Part:BBa_K3815015

AANDENYALGA. mutant SsrA degradation tag

Usage and Biology

This is an engineered derivative of wildtype ssrA tag from Escherichia coli, where three C-terminal amino acids LAA in WT are replaced with LGA. Refer to BBa_M0050 for the biological function of the tag.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]

Result

For a flexible control of protein half-life, we aimed to obtain a collection of mutant tags with various degradation efficiencies.

Fig.1 mutagenesis strategy

We fused the ssrA tag sequence to GFP while introducing mutations in the tag by random-base primers, and cloned the mutant library of ssrA-tagged GFP into a plasmid vector, so that mutant tags of different activity can be identified by comparing GFP intensity of E.coli transformants.

The wildtype ssrA tag amino acid sequence is AANDENYALAA. It was reported that the three amino acids at the C terminus of the tag (LAA in wildtype) have a great impact on the degradation rate of tagged protein. Therefore, we chose these three amino acids as the targets for mutagenesis.

Fig.2 primer and amino acid sequences for mutagenesis

As a result of transformation, colonies of various fluorescence intensity were obtained on the LB plates. 72 colonies in total were picked from plates, and cultured overnight in LB media. The images of E.coli cultures were taken under the blue light.

Fig.3 E.coli cultures of various GFP intensity. A10: LB media only, B10: E.coli culture not expressing GFP, B7: E.coli culture expressing non ssrA-tagged GFP, C7: E.coli culture expressing WT ssrA-tagged GFP

Plasmid was extracted from each bacterial culture by miniprep, and then Sanger-sequenced to identify ssrA tag sequence. Furthermore, to quantify protein degradation efficiency of each mutant, GFP Fluorescence of each bacterial overnight culture was imaged on Typhoon 9410 (GE healthcare).

Fig.4 Left: GFP fluorescence image of each bacterial overnight culture. Right: sequenced three C-terminal amino acids of each culture

The mutant ssrA tag sequence of each clone was sequenced, and biological triplicate of each bacterial overnight culture was imaged for GFP fluorescence, including controls (LB media only, bacterial culture not expressing GFP (no GFP), and bacterial culture expressing non ssrA-tagged GFP (no ssrA tag)).

Fig.5 The fluorescence of each culture was quantified by ImageJ as inverted mean gray value. Measured value of each culture was then normalized to the level of the culture expressing non ssrA-tagged GFP (no ssrA tag), and presented as mean ± SD from three biological replicates. WT (LAA) and two mutants reported in a previous research are shown in red boxes.

Conclusion

We mutagenized ssrA tag by PCR with mixed primers, and successfully obtained a mutant collection of engineered ssrA tag derivatives which show various protein degradation efficiencies.

Part collection of mutant ssrA tags

In our mutagenesis experiments, we identified 17 mutant tags which show various protein degradation efficiencies (refer to Result). The other mutant tags are listed below.

Name	Type	Part Name	Designer
BBa_K3815015	Tag	AANDENYALGA.mutant SsrA degradation tag	Alexander Liu
BBa_K3815016	Tag	AANDENYAKWA.mutant SsrA degradation tag	Alexander Liu
BBa_K3815017	Tag	AANDENYALAK.mutant SsrA degradation tag	Alexander Liu
BBa_K3815018	Tag	AANDENYAHPK.mutant SsrA degradation tag	Alexander Liu
BBa_K3815019	Tag	AANDENYALAL.mutant SsrA degradation tag	Alexander Liu
BBa_K3815020	Tag	AANDENYANDK.mutant SsrA degradation tag	Alexander Liu
BBa_K3815021	Tag	AANDENYANEN.mutant SsrA degradation tag	Alexander Liu
BBa_K3815022	Tag	AANDENYAYES.mutant SsrA degradation tag	Alexander Liu
BBa_K3815023	Tag	AANDENYAHAK.mutant SsrA degradation tag	Alexander Liu
BBa_K3815024	Tag	AANDENYALAS.mutant SsrA degradation tag	Alexander Liu
BBa_K3815025	Tag	AANDENYATAP.mutant SsrA degradation tag	Alexander Liu
BBa_K3815026	Tag	AANDENYANAA.mutant SsrA degradation tag	Alexander Liu
BBa_K3815027	Tag	AANDENYAKLA.mutant SsrA degradation tag	Alexander Liu
BBa_K3815028	Tag	AANDENYALPA.mutant SsrA degradation tag	Alexander Liu
BBa_K3815029	Tag	AANDENYALAM.mutant SsrA degradation tag	Alexander Liu
BBa_K3815030	Tag	AANDENYALAI.mutant SsrA degradation tag	Alexander Liu
BBa_K3815031	Tag	AANDENYAPHA.mutant SsrA degradation tag	Alexander Liu

Improvement from an Existing Part

This is a part improved from BBa_K1051206. In this part, three C-terminal amino acids LAA are replaced with LGA, resulting in a reduced protein degradation efficiency. Therefore, this part show an increased half-life of fused proteins compared to WT. This part, together with the other mutants described in the part collection above, consists of a large repertoire of protein degradation tags of various efficiencies (refer to Result), which can be applied for fine-tuning of many kinds of synthetic systems that require a precise control of proteins.

Reference

1. Flynn, J.M., Levchenko, I., Seidel, M., Wickner, S.H., Sauer, R.T., and Baker, T.A. (2001). Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc. Natl. Acad. Sci. U. S. A. 98, 10584–10589.