Rapid Translation of the Early Coding Region Promotes Premature Transcription Termination, Reducing Protein Expression in Escherichia coli

Slowly translated codons are overrepresented among the first approximately 30 codons of natural genes across all domains of life, yet the functional basis for this conserved feature remains incompletely understood. Using the Escherichia coli lacZ gene as a model, we previously showed that insertion of fast-translated codons into the early coding region dramatically reduces β-galactosidase production by increasing premature transcription termination and decreasing mRNA stability. Here we show that premature transcription termination events occur several nucleotides downstream of the fast-codon inserts, at positions coinciding with previously characterized Rho-dependent intragenic termination sites in lacZ. To exclude the possibility that the specific amino acid sequence of the inserts-rather than their translation speed-was responsible for termination, we constructed two additional lacZ variants with distinct fast-translated sequences, including one replacing the 30 earliest lacZ codons with their fastest synonymous alternatives. Both variants showed premature transcription termination of comparable magnitude to the original inserts, demonstrating that it is the high translation rate itself which causes premature termination. Analysis of a conservative set of seven high-confidence fast-translated codons across natural highly expressed genes and the synthetic constructs revealed that a run of consecutive fast codons is the feature that most clearly distinguishes the terminating sequences from natural genes. We propose that excessively rapid synthesis of the N-terminal part of a polypeptide may impair its proper entry into the ribosomal exit tunnel, thereby disrupting transcription-translation coupling and exposing downstream mRNA to Rho-dependent termination.