Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives

Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom

We conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis presented in our study suggests a correlation, which is negative but highly correlated between Axis 1 and GC3s (r=-0.827, P<0.01), indicating that mutational bias has a significant and dominant repressive role to the choices of GC3. We also observed a strong positive correlation between codon adaptation index (CAI) and translational adaptation index (tAIg) (0.407, P<0.01), which demonstrates the facilitation of efficient translation by the optimal codon usage patterns of the highly expressed genes. We believe that the complete set of optimal codon usage patterns detected in this study will serve as a model to enhance the transgenesis in the studied cultivar of Solanum lycopersicum.

Isolation of a Δ5 desaturase gene from Euglena gracilis and functional dissection of its HPGG and HDASH motifs

Delta (Δ) 5 desaturase is a key enzyme for the biosynthesis of health-beneficial long chain polyunsaturated fatty acids such as arachidonic acid (ARA, C20:4n-6), eicosapentaenoic acid (C20:5n-3) and docosahexaenoic acid (C22:6n-3) via the “desaturation and elongation” pathways. A full length Δ5 desaturase gene from Euglena gracilis (EgΔ5D) was isolated by cloning the products of polymerase chain reaction with degenerate oligonucleotides as primers, followed by 5′ and 3′ rapid amplification of cDNA ends. The whole coding region of EgΔ5D was 1,350 nucleotides in length and encoded a polypeptide of 449 amino acids. BlastP search showed that EgΔ5D has about 39 % identity with a Δ5 desaturase of Phaeodactylum tricornutum. In a genetically modified dihomo-gamma-linoleic acid (DGLA, C20:3n-6) producing Yarrowia lipolytica strain, EgΔ5D had strong Δ5 desaturase activity with DGLA to ARA conversion of more than 24 %. Functional dissection of its HPGG and HDASH motifs demonstrated that both motifs were important, but not necessary in the exact form as encoded for the enzyme activity of EgΔ5D. A double mutant EgΔ5D-34G158G with altered sequences within both HPGG and HDASH motifs was generated and exhibited Δ5 desaturase activity similar to the wild type EgΔ5D. Codon optimization of the N-terminal region of EgΔ5D-34G158G and substitution of the arginine with serine at residue 347 improved substrate conversion to 27.6 %.