Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities

Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer.
In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level.
Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication.

The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.

The dataset contains all 45 raw data files from the mass spectrometry analysis (LC-MS/MS) of the cultures of the alga Guillardia theta, which were analyzed in this study. These files have Waters raw format and can be processed with commercial software such as ProteinLynx Global server 3.0 and Mascot Distiller 2.5. The algae, which were grown under optimal light, were analyzed in the NL-series. The algae, which were grown under high light intensity, were analyzed in the HL-series, and the algae, which were grown under low light intensity, were analyzed in the LL-series. The details of the growth conditions are described in doi: 10.1007/s11120-017-0400-0. Each series of samples contained five biological replicates, of which each was analyzed in triplicate. In total, 45 samples were analyzed. In addition to the raw data files, the dataset contains the peaklist-files (PKL, text file), which were used for the database searches using the Mascot search engine and the mzid-files (XML files) of the individual database searches. The dataset includes also the fast-files of the sequence databases, which were used for the database searches (text files). The other data of this study are not included in this dataset.

An important scientific application of these data in this study is providing experimental evidence for the expression of the phycobili antenna proteins of Guillardia theta and a tool for correcting and optimizing their gene models. Show less..