Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships

Abstract

Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.

Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli

“…Recently, Duarte-Velázquez et al . 23 suggested either gene duplication or horizontal gene transfer as the main factors driving evolution of several transcription regulators in E. coli , including CsqR. Our observation on the phylogeny of CsqR extends and clarifies this assumption (Fig.…”

“…Indeed, CsqR acted as a repressor for yihV , yihT, and yihS during growth with glucose, and had no effect during growth on lactose 12 . Recently, a microarray study on E. coli also showed activation of the csqR gene in response to lactose during glucose-lactose diauxic shift at the growth arrest phase 22 , 23 . These observations suggest that lactose might serve, together with SQ, as an effector molecule for CsqR.…”

Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli

“…S4 ). The YafC is predicted to be a transcription factor that regulates genes related to metabolism and chlorine resistance 31 , and RcsB is a response regulator involved in biofilm and exopolysaccharide formation 32 . The changes in these two transcriptional regulatory proteins, i.e., upregulation of yafC and downregulation of rcsB , certainly seem to have a favourable impact on rAAR expression.…”

Synergistic application of atmospheric and room temperature plasma mutagenesis and adaptive laboratory evolution improves the tolerance of Escherichia coli to L‐cysteine

“…[25] The gene yfiE, a lysR-type DNA-binding transcriptional regulator, is predicted to be involved in regulating genes associated with the export of Lcysteine and O-acetyl-L-serine. [26,27] To further validate the roles of eamB and yfiE, mutants yfiE N127K and eamB N157S were simultaneously introduced into the parental strain AT-1, resulting in the strain AT-1(eamB N157S )(yfiE N127K ). Surprisingly, the growth phenotype of the strain AT-1(eamB N157S )(yfiE N127K ) closely resembled that of the strain AT-1(eamB N157S ), indicating that the integration of yfiE N127K did not further improve the L-cysteine tolerance (Figure 5G).…”