS/MS.

Prepared (sub-)cellular fractions were separated by gradient SDS-PAGE and entire sample lanes cut into pieces prior to in-gel digest and nanoLC separation coulpled to iontrap MS/MS detection.

Prorocentrum cordatum was subjected to whole cell shotgun analyses (in-solution digest) unsing nanoLC ESI-intrap MS/MS

Detailed description of the methods applied for proteomic analyses of P. cordatum heat stress response