Codon Usage in Higher Plants, Green Algae, and Cyanobacteria

Abstract

Codon usage is the selective and nonrandom use of synonymous codons by an organism to encode the amino acids in the genes for its proteins. During the last few years, a large number of plant genes have been cloned and sequenced, which now permits a meaningful comparison of codon usage in higher plants, algae, and cyanobacteria. For the nuclear and organellar genes of these organisms, a small set of preferred codons are used for encoding proteins. Codon usage is different for each genome type with the variation mainly occurring in choices between codons ending in cytidine (C) or guanosine (G) versus those ending in adenosine (A) or uridine (U). For organellar genomes, chloroplastic and mitochrondrial proteins are encoded mainly with codons ending in A or U. In most cyanobacteria and the nuclei of green algae, proteins are encoded preferentially with codons ending in C or G. Although only a few nuclear genes of higher plants have been sequenced, a clear distinction between Magnoliopsida (dicot) and Liliopsida (monocot) codon usage is evident. Dicot genes use a set of 44 preferred codons with a slight preference for codons ending in A or U. Monocot codon usage is more restricted with an average of 38 codons preferred, which are predominantly those ending in C or G. But two classes of genes can be recognized in monocots. One set of monocot genes uses codons similar to those in dicots, while the other genes are highly biased toward codons ending in C or G with a pattem similar to nuclear genes of green algae. Codon usage is discussed in relation to evolution of plants and prospects for intergenic transfer of particular genes.

Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

“…Notwithstanding our small sample, the gymnosperm nuclear genes can very roughly be divided into two classes--a GC-rich class with >60% GC at third positions and a GC-poor class with <60% GC at third positions. This distribution is more or less intermediate with regard to the distributions found in monocots and dicots, respectively (Salinas et al 1988;Campbell and Gowri et al 1990). Both the GC-rich and the GC-poor group of conifer genes are somewhat lower in third-position GC content than their graminaceous counterparts.…”

“…CpG suppression is found to varying extents in different plant genomes (Hepburn et al 1987;Quigley et al 1989;Campbell and Gowri 1990;. Lack of suppression has been attributed to both protection against methylation (Bird 1986) as well as specific G-T mismatch repair (Hepburn et al 1987); for the purpose of our model, a distinction between these (Brinkmann et al 1987) and tobacco (Shih et al 1986), GapC from maize (Brinkmann et al 1987) and tobacco (Shih et al 1986), Lhcbl from rice (Lhcbl*l or 2120, Matsouka 1990) and tomato (Lhcbl*2 or Cab-lB, Pichersky et al 1985), Lhcb2 from rice (Lhcb2*l or 2123, Matsouka 1990) and tomato , Lhcb5 from barley (SCrensen et al 1992) and tomato , Pal from rice (Minami et al 1989) and tomato (EMBL M90692), Pcr from barley (Schultz et al 1989) and pea (Spano et al 1992a), and…”

“…In the nuclear genomes of monocotyledons, two distinct types of genes are found: GC-biased genes, in which codon usage is strongly biased toward G and C in the third codon position, and nonbiased genes, in which codon usage is relaxed and the four nucleotides appear in approximately equal frequencies in the third codon position (Campbell and Gowri 1990;Brinkmann et al 1987). In dicotyledons, GC-biased genes are very rare and the codon usage of most genes resembles that of nonbiased genes in monocots ).…”

Combining Machine Learning and Homology-Based Approaches to Accurately Predict Subcellular Localization in Arabidopsis

“…As it was reported earlier that the overall bias in synonymous codon usage of a genome is species specific (Campbell and Gowri, 1990;Fennoy and Bailey-Serres, 1993;Sandberg et al, 2003;Liu and Xue, 2005), this possibility could also be elaborated to make use of "genome signatures" for the species-specific prediction systems. Therefore, the present bioinformatics analysis should not be interpreted to reach some biological conclusion(s), such as if protein targeting is species specific.…”

Codon Usage Bias of the Wheat Flower Development Gene WAG-2 and Other AGAMOUS Group Genes

“…Higher plants are like other organisms in that each species has a unique codon bias with plants of the same taxonomic class maintaining a similar codon usage pattern (Campbell & Gowri, 1990). Species with near genetic relationship share the near codon usage frequency and preference.…”