Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain

Table 1 Rare codon frequencies of the coding sequences used in this study

Coding sequence	Total codons	RIL codon content^a			% of RIL codons	% of Rare codons^b	GC Content (%)	Description^c
		Arg AGA/AGG	Ile ATA	Leu CTA
fd	97	1/1	0/4	1/6	2.1	24.7	40	pea ferredoxin
clpt1	178	3/4	1/8	2/20	3.4	9.6	48	05-08-O17 – accessory protein of the chloroplastic ClpP protease complex
fnr	308	7/8	2/12	2/21	3.6	19.8	42	pea ferredoxin-NADP(H) reductase
clpp4	235	6/11	4/26	0/18	4.3	20.4	44	04-15-O12 – component of the chloroplastic ClpP protease complex
clpc2	834	32/64	10/61	9/82	6.1	12.6	46	09-19-G11 – chloroplastic chaperone
clpd	865	33/56	16/62	8/85	6.4	15.1	46	05-05-I08 – chloroplastic chaperone
clpr2	224	10/18	4/13	4/19	8.0	21.9	47	06-10-N03 – component of the chloroplastic ClpP protease complex
dsRBD2	82	6/6	0/2	7/19	8.5	23.2	43	Second double-stranded RNA-binding domain of DICER1 (Arabidopsis thaliana)
trx	109	0/1	0/9	0/13	0.0	3.7	52	E. coli thioredoxin
E. coli	-	-	-	-	-	-	51	Escherichia coli K12 NCBI RefSeq Accession NC000913
A. thaliana	-	-	-	-	-	-	36^d	Whole genome data at NCBI

^aRatio of RIL codon(s) for the indicated amino acid to the number of total codons encoding each amino acid, respectively. RIL codons are indicated in parenthesis below each amino acid.
^bPercentage of codons previously defined as rare in E. coli because they occur at frequency below 10% [8, 9]
^cNumbers indicate clone number from the RIKEN Arabidopsis full length cDNA bank. All clp coding sequences are from A. thaliana
^dAll genome data with the exception of mitochondrial DNA.