Codon bias

Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection

J. L. Liu, Ma, Y. H., Xu, J. Y., Chen, Y. X., Chen, S. E., and Ma, Z. R., “Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection”, vol. 14, pp. 16803-16812, 2015.

The mechanism of alternative AUG usage in foot-and-mouth disease virus is not completely understood. Using simple computational approaches, we evaluated the contributions of overall codon bias, quantitative codon bias, and %GC of the region between the two alternative AUGs, Region-La, as well as the nucleotide bias of the sequence context flanking each AUG with respect to translation initiation efficiency. For all serotypes of this virus, we found that only a small component of the effect of RNA secondary structure on ribosome scanning was due to the low %GC of Region-La.

Molecular cloning and characterization of the glyceraldehyde-3-phosphate dehydrogenase gene from Penicillium expansum PE-12

T. Zhang, Qi, Z., Yu, Q. S., and Tang, K. X., “Molecular cloning and characterization of the glyceraldehyde-3-phosphate dehydrogenase gene from Penicillium expansum PE-12”, vol. 12, pp. 2442-2454, 2013.

Penicillium expansum produces large amounts of lipase, which is widely used in laundry detergent and leather industry. We isolated the glyceraldehyde-3-phosphate dehydrogenase gene (PeGPD) from P. expansum PE-12 through reverse transcriptase PCR and 5ꞌ-3ꞌ-rapid amplification of cDNA ends (RACE-PCR). The gene is 1266 bp long, including an ORF of 1014 bp, encoding a polypeptide chain of 337 amino acids. A phylogenetic tree based on GPD proteins showed that P. expansum is close to Aspergillus species, but comparatively distant from P.