Open Access Research article

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids

Sabine Sturm1, Johannes Engelken23, Ansgar Gruber14*, Sascha Vugrinec1, Peter G Kroth1, Iwona Adamska2 and Johann Lavaud15

Author Affiliations

1 Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany

2 Biochemie und Physiologie der Pflanzen, Fach 602, Universität Konstanz 78457 Konstanz, Germany

3 Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona,Spain

4 Present address: Department of Biochemistry & Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia B3H 4R2, Canada

5 Present address: UMR 7266 CNRS-ULR ’LIENSs’, CNRS/University of La Rochelle, Institute for Coastal and Environmental Research, La Rochelle Cedex, France

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BMC Evolutionary Biology 2013, 13:159  doi:10.1186/1471-2148-13-159

Published: 30 July 2013

Additional files

Additional file 1:

List of sequences, pdf file. Table S1. List of sequences analysed in Figure 1 and Figure S1 (see Additional file 3).

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Additional file 2:

Sequence alignment, text file (FASTA format). Sequence alignment used to build the phylogenetic tree of three- and four-helices protein families of the extended LHC protein superfamily (Figure S3, see Additional file 5), 51 positions, 55 taxa.

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Additional file 3:

Annotated sequence alignments, pdf file. Figure S1. (A) Sequence alignment of helices I and III of RedCAPs with red lineage LHCF, CAC/LHCR and LHCX/LI818 proteins. (B) Sequence alignment of helices I and III of RedCAPs with green lineage CAB (LHCa, LHCb and LHCP), LHCSR/LI818, ELIP and LHL4 proteins. (C) Full-length sequence alignment of identified RedCAP amino acid sequences. Identical amino acids are surrounded by black and similar amino acids by grey boxes. Chl-binding motifs located in transmembrane helices I and III are marked with a green bar above the alignment, and the approximate position of transmembrane helix II is marked with a grey bar. Accession numbers of aligned sequences are given in Table S1 (see Additional file 1).

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Additional file 4:

Putative chlorophyll-binding sites in RedCAPs, pdf file. Figure S2. Putative chlorophyll-binding sites in members of the LHC (light-harvesting complex) and the RedCAP protein families. Experimentally derived chlorophyll binding sites from Arabidopsis thaliana LHCII proteins are indicated in green according to [104-106]. Conserved amino acid positions that may represent putative binding sites for chlorophylls or carotenoids in RedCAPs are indicated in blue. Note that the second helix (helix II) is poorly conserved between distant members of the LHC protein family and not conserved between LHC and RedCAP, therefore the alignment of different helices II does not necessarily show homologous positions.

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Additional file 5:

Phylogenetic tree, pdf file. Figure S3. Phylogenetic tree of three- and four-helices protein families of the extended LHC protein superfamily. Robust internal nodes were labelled according to their corresponding statistical support (Maximum likelihood, ML; Neighbor-joining, NJ and bayesian posterior probability). Accession numbers of analysed sequences are listed in Table S1 (see Additional file 1); for the sequence alignment see Additional file 2.

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Additional file 6:

Sequence alignment, text file (FASTA format). Sequence alignment used to build the phylogenetic tree of RedCAPs (Figure 1), 146 positions, 13 taxa.

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Additional file 7:

References for Figure2, pdf file. Table S2. Reference table for the proposed evolutionary history of RedCAP, LHC and LHC-like genes (Figure 2). Findings for cyanobacteria, green algae and plants have been generalised according to published studies, while findings for red algae, cryptophytes and diatoms are specific for representative species of which the plastid-, nucleomorph-, and nuclear genomes (or large transcriptome datasets in the case of “present” statements) have been sequenced and published (see footnotes in table). Genes are marked as “present” if their existence has been reported in the literature; “absent” means that these genes were neither identified in our analyses, nor—to our knowledge—have been reported to exist before (hence no references for “absent” statements). For RedCAP sequence identifiers see also Table 1 of this study.

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Additional file 8:

Localisation of the RedCAP protein in complex plastids of diatoms II, pdf file. Figure S4. Expression of the full-length RedCAP:GFP fusion constructs in P. tricornutum. Microscopical images of transmitted light (differential interference contrast, DIC), Chlorophyll autofluorescence, GFP fluorescence and a merged image are shown from left to right, fluorescence images are maximum intensity projections of seven slices of a 3.08 μm image stack, scale bars represent 10 μm.

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Additional file 9:

RedCAP, LHCF and LHC-like gene expression analysis as given by REST, pdf file. Table S3. RedCAP, LHCF and LHC-like gene expression analysis as given by REST [102]. (A) Data for dark-treated cells (experimental condition D). (B) Data for low light grown cells (experimental condition LL). (C) Data for moderate high light grown cells (experimental condition ML). (D) Data for cells exposed to high light for 2 h (condition HL). Experiments were performed in four replicates as described in the Methods section of the manuscript. For details of the software see [102]; the column “P(H1)” lists the results of REST‘s hypothesis test (the probability that the difference between the sample and control occurs only by chance), the “Result” column lists those up- or down-regulations (relative to the first sample) that are indicated as significant by the statistical randomisation tests by REST.

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Additional file 10:

Changes in RedCAP, LHC and LHC-like transcript abundance, pdf file. Figure S5. Changes in RedCAP, LHC and LHC-like transcript abundance. Abbreviations and symbols: upward arrow, up-regulation; rightward arrow, no changes in the expression; downward arrow, down-regulation; CR, diurnal rhythm; HL, high light; LL, low light; ML, moderate high light; n.c., not clear; a, a transient, statistically significant up-regulation at the beginning of the previous light phase; b, diurnal rhythm under LL but not under ML conditions; c, up-regulation in the late phase of illumination; d, up-regulation in the early phase of illumination; e, short-term moderate up-regulation.

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Additional file 11:

Primers used for the RT-qPCR, pdf file. Table S4. Primer sequences used for the real-time quantitative PCR analysis in P. tricornutum, the LHCF2 gene has been analysed with the primers designed by Siaut et al. [36] (the gene is called “FcpB” in the cited study).

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