SBOL Visual: A Graphical Language for Genetic Designs

Abstract

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

Fig 1. SBOL Visual aids rapid communication of variant synthetic DNA designs: multi-color reporter variants.

In this figure we present an example genetic reporter device [17,21] to show how a common symbology can highlight the differences between a series of related DNA constructs. (A) The three-color, green fluorescent protein (GFP)-based genetic reporter was designed for easy swapping of each cassette’s promoter by methods based on restriction cloning or recombination, allowing it to be modified to measure promoters for analyzing the effects of growth condition on circuit performance variation (figure modified from [20]). The SBOL Visual symbology (right) highlights that the promoters are variable, and the coloring of the CDS (which is not constrained by SBOL Visual) is used to keep track of which genetic reporter is at which position, including three fluorescent proteins (CFP: cyan, YFP: yellow, RFP: red). Equivalent means for distinguishing sequences include fill/hatch patterns (e.g., for black-and-white publication) or textual labels above the components. (B) The three-color reporter was modified to make a protein fusion between the Yellow Fluorescent Protein gene and the cI repressor from phage lambda (modified from [21] gray and yellow in the SBOL Visual diagram). This shows how the user-specified coloring can add new information to the basic glyphs. This design also swapped around the positions of the different reporter genes, as well as replacing the promoters, to create a regulatory circuit in which the regulatory protein could be directly observed via the protein fusion with YFP. (C) The three-color reporter was modified to a two-color system, and the YFP gene was replaced with a GFP variant, to optimize two-color measurement. This system was used to systematically measure all combinations of 114 promoters and 111 ribosome binding sites (modified from [18]). (D) The DNA sequence of the three-color reporter construct presented in [17]. Here the promoter and terminator sequences are underlined, and the three color fluorescent genes are indicated by highlighting the text as cyan, yellow, or red. The purple sequences denote ribosome binding sites. This highlights how the SBOL Visual notation in (A) is much easier to quickly understand than the raw sequence, while still clearly communicating the organization of genetic parts.