Translation initiation from sequence variants of the bacteriophage T7 g10RBS in Escherichia coli and Agrobacterium fabrum

Background The bacteriophage T7 gene 10 ribosome binding site (g10RBS) has long been used for robust expression of recombinant proteins in Escherichia coli. This RBS consists of a Shine–Dalgarno (SD) sequence augmented by an upstream translational “enhancer” (Enh) element, supporting protein production at many times the level seen with simple synthetic SD-containing sequences. The objective of this study was to dissect the g10RBS to identify simpler derivatives that exhibit much of the original translation efficiency. Methods and results Twenty derivatives of g10RBS were tested using multiple promoter/reporter gene contexts. We have identified one derivative (which we call “CON_G”) that maintains 100% activity in E. coli and is 33% shorter. Further minimization of CON_G results in variants that lose only modest amounts of activity. Certain nucleotide substitutions in the spacer region between the SD sequence and initiation codon show strong decreases in translation. When testing these 20 derivatives in the alphaproteobacterium Agrobacterium fabrum, most supported strong reporter protein expression that was not dependent on the Enh. Conclusions The g10RBS derivatives tested in this study display a range of observed activity, including a minimized version (CON_G) that retains 100% activity in E. coli while being 33% shorter. This high activity is evident in two different promoter/reporter sequence contexts. The array of RBS sequences presented here may be useful to researchers in need of fine-tuned expression of recombinant proteins of interest. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06891-z.


Introduction
Recombinant protein expression in Escherichia coli is often optimized by engineering two control points: transcription (promoter optimization) and translation (ribosome binding site, or RBS, optimization) [1,2]. The RBS from the bacteriophage T7 gene 10 (g10RBS) has been used extensively in commercially available plasmids to stimulate recombinant protein expression in E. coli. It was previously shown that when g10RBS is placed upstream of recombinant genes, protein expression is increased 40-fold or more than when a synthetic consensus RBS sequence is used [3]. Within this 45-nucleotide (nt) sequence, an A/U-rich 9-nt enhancer element (Enh) upstream of the Shine-Dalgarno (SD) region is found to stimulate translation, even when its position relative to the SD region is changed [4]. Several studies have examined the effects of this Enh element on translation rates [3][4][5][6][7][8][9][10]. Homology between the Enh and nucleotides 458-466 in the 16S rRNA led to an initial proposal that base-pairing underlies the increased translation rates [4,8]. Modifications to nucleotides 458-466 of the 16S rRNA, however, did not support that hypothesis [6]. Subsequent proposals suggest, instead, that Enh or similar elements interact with ribosomal protein S1 [11][12][13]. Beyond E. coli, the g10RBS has been shown to support high expression of recombinant proteins in other gammaproteobacteria such as Pseudomonas, Erwinia, and Serratia [14]. The objective of the present study is to more thoroughly dissect this phage-derived RBS to identify shorter derivatives that retain translational activity in E. coli, and to test these derivatives in the more distantly related alphaproteobacterial species, Agrobacterium fabrum.

Results and discussion
The full-length g10RBS used in commercial vectors to enhance translation is referred to in this study as "FL_A," which includes (from the 5' end) an XbaI site, an 11-nt A/U-rich sequence, the 9-nt Enh element, a 4-nt potential "standby" site, the SD sequence (GGA GAT ), and the SD-initiation codon spacer. The g10RBS and its potential to hybridize with the E. coli 16S rRNA are depicted in Fig. 1a. The anti-Enh region within the 16S sequence is not found in the alphaproteobacterial rRNAs from A. fabrum and Sinorhizobium meliloti (Fig. 1b).
A total of 21 RBS sequences, including FL_A, were ligated individually into a test plasmid that replicates in both E. coli and A. fabrum, and encodes the mScarlet-I fluorescent protein [15], driven by a synthetic lacT5 promoter. Because the plasmid does not encode the LacI repressor, the lacT5 promoter behaves constitutively in these strains. Fluorescent output for each RBS was measured in E. coli and A. fabrum (Fig. 2) and are presented as normalized values with the FL_A measurement in E. coli calibrated to "100". All other fluorescence measurements presented are normalized to that standard.
The SD sequence within FL_A (GGAG AT) does not match perfectly with the anti-SD at the 3' end of 16S in E. coli or A. fabrum, so the A nucleotide was changed to G to make a perfect match (GGAG GT). We refer to this derivative as "FL_G." For FL_G and FL_A, a series of three 5' truncations were made. Next, the 11-nt A/U-rich sequence upstream of Enh and the 4-nt potential standby site were simultaneously removed from FL_A and FL_G to form a condensed RBS. These are called "CON_A" and "CON_G", respectively. Then, four single-base truncations were made from the 5' end of Enh in the FL_G derivative. Finally, in the derivative with 4 bases truncated from the 5' end of Enh (termed "CON_GT4"), we made several modifications to the spacer between the SD and the initiation codon by either removing bases or replacing them to incorporate various restriction sites (see Fig. 2).
In E. coli, the A-to-G base substitution in the SD sequence (FL_A vs FL_G) led to a 20% drop in expression. Each of the three truncations within the FL_A sequence ("T1_A", "T2_A", and "T3_A") led to 9%, 29%, and 67% reductions in expression, respectively. In contrast, the same three truncations within the FL_G sequence ("T1_G", "T2_G", and "T3_G") led to a 2% increase, and 9% and 44% decreases, respectively. When comparing CON_A and CON_G to FL_A, we observed, surprisingly, that the CON_G derivative yielded expression levels nearly identical to the parental FL_A sequence despite being 33% (15 nt) shorter, while expression from the CON_A derivative was 12% lower than FL_A. This observation is consistent with data from two high-throughput studies on the 5' untranslated regions of mRNAs in E. coli, where it was determined that there is a preference for a G nucleotide eight bases upstream of the initiation codon [16,17]. For this reason, subsequent RBS modifications were made to the highly efficient CON_G sequence. Four single-base deletions from the 5' end of the enhancer element in CON_G ("CON_GT1", "CON_GT2", "CON_GT3", and "CON_GT4") led to 17%, 26%, 55%, and 31% reductions in expression, respectively. Modifying the spacer between the SD and the initiation codon to incorporate restriction sites ("Spc_KpnI", "Spc_EcoRI", "Spc_ BamHI", and "Spc_SacI") led to 33%, 61%, 97%, and 89% reductions in expression, respectively. Removing 1 and 2 bases ("Spc_T1" and "Spc_T2") from the spacer led to 6% and 12% reductions in expression, respectively (see Fig. 2).
In A. fabrum, FL_A and FL_G gave nearly identical expression levels and truncations of these yielded even higher levels of translation. In fact, the 22-nt T3_A sequence supported the highest level of translation of all 21 sequences tested. The CON_A and CON_G RBS sequences yielded 33% and 24% (respectively) more fluorescence than FL_A, with CON_A exhibiting 94% of the activity as T3_A. The CON_GT series of Enh truncations had similar effects in A. fabrum as in E. coli, with the CON_GT4 variant unexpectedly giving higher expression than CON_GT3. Levels of expression in A. fabrum remained high in most cases when modifying the spacer between the SD and initiation codon, two exceptions being the Spc_BamHI and Spc_SacI variants, which led to 88% and 54% decreases in expression, respectively. These are also the variants that gave the lowest expression values in E. coli. Interestingly, cultures of A. fabrum harboring a few of the most active RBS sequences (T1_A, T2_A, T3_A, and CON_A) initially had high levels of fluorescence and somewhat decreased cell density. In subsequent passages of these cultures, normal cell density was restored, but fluorescence decreased-suggesting a fitness cost associated with such high-level expression of the reporter gene. Consistent with this, colonies from these high-expressing strains appeared slightly smaller compared to the other strains (see Supplementary Fig. S1a-c). Suppression of fitness defects was possibly due to mutations in the promoter, RBS, reporter gene, or plasmid origin of replication, though the precise cause was not investigated.
To determine if the effect of RBS variants on reporter gene expression is in part due to flanking sequences, we selected four RBS variants to test in a new promoter/reporter context. The RBS sequences were selected to represent a AFU   FL_A  T1_A  T2_A  T3_A  FL_G  T1_G  T2_G  T3_G  CON_A  CON_G  CON_GT1  CON_GT2  CON_GT3  CON_GT4  Spc_KpnI  Spc_EcoRI  Spc_BamHI  Spc_SacI  Spc_T1  Spc_T2  GGT   TCTAGAaataattttgtttaactttaagaaggagatatacatATG  TCTAGA  tttaactttaagaaggagatatacatATG  TCTAGA  tttaagaaggagatatacatATG  TCTAGA  aggagatatacatATG  TCTAGAaataattttgtttaactttaagaaggaggtatacatATG  TCTAGA  tttaactttaagaaggaggtatacatATG  TCTAGA  tttaagaaggaggtatacatATG  TCTAGA  aggaggtatacatATG  TCTAGA  ttaacttta  ggagatatacatATG  TCTAGA  ttaacttta  ggaggtatacatATG  TCTAGA  taacttta  ggaggtatacatATG  TCTAGA  aacttta  ggaggtatacatATG  TCTAGA  acttta  ggaggtatacatATG  TCTAGA  cttta  ggaggtatacatATG  TCTAGA  cttta  wide range of translation enhancement. Whereas the original system employs the lacT5 promoter and mScarlet-I reporter, the alternative system uses the constitutive Pkan promoter (from the Tn5 transposon) and a monomeric superfolder GFP (msfGFP) reporter. The dissimilarity of flanking sequences in these two systems is shown in Fig. 3a. In E. coli, no differences in relative RBS activity could be seen between these sequence contexts (Fig. 3b). In A. fabrum, the relative values differ somewhat. For example, CON_GT4 gives slightly higher translation than CON_G in the mScarlet-I context (a ~ 5% increase), but substantially lower activity in the msfGFP context (a 33% decrease; see Fig. 3c).
To test the influence of the four RBS variants on protein expression and purification from E. coli, the msfGFP gene was modified to encode a C-terminal His 6 tag in each expression plasmid. Expression and purification according to conventional methods (see Materials and Methods) was carried out, and gel analysis of purified products is shown in Fig. 3d. Consistent with the fluorescence-based analysis, CON_G and CON_GT4 gave the highest yield of recombinant protein, with T3_G yielding a lower amount, and GGT yielding undetectable levels of recombinant protein.
Among the most notable RBS variants tested in this study, the SD-initiator spacer variants were rather surprising, though consistent with recent work indicating that adenosine nucleotides in this region can enhance translation, while cytidine nucleotides are unfavorable [18]. The most detrimental spacer substitutions in our analysis were Spc_SacI (ATA CAT to GAG CTC ) and Spc_BamHI (ATA CAT to GGA TCC ). Both of these changes reduce the number of A nucleotides and increase the number of C nucleotides. We acknowledge, however, that the effect of spacer sequence on translation efficiency is idiosyncratic, as recent high-throughput studies identified efficient RBS sequences that deviate from this rule [19,20].
In both E. coli and A. fabrum, we expected the CON_ GT1/2/3/4 truncation series (which removes 1 to 4 nucleotides from Enh) to exhibit a downward trend in expression level compared to CON_G. While this was partly true, CON_GT4 showed a rebounded level of expression compared to CON_GT3. This observation bolsters the model in which the effect of Enh does not necessarily depend on its propensity to hybridize to the complementary sequence on 16S [6]. High levels of expression in A. fabrum for T3_A and T3_G indicate the dispensability of Enh in this organism.
The g10RBS derivatives tested in this study display a range of observed activity, including a minimized version (CON_G) that retains 100% activity in E. coli while being 33% shorter. This high activity is evident in two different promoter/reporter sequence contexts. A. fabrum appears  Error bars indicate the standard deviation. d His 6 tagged GFP was purified from E. coli cells harboring the selected RBS sequences to be less influenced by the varying RBS sequences tested here which may be related to the parental sequence not being native to this species. The set of RBS sequences presented here may be useful to researchers in need of fine-tuned expression of recombinant proteins of interest in diverse species.

Bacterial genetic manipulations and growth conditions
Escherichia coli DH5α (Sharon Long collection) and A. fabrum B527 (a streptomycin-resistant derivative of C58, Griffitts lab collection) strains were grown in lysogeny broth (LB) at 37 °C or 30 °C, respectively. Fluorescent protein expression plasmids were constructed in vitro, transformed into DH5α, sequence-verified, and transferred to A. fabrum by conjugation using helper strain B001 [21].
Plasmid selection was carried out in lysogeny broth (LB) containing 30 μg/ml kanamycin (GoldBio K-120-5) (E. coli) or 100 μg/ml neomycin (Sigma N1876-25G) (A. fabrum). Full sequences for the FL_A-containing starting plasmids (pJG1082 for mScarlet-I expression and pAB215 for msfGFP expression) are given as supplementary information, with the g10RBS and initiation codon capitalized. Variants of these plasmids, and primers used for their construction, are documented in Supplementary Tables S1 and S2.  Funding Funding for this study was provided by the National Science Foundation through a Collaborative Research Grant to J.S.G.

Measurement of fluorescent output
Data availability All data used for figures can be made available upon request.
Code availability Not applicable.

Conflict of interest
The authors declare there are no conflicting or competing interests.
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/.