title: Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii.
abstract: The efficiency of gene expression in all organisms depends on the nucleotide composition of the coding region. GC content and codon usage are the two key sequence features known to influence gene expression, but the underlying molecular mechanisms are not entirely clear. Here we have determined the relative contributions of GC content and codon usage to the efficiency of nuclear gene expression in the unicellular green alga Chlamydomonas reinhardtii. By comparing gene variants that encode an identical amino acid sequence but differ in their GC content and/or codon usage, we show that codon usage is the key factor determining translational efficiency and, surprisingly, also mRNA stability. By contrast, unfavorable GC content affects gene expression at the level of the chromatin structure by triggering heterochromatinization. We further show that mutant algal strains that permit high-level transgene expression are less susceptible to epigenetic transgene suppression and do not establish a repressive chromatin structure at the transgenic locus. Our data disentangle the relationship between GC content and codon usage, and suggest simple strategies to overcome the transgene expression problem in Chlamydomonas.
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany.
authors.forename: Rouhollah
authors.initials: R
authors.lastname: Barahimipour
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Genomics and Proteomics, University of California Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA, 90095, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Strenkert
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany.
authors.forename: Juliane
authors.initials: J
authors.lastname: Neupert
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schroda
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Genomics and Proteomics, University of California Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA, 90095, USA.
authors.forename: Sabeeha S
authors.initials: SS
authors.lastname: Merchant
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany.
authors.forename: Ralph
authors.initials: R
authors.lastname: Bock
mesh_terms: D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism; D001482:Base Composition / Q000235:genetics*; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000378:metabolism; D003062:Codon / Q000235:genetics*; D015870:Gene Expression; D015151:Immunoblotting; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D018613:Microscopy, Confocal; D009154:Mutation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D019076:Transgenes
chemical_list: D020418:Algal Proteins; D003062:Codon; D008164:Luminescent Proteins; D012333:RNA, Messenger
keywords: Chlamydomonas reinhardtii; GC content; RNA stability; codon usage; epigenetics; histone modification; translation