Codon usage in plant genes

Abstract

We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general.

Molecular Cloning and Evidence for Osmoregulation of the Δ1-Pyrroline-5-Carboxylate Reductase (proC) Gene in Pea (Pisum sativum L.)

“…The ORF encoded a polypeptide of 273 amino acids with a predicted molecular mass of 28,242 Da. Codon usage in the pea P5CR gene was not significantly different from that reported for other dicot genes (24).…”

“…5). Root P5CR mRNA levels remained 4-and 3-fold higher in salt-stressed plants at 24 and 72 h, respectively. In contrast, there was no significant influence of salinization on levels of the 1.3-kb transcript in leaf tissues of these seedlings.…”

Sequence Architecture Downstream of the Initiator Codon Enhances Gene Expression and Protein Stability in Plants

“…The preferred occurrence of T at ϩ6, which is the wobble position in the codon for Ala, is characteristic of the penultimate N-terminal codon in the dataset developed by us. In an earlier study (Murray et al, 1989), the frequency of GCT employed for Ala in plant gene database was calculated at 37%. Quite comparably, the dataset of highly expressed nuclear genes analyzed by us also showed GCT for Ala at 39% positions in the reading frame.…”

High level accumulation of α-glucan in maize kernels by expressing the gtfD gene from Streptococcus mutans

“…In general, genes in monocots including maize contain a high G + C content at the degenerate third base; 16 out of 18 amino acids favor G or C in this position (Murray et al 1989). However, bacterial genes, such as gtfD, follow a different codon bias pattern.…”

“…Increased recombinant protein accumulation due to codon optimization is reported in other cases (Horvath, et al 2000 andKarasev et al 2005). Following the maize codon usage guidelines of Murray et al (1989), we optimized gtfD N471D with maizepreferred codons and produced a synthetic gene. The resulting sequence (Genbank accession number DQ659099), which has the exact same deduced amino acid sequence as the original enzyme, differs from the original bacterial gene in the following three ways: (1) the sequence encoding the 36 amino acid signal peptide was removed and replaced with ATG-an initiator methionine codon, (2) 29% of gtfD/N471D's bases were changed according to maize preferred codon usage increase GC content from 38.5% to 62.8%, (3) several putative polyadenylation sites were eliminated.…”