Journal article

Gene functionality's influence on the second codon: A large-scale survey of second codon composition in three domains

Sen-Lin Tang, Bill CH Chang, Saman K Halgamuge

GENOMICS | ACADEMIC PRESS INC ELSEVIER SCIENCE | Published : 2010

Abstract

The second codon of a transcript, besides encoding for an amino acid, is now known to also have multiple molecular functions and is involved in translation efficiency and protein turn-over and maturation processing. These multiple purposes therefore make the selection constraints on this codon's composition more complex. To examine the biological significance of various permutations of the second codon, we conducted a systematic survey of second codon composition from 442 selected genomes across three domains. The amino acid bias of the second codon is associated with specific protein functions. The most common amino acids (S, A, K and T) are significantly avoided in Cell Envelope-related ge..

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Grants

Funding Acknowledgements

This work was supported by the Biodiversity Research Center and the Institute of Plant and Microbial Biology, Academia Sinica, Taiwan. We would like to show our appreciation to Mr. Yu-Hsiung Lin in assisting with data collection and Ms. Hsiao-Chi Chen and Dr. Harry Wilson for proofreading and scientific suggestions and comments.