title: Promoter element arising from the fusion of standard BioBrick parts.
abstract: We characterize the appearance of a constitutive promoter element in the commonly used cI repressor-encoding BioBrick BBa_C0051. We have termed this promoter element pKAT. Full pKAT activity is created by the ordered assembly of sequences in BBa_C0051 downstream of the cI gene encoding the 11 amino acid LVA proteolytic degradation tag, a BioBrick standard double-TAA stop codon, a genetic barcode, and part of the RFC10 SpeI-XbaI BioBrick scar. Placing BBa_C0051 or other pKAT containing parts upstream of other functional RNA coding elements in a polycistronic context may therefore lead to the unintended transcription of the downstream elements. The frequent reuse of pKAT or pKAT-like containing basic parts in the Registry of Biological Parts has resulted in approximately 5% of registry parts encoding at least one instance of a predicted pKAT promoter located directly upstream of a ribosome binding site and ATG start codon. This example highlights that even seemingly simple modifications of a part's sequence (in this case addition of degradation tags and barcodes) may be sufficient to unexpectedly change the contextual behavior of a part and reaffirms the inherent challenge in carefully characterizing the behavior of standardized biological parts across a broad range of reasonable use scenarios.
authors: Department of Biomedical Engineering, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
authors: Andrew I
authors: AI
authors: Yao
authors: Timothy A
authors: TA
authors: Fenton
authors: Keegan
authors: K
authors: Owsley
authors: Phillip
authors: P
authors: Seitzer
authors: David J
authors: DJ
authors: Larsen
authors: Holly
authors: H
authors: Sit
authors: Jennifer
authors: J
authors: Lau
authors: Arjun
authors: A
authors: Nair
authors: Justin
authors: J
authors: Tantiongloc
authors: Ilias
authors: I
authors: Tagkopoulos
authors: Marc T
authors: MT
authors: Facciotti
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012270:Ribosomes / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic