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Synthetic biology challenges long‐held hypotheses in translation, codon bias and transcription
Author(s) -
Forster Anthony C.
Publication year - 2012
Publication title -
biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.144
H-Index - 84
eISSN - 1860-7314
pISSN - 1860-6768
DOI - 10.1002/biot.201200002
Subject(s) - biology , translation (biology) , transcription (linguistics) , computational biology , synthetic biology , codon usage bias , genetics , evolutionary biology , gene , messenger rna , genome , linguistics , philosophy
Synthetic biology is a powerful experimental approach, not only for developing new biotechnology applications, but also for testing hypotheses in basic biological science. Here, examples from our research using the best model system, Escherichia coli , are reviewed. New evidence drawn from synthetic biology has overturned several long‐standing hypotheses regarding the mechanisms of transcription and translation: (i) all native aminoacyl‐tRNAs are not equally efficient in translation at equivalent concentrations; (ii) accommodation is not always rate limiting in translation, and may not be for any aminoacyl‐tRNA; (iii) proline is the only N‐alkyl‐amino acid in the genetic code not because of special suitability for protein structure, but because of its comparatively high nucleophilicity; (iv) the usages of most sense codons in E. coli do not correlate with cognate tRNA abundances and (v) class II transcriptional pausing and termination by T7 RNA polymerase cannot be assumed to occur in vivo based on in vitro data. Implications of these conclusions for the biotechnology field are discussed.