Effects of rare codon clusters on the expression of a high-turnover chloroplast protein in Chlamydomonas reinhardtii

Weiß, Caroline; Bertalan, Ivo; Johanningmeier, Udo

doi:10.1016/j.jbiotec.2012.04.008

Cited by 8 publications

(1 citation statement)

References 37 publications

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“…The Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity characteristics of SCUB have been widely analyzed in the plastid genomes of different plants. [13][14][15][16][17][18] However, the difference among SCUB in plastid genomes from lower to higher plants has not been well examined.…”

Section: Introductionmentioning

confidence: 99%

Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

Tian

et al. 2015

Evol Bioinform Online

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Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

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Section: Introductionmentioning

confidence: 99%

Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

Tian

et al. 2015

Evol Bioinform Online

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Analysis of heterologous regulatory and coding regions in algal chloroplasts

Gimpel

Mayfield

2012

Appl Microbiol Biotechnol

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The basic photosynthetic apparatus is highly conserved across all photosynthetic organisms, and this conservation can be seen in both protein composition and amino acid sequence. Conservation of regulatory elements also seems possible in chloroplast genes, as many mRNA untranslated regions (UTRs) appear to have similar structural elements. The D1 protein of Photosystem II (psbA gene) is a highly conserved core reaction center protein that shows very similar regulation from cyanobacteria through higher plants. We engineered full and partial psbA genes from a diverse set of photosynthetic organisms into a psbA deficient strain of Chlamydomonas reinhardtii. Analysis of D1 protein accumulation and photosynthetic growth revealed that coding sequences and promoters are interchangeable even between anciently diverged species. On the other hand functional recognition of 5' UTRs is limited to closely related organisms. Furthermore transformation of heterologous promoters and 5' UTRs from the atpA, tufA and psbD genes conferred psbA mRNA accumulation but not translation. Overall, our results show that heterologous D1 proteins can be expressed and complement Photosystem II function in green algae, while RNA regulatory elements appear to be very specific and function only from closely related species. Nonetheless, there is great potential for the expression of heterologous photosynthetic coding sequences for studying and modifying photosynthesis in C. reinhardtii chloroplasts.

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Enhancing resistance of Chlamydomonas reinhardtii to oxidative stress fusing constructs of heterologous antioxidant peptides into D1 protein

et al. 2021

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Effects of rare codon clusters on the expression of a high-turnover chloroplast protein in Chlamydomonas reinhardtii

Cited by 8 publications

References 37 publications

Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

Analysis of heterologous regulatory and coding regions in algal chloroplasts

Enhancing resistance of Chlamydomonas reinhardtii to oxidative stress fusing constructs of heterologous antioxidant peptides into D1 protein

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