Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells

Chen Deng; Xueqin Lv; Jianghua Li; Yanfeng Liu; Guocheng Du; Rodrigo Ledesma Amaro; Long Liu

doi:10.1002/bit.26841

Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells

Biotechnol Bioeng. 2019 Jan;116(1):5-18. doi: 10.1002/bit.26841. Epub 2018 Oct 27.

Authors

Chen Deng^{1

2}, Xueqin Lv^{1

2}, Jianghua Li², Yanfeng Liu^{1

2}, Guocheng Du¹, Rodrigo Ledesma Amaro³, Long Liu^{1

2}

Affiliations

¹ Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
² Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
³ Department of Bioengineering, Imperial College London, London, UK.

PMID: 30229865
DOI: 10.1002/bit.26841

Abstract

In prokaryotic cells, 3'-5' exonucleases can attenuate messenger RNA (mRNA) directionally from the direction of the 3'-5' untranslated region (UTR), and thus improving the stability of mRNAs without influencing normal cell growth and metabolism is a key challenge for protein production and metabolic engineering. Herein, we significantly improved mRNA stability by using synthetic repetitive extragenic palindromic (REP) sequences as an effective mRNA stabilizer in two typical prokaryotic microbes, namely, Escherichia coli for the production of cyclodextrin glucosyltransferase (CGTase) and Corynebacterium glutamicum for the production of N-acetylglucosamine (GlcNAc). First, we performed a high-throughput screen to select 4 out of 380 REP sequences generated by randomizing 6 nonconservative bases in the REP sequence designed as the degenerate base "N." Secondly, the REP sequence was inserted at several different positions after the stop codon of the CGTase-encoding gene. We found that mRNA stability was improved only when the space between the REP sequence and stop codon was longer than 12 base pairs (bp). Then, by reconstructing the spacer sequence and secondary structure of the REP sequence, a REP sequence with 8 bp in a stem-loop was obtained, and the CGTase activity increased from 210.6 to 291.5 U/ml. Furthermore, when this REP sequence was added to the 3'-UTR of glucosamine-6-phosphate N-acetyltransferase 1 ( GNA1), which is a gene encoding a key enzyme GNA1 in the GlcNAc synthesis pathway, the GNA1 activity was increased from 524.8 to 890.7 U/mg, and the GlcNAc titer was increased from 4.1 to 6.0 g/L in C. glutamicum. These findings suggest that the REP sequence plays an important function as an mRNA stabilizer in prokaryotic cells to stabilize its 3'-terminus of the mRNA by blocking the processing action of the 3'-5' exonuclease. Overall, this study provides new insight for the high-efficiency overexpression of target genes and pathway fine-tuning in bacteria.

Keywords: mRNA stability; metabolic engineering; protein engineering; repetitive extragenic palindromic sequence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acetylglucosamine / biosynthesis
Corynebacterium glutamicum / genetics
Corynebacterium glutamicum / metabolism*
Escherichia coli / genetics
Escherichia coli / metabolism*
Glucosyltransferases / biosynthesis
Glucosyltransferases / genetics
Inverted Repeat Sequences*
Metabolic Engineering / methods*
RNA Stability*
RNA, Messenger / genetics
RNA, Messenger / metabolism*
Recombinant Proteins / biosynthesis*
Recombinant Proteins / genetics

Substances

RNA, Messenger
Recombinant Proteins
Glucosyltransferases
cyclomaltodextrin glucanotransferase
Acetylglucosamine