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Transcriptional response to copper excess and identification of genes involved in heavy metal tolerance in the extremophilic microalga Chlamydomonas acidophila

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Abstract

High concentrations of heavy metals are typical of acidic environments. Therefore, studies on acidophilic organisms in their natural environments improve our understanding on the evolution of heavy metal tolerance and detoxification in plants. Here we sequenced the transcriptome of the extremophilic microalga Chlamydomonas acidophila cultivated in control conditions and with 500 μM of copper for 24 h. High-throughput 454 sequencing was followed by de novo transcriptome assembly. The reference transcriptome was annotated and genes related to heavy metal tolerance and abiotic stress were identified. Analyses of differentially expressed transcripts were used to detect genes involved in metabolic pathways related to abiotic stress tolerance, focusing on effects caused by increased levels of copper. Both transcriptomic data and observations from PAM fluorometry analysis suggested that the photosynthetic activity of C. acidophila is not adversely affected by addition of high amounts of copper. Up-regulated transcripts include several transcripts related to photosynthesis and carbohydrate metabolism, transcripts coding for general stress response, and a transcript annotated as homologous to the oil-body-associated protein HOGP coding gene. The first de novo assembly of C. acidophila significantly increases transcriptomic data available on extremophiles and green algae and thus provides an important reference for further molecular genetic studies. The differences between differentially expressed transcripts detected in our study suggest that the response to heavy metal exposure in C. acidophila is different from other studied green algae.

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Acknowledgments

Funding was provided by the Spanish Ministry of Economy and Competitivity (MINECO) under Grant CGL-2011-22540. We acknowledge the Data Intensive Academic Grid (DIAG) computing infrastructure [funded by National Science Foundation under Grant No. 0959894 titled MRI-R2: Acquisition of Data Intensive Academic Grid (DIAG)] as well as CSC–Finnish IT Center for Science and the Finnish Grid Infrastructure (FGI) for the allocation of computational resources. F. Puente-Sánchez enjoys a JAE-pre fellowship from the Spanish Consejo Superior de Investigaciones Científicas (CSIC). Daniel Barshis and Kimmo Mattila are acknowledged for help with the taxonomic annotation of transcripts.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland

    Sanna Olsson

  2. Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, 28040, Madrid, Spain

    Sanna Olsson

  3. INTA-CSIC, Astrobiology Center (CAB, INTA-CSIC), Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain

    Fernando Puente-Sánchez, Manuel J. Gómez & Angeles Aguilera

  4. Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029, Madrid, Spain

    Manuel J. Gómez

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  1. Sanna Olsson
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  2. Fernando Puente-Sánchez
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  3. Manuel J. Gómez
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  4. Angeles Aguilera
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Correspondence to Sanna Olsson.

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Communicated by L. Huang.

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Availability of supporting data: The Transcriptome Shotgun Assembly project supporting the results of this article is available in the National Center for Biotechnology Information (GBAH00000000, http://www.ncbi.nlm.nih.gov/nuccore/GBAH00000000). The data sets supporting the results of this article are included within the article and its supplementary files except for the phylogenetic trees for transcripts contig03072, contig03074, contig12255 and contig13050 as well as corresponding alignments used for the analyses, which are available in the LabArchives (DOI 10.6070/H4VD6WDR, https://mynotebook.labarchives.com/doi/NTI4ODQuMHw0MDY4MC80MDY4MC9Ob3RlYm9vay80MTkyMjc0OTc3fDEzNDI0NC4w/10.6070/H4VD6WDR). Online Resource 1 Housekeeping genes used for normalization in differential gene expression analysis. Reads are indicated as number of raw reads and normalized FPKM values. (PDF 184 kb)

Online Resource 2Summary of GO-terms of assembled Chlamydomonas acidophila transcripts (PDF 2141 kb)

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Online Resource 3Transcripts in Chlamydomonas acidophila functionally associated to stress. Information on length, top match organism in BLASTx to nr database, best BLAST hit accession number, E-value and functional annotation based on BLASTx searches is indicated (PDF 548 kb)

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Online Resource 4Putative foreign transcripts in Chlamydomonas acidophila functionally associated to metal stress and detoxification. The transcripts get a first BLAST hit in other organisms than green algae or plants. Transcript length, top match organism in BLASTx to nr database, best BLAST hit accession number, E-value and putative functions are also reported (PDF 294 kb)

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Online Resource 5Chlamydomonas acidophila transcripts that get a different first BLAST hit and consensus taxonomy. The transcripts get a first blast hit in other organisms than green algae or plants but get a consensus taxonomy annotation as green algae with TAXAassign using consensus threshold -t 70 (PDF 277 kb)

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Olsson, S., Puente-Sánchez, F., Gómez, M.J. et al. Transcriptional response to copper excess and identification of genes involved in heavy metal tolerance in the extremophilic microalga Chlamydomonas acidophila . Extremophiles 19, 657–672 (2015). https://doi.org/10.1007/s00792-015-0746-1

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