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Chernyshov SV, Masulis IS, Mikoulinskaia GV. From DNA to lytic proteins: transcription and translation of the bacteriophage T5 holin/endolysin operon. World J Microbiol Biotechnol 2024; 40:256. [PMID: 38926173 DOI: 10.1007/s11274-024-04063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
The analysis of transcriptional activity of the bacteriophage T5 hol/endo operon conducted in the paper revealed a strong constitutive promoter recognized by E. coli RNA polymerase and a transcription initiation point of the operon. It was also shown that the only translational start codon for holin was a non-canonical TTG. Translation initiation regions (TIRs) of both genes of the operon (hol and endo) were further analyzed using chimeric constructs, in which parts of the hol/endo regulatory regions were fused with the gene of a reporter protein (EGFP). It was found that TIR of hol was 20 times less effective than that of endo. As it turned out, the level of EGFP production was influenced by the composition of the constructs and the type of the hol start codon. Apparently, the translational suppression of holin's accumulation and posttranslational activation of endolysin by Ca2+ are the main factors ensuring the proper timing of the host cell lysis by bacteriophage T5. The approach based on the use of chimeric constructs proposed in the paper can be recommended for studying other native or artificial operons of any complexity: analyzing the impacts of separate DNA regions, as well as their coupled effect, on the processes of transcription and translation of recombinant protein(s).
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Affiliation(s)
- Sergei V Chernyshov
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS, Prospekt Nauki, 6, Pushchino, Moscow region, Pushchino, Moscow region, 142290, Russia
| | - Irina S Masulis
- Institute of Cell Biophysics RAS PBC RAS, Institutskaya ul., 3, Pushchino, Pushchino, Moscow region, 142290, Russia
| | - Galina V Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS, Prospekt Nauki, 6, Pushchino, Moscow region, Pushchino, Moscow region, 142290, Russia.
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Sun M, Gao AX, Li A, Liu X, Wang R, Yang Y, Li Y, Liu C, Bai Z. Bicistronic design as recombinant expression enhancer: characteristics, applications, and structural optimization. Appl Microbiol Biotechnol 2021; 105:7709-7720. [PMID: 34596722 DOI: 10.1007/s00253-021-11611-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022]
Abstract
The bicistronic design (BCD) is characterized by a short fore-cistron sequence and a second Shine-Dalgarno (SD2) sequence upstream of the target gene. The outstanding performance of this expression cassette in promoting recombinant protein production has attracted attention. Recently, the application of the BCD has been further extended to gene expression control, protein translation monitoring, and membrane protein production. In this review, we summarize the characteristics, molecular mechanisms, applications, and structural optimization of the BCD expression cassette. We also specifically discuss the challenges that the BCD system still faces. This is the first review of the BCD expression strategy, and it is believed that an in-depth understanding of the BCD will help researchers to better utilize and develop it. KEY POINTS: • Summary of the characteristics and molecular mechanisms of the BCD system. • Review of the actual applications of the BCD expression cassette. • Summary of the structural optimization of the BCD system.
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Affiliation(s)
- Manman Sun
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - An Li
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiuxia Liu
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Rongbing Wang
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Chunli Liu
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhonghu Bai
- National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, 214112, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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Xu L, Liu P, Dai Z, Fan F, Zhang X. Fine-tuning the expression of pathway gene in yeast using a regulatory library formed by fusing a synthetic minimal promoter with different Kozak variants. Microb Cell Fact 2021; 20:148. [PMID: 34320991 PMCID: PMC8317321 DOI: 10.1186/s12934-021-01641-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Tailoring gene expression to balance metabolic fluxes is critical for the overproduction of metabolites in yeast hosts, and its implementation requires coordinated regulation at both transcriptional and translational levels. Although synthetic minimal yeast promoters have shown many advantages compared to natural promoters, their transcriptional strength is still limited, which restricts their applications in pathway engineering. RESULTS In this work, we sought to expand the application scope of synthetic minimal yeast promoters by enhancing the corresponding translation levels using specific Kozak sequence variants. Firstly, we chose the reported UASF-E-C-Core1 minimal promoter as a library template and determined its Kozak motif (K0). Next, we randomly mutated the K0 to generate a chimeric promoter library, which was able to drive green fluorescent protein (GFP) expression with translational strengths spanning a 500-fold range. A total of 14 chimeric promoters showed at least two-fold differences in GFP expression strength compared to the K0 control. The best one named K528 even showed 8.5- and 3.3-fold increases in fluorescence intensity compared with UASF-E-C-Core1 and the strong native constitutive promoter PTDH3, respectively. Subsequently, we chose three representative strong chimeric promoters (K540, K536, and K528) from this library to regulate pathway gene expression. In conjunction with the tHMG1 gene for squalene production, the K528 variant produced the best squalene titer of 32.1 mg/L in shake flasks, which represents a more than 10-fold increase compared to the parental K0 control (3.1 mg/L). CONCLUSIONS All these results demonstrate that this chimeric promoter library developed in this study is an effective tool for pathway engineering in yeast.
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Affiliation(s)
- Liping Xu
- School of Life Science, University of Science and Technology of China, No. 96, JinZhai Road, Baohe District, Hefei, Anhui, 230026, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China
| | - Zhubo Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China.
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Liu X, Zhao Z, Zhang W, Sun Y, Yang Y, Bai Z. Bicistronic expression strategy for high-level expression of recombinant proteins in Corynebacterium glutamicum. Eng Life Sci 2017; 17:1118-1125. [PMID: 32624739 DOI: 10.1002/elsc.201700087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/23/2017] [Accepted: 07/13/2017] [Indexed: 12/22/2022] Open
Abstract
Directly using the promoter associated with 5'-untranslated region of a high-protein-abundance gene from the genome may cause low expression activity of an expression system. A bicistronic expression part containing the short 5' coding sequence of the source gene and an embedded Shine-Dalgarno sequence can cause higher expression levels of the recombinant gene in a bicistronic cassette. Here, we evaluated two methods to construct expression parts and exploited genomic sequence sources to provide specific functional sequences to complete the expression system. The architecture of the bicistronic part increased the expression levels of target genes and performed more reliably than conventional expression parts with the same promoter and 5' untranslated region. For Corynebacterium glutamicum, the strongest bicistronic part, HP-BEP4, was obtained from a heterologous sequence source, leading to a 2.24-fold increase in the expression level of fluorescent protein over constitutively expressed pXMJ19 or the production of more than 100 mg/L single-chain variable fragment (scFv). It could meet the needs of overexpressing key genes in C. glutamicum.
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Affiliation(s)
- Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Zihao Zhao
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Wei Zhang
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Yang Sun
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University Wuxi P. R. China
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Dual toxic-peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally. Cell Rep 2014; 7:424-435. [PMID: 24703849 DOI: 10.1016/j.celrep.2014.03.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/05/2014] [Accepted: 03/05/2014] [Indexed: 12/20/2022] Open
Abstract
Produced from the pathogenicity islands of Staphylococcus aureus clinical isolates, stable SprG1 RNA encodes two peptides from a single internal reading frame. These two peptides accumulate at the membrane, and inducing their expression triggers S. aureus death. Replacement of the two initiation codons by termination signals reverses this toxicity. During growth, cis-antisense RNA SprF1 is expressed, preventing mortality by reducing SprG1 RNA and peptide levels. The peptides are secreted extracellularly, where they lyse human host erythrocytes, a process performed more efficiently by the longer peptide. The two peptides also inactivate Gram-negative and -positive bacteria, with the shorter peptide more effective against S. aureus rivals. Two peptides are secreted from an individual RNA containing two functional initiation codons. Thus, we present an unconventional type I toxin-antitoxin system expressed from a human pathogen producing two hemolytic and antibacterial peptides from a dual-coding RNA, negatively regulated by a dual-acting antisense RNA.
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