CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences

Abstract

Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often "optimized" as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in Escherichia coli, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education.

Regulated N-Terminal Modification of Proteins Synthesized Using a Reconstituted Cell-Free Protein Synthesis System

“…All template DNA sequences for cell-free protein synthesis were designed using CodHonEditor based on E. coli codon usage and synthesized by GenScript (Supplementary Table 1).…”

“…■ METHODS Preparation of Template DNA for Protein Synthesis. All template DNA sequences for cell-free protein synthesis were designed using CodHonEditor 18 based on E. coli codon usage and synthesized by GenScript (Supplementary Table 1). The template DNA contained the 5′-UTR (5′-GAAATTAATACG-ACTCACTATAGGGAGACCACAACGGTTTCCCTCTAG-AAATAATTTTGTTTAACTTTAAGAAGGAGATATACCA-ORF-3′), including the T7 promoter and Shine−Dalgarno sequence, and the 3′-UTR (5′-ORF-TAATGAATAACTAA-TCC-3′).…”

N-Terminal Amino Acid Affects the Translation Efficiency at Lower Temperatures in a Reconstituted Protein Synthesis System

“…Firstly, we synthesized four model proteins, including dihydrofolate reductase (DHFR) and alkaline phosphatase (ALP) from E. coli and superfolder green fluorescent protein (sfGFP) and firefly luciferase (Luc), using the PURE system at 23, 30, and 37 • C to determine the effect of synthesis temperature on synthesis efficacy (Figure 1). To reduce the influence of codon usage, the DNA sequences of Luc and sfGFP, which were derived from organisms other than E. coli, were designed based on the codon usage frequency in E. coli [25]. When the four proteins were synthesized at 37 • C, the yields of DHFR and sfGFP were markedly greater than those of Luc and ALP.…”

“…Only the mature region was used for ALP. Wild-type sfGFP and Luc template DNA were designed using the CodHonEditor [25] based on E. coli codon usage and synthesized by Eurofins Genomics (Tokyo, Japan). Trastuzumab HC DNA was designed and synthesized by GenScript (Tokyo, Japan).…”

Rethinking the D'Hondt method

“…Most national proportional representation systems and one in five mixed ones now use the D'Hondt method (Bormann and Golder 2013), as do some other elections or allocations of parliamentary committee chairs and executive body seats (O'Leary, Grofman, and Elklit 2005). Its uses extend into a variety of domains, including allocating claims on indivisibilities (Herrero and Martínez 2008) and constrained portfolio selection (Baixauli-Soler, Alfaro-Cid, and Fernandez-Blanco 2011) in economics, rounding numbers in statistics (Dorfleitner and Klein 1999), codon usage fitting in biochemistry (Takai 2016), and within algorithms in computer science (Kruse et al 2016;Zhang et al 2016;Aritsugi and Kubota 2017). It is also one of the oldest proportional apportionment methodsthe Jefferson method, which apportions identically, was first used two and a quarter centuries ago.…”