title: Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology.
abstract: Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks. In genetic terms, these informational phrases correspond to transcription units, which are the minimal genetic information expressed consistently from initiation to termination marks. Between the start and final punctuation marks, additional marks are present that are read by the transcriptional and translational machineries. In this work, we look at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and define a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.
authors.affiliation: Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico. agustino.martinez@cinvestav.mx.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Rangel-Chavez
authors.affiliation: Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico. agustino.martinez@cinvestav.mx.
authors.forename: Edgardo
authors.initials: E
authors.lastname: Galan-Vasquez
authors.affiliation: Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico. agustino.martinez@cinvestav.mx.
authors.forename: Agustino
authors.identifier: http://orcid.org/0000-0003-2231-5014
authors.initials: A
authors.lastname: Martinez-Antonio
mesh_terms: D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D005818:Genetic Engineering / Q000379:methods; D016680:Genome, Bacterial; D059372:Nucleotide Motifs; D009876:Operon; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012808:Sigma Factor / Q000378:metabolism; D058615:Synthetic Biology / Q000379:methods; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D012808:Sigma Factor