GC3 biology in corn, rice, sorghum and other grasses

• Published in: BMC genomics Vol. 11; no. 1; p. 308
• Main Authors: Tatarinova, Tatiana V, Alexandrov, Nickolai N, Bouck, John B, Feldmann, Kenneth A
• Format: Journal Article
• Language: English
• Published: London BioMed Central 16.05.2010; Springer Nature B.V; BMC
• Subjects: Agricultural biotechnology; Algorithms; Animal Genetics and Genomics; Base Composition; Bias; Biology; Biomedical and Life Sciences; Biotechnology industry; Codon - chemistry; Codon - genetics; Computer science; DNA Methylation; Gene Conversion; Gene Expression Regulation, Plant; Genes, Plant - genetics; Genetic Variation; Genetics; Genomes; Genomics; Grasses; Introns - genetics; Life Sciences; Microarrays; Microbial Genetics and Genomics; Oryza - genetics; Oryza sativa; Plant Genetics and Genomics; Plant species; Poaceae - genetics; Proteomics; Research Article; Sequence Homology, Nucleic Acid; Sorghum; Sorghum - genetics; TATA Box - genetics; Vertebrates; Zea mays - genetics; Rice Gene; Codon Usage; Codon Usage Pattern; Wobble Position; Codon Usage Bias
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-11-308

Background The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. Results Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC 3 ) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC 3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC 3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC 3 bimodality in grasses. Conclusions Our findings suggest that high levels of GC 3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC 3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.