GC3 biology in corn, rice, sorghum and other grasses

BMC Genomics

Research Article

John B Bouck¹  Nickolai N Alexandrov¹  Kenneth A Feldmann²  Tatiana V Tatarinova³ 

[1] Ceres, Inc, 1535 Rancho Conejo Rd, 91320, Thousand Oaks, CA, USA;Ceres, Inc, 1535 Rancho Conejo Rd, 91320, Thousand Oaks, CA, USA;School of Plant Sciences, University of Arizona, 85721, Tucson, AZ, USA;Department of Biomedical Engineering, Georgia Institute of Technology, 30332, Atlanta, Georgia, USA;Division of Mathematics and Statistics, University of Glamorgan, CF37 1DL, Pontypridd, UK;

关键词: Codon Usage;    Rice Gene;    Codon Usage Bias;    Codon Usage Pattern;    Wobble Position;   

DOI  :  10.1186/1471-2164-11-308

 received in 2009-09-16, accepted in 2010-05-16,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 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 GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses.ConclusionsOur findings suggest that high levels of GC3 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 GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.

【 授权许可】

CC BY   
© Tatarinova et al; licensee BioMed Central Ltd. 2010