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Jain PM, Nellikka A, Kammara R. Understanding bacteriocin heterologous expression: A review. Int J Biol Macromol 2024; 277:133916. [PMID: 39033897 DOI: 10.1016/j.ijbiomac.2024.133916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.
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Affiliation(s)
- Priyanshi M Jain
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Anagha Nellikka
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Rajagopal Kammara
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India.
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2
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Jacobebbinghaus N, Lauersen KJ, Kruse O, Baier T. Bicistronic expression of nuclear transgenes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1400-1412. [PMID: 38415961 DOI: 10.1111/tpj.16677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
In eukaryotic organisms, proteins are typically translated from monocistronic messenger RNAs containing a single coding sequence (CDS). However, recent long transcript sequencing identified 87 nuclear polycistronic mRNAs in Chlamydomonas reinhardtii natively carrying multiple co-expressed CDSs. In this study, we investigated the dynamics of 22 short intergenic sequences derived from these native polycistronic loci by their application in genetic constructs for synthetic transgene expression. A promising candidate sequence was identified based on the quantification of transformation efficiency and expression strength of a fluorescence reporter protein. Subsequently, the expression of independent proteins from one mRNA was verified by cDNA amplification and protein molecular mass characterization. We demonstrated engineered bicistronic expression in vivo to drive successful co-expression of several terpene synthases with the selection marker aphVIII. Bicistronic transgene design resulted in significantly increased (E)-α-bisabolene production of 7.95 mg L-1 from a single open reading frame, 18.1× fold higher than previous reports. Use of this strategy simplifies screening procedures for identification of high-level expressing transformants, does not require the application of additional fluorescence reporters, and reduces the nucleotide footprint compared to classical monocistronic expression cassettes. Although clear advantages for bicistronic transgene expression were observed, this strategy was found to be limited to the aphVIII marker, and further studies are necessary to gain insights into the underlying mechanism that uniquely permits this co-expression from the algal nuclear genome.
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Affiliation(s)
- Nick Jacobebbinghaus
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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3
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Bryant OJ, Lastovka F, Powell J, Chung BYW. The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria. Nat Commun 2023; 14:8167. [PMID: 38071303 PMCID: PMC10710512 DOI: 10.1038/s41467-023-43759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Translational control in pathogenic bacteria is fundamental to gene expression and affects virulence and other infection phenotypes. We used an enhanced ribosome profiling protocol coupled with parallel transcriptomics to capture accurately the global translatome of two evolutionarily distant pathogenic bacteria-the Gram-negative bacterium Salmonella and the Gram-positive bacterium Listeria. We find that the two bacteria use different mechanisms to translationally regulate protein synthesis. In Salmonella, in addition to the expected correlation between translational efficiency and cis-regulatory features such as Shine-Dalgarno (SD) strength and RNA secondary structure around the initiation codon, our data reveal an effect of the 2nd and 3rd codons, where the presence of tandem lysine codons (AAA-AAA) enhances translation in both Salmonella and E. coli. Strikingly, none of these features are seen in efficiently translated Listeria transcripts. Instead, approximately 20% of efficiently translated Listeria genes exhibit 70 S footprints seven nt upstream of the authentic start codon, suggesting that these genes may be subject to a novel translational initiation mechanism. Our results show that SD strength is not a direct hallmark of translational efficiency in all bacteria. Instead, Listeria has evolved additional mechanisms to control gene expression level that are distinct from those utilised by Salmonella and E. coli.
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Affiliation(s)
- Owain J Bryant
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Centre for Structural Biology, National Cancer Institute, 21702, Frederick, MD, USA
| | - Filip Lastovka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Jessica Powell
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Betty Y-W Chung
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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Trautmann HS, Schmidt SS, Gregory ST, Ramsey KM. Ribosome heterogeneity results in leader sequence-mediated regulation of protein synthesis in Francisella tularensis. J Bacteriol 2023; 205:e0014023. [PMID: 37676009 PMCID: PMC10521369 DOI: 10.1128/jb.00140-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/07/2023] [Indexed: 09/08/2023] Open
Abstract
Although ribosomes are generally examined in aggregate, ribosomes can be heterogenous in composition. Evidence is accumulating that changes in ribosome composition may result in altered function, such that ribosome heterogeneity may provide a mechanism to regulate protein synthesis. Ribosome heterogeneity in the human pathogen Francisella tularensis results from incorporation of one of three homologs of bS21, a small ribosomal subunit protein demonstrated to regulate protein synthesis in other bacteria. Loss of one homolog, bS21-2, results in genome-wide post-transcriptional changes in protein abundance. This suggests that bS21-2 can, either directly or indirectly, lead to preferential translation of particular mRNAs. Here, we examine the potential of bS21-2 to function in a leader sequence-dependent manner and to function indirectly, via Hfq. We found that the 5´ untranslated region (UTR) of some bS21-2-responsive genes, including key virulence genes, is sufficient to alter translation in cells lacking bS21-2. We further identify features of a 5´ UTR that allow responsiveness to bS21-2. These include an imperfect Shine-Dalgarno sequence and a particular six nucleotide sequence. Our results are consistent with a model in which a bS21 homolog increases the efficiency of translation initiation through interactions with specific leader sequences. With respect to bS21-2 indirectly regulating translation via the RNA-binding protein Hfq, we found that Hfq controls transcript abundance rather than protein synthesis, impacting virulence gene expression via a distinct mechanism. Together, we determined that ribosome composition in F. tularensis regulates translation in a leader sequence-dependent manner, a regulatory mechanism which may be used in other bacteria. IMPORTANCE Ribosome heterogeneity is common in bacteria, and there is mounting evidence that ribosome composition plays a regulatory role in protein synthesis. However, mechanisms of ribosome-driven gene regulation are not well understood. In the human pathogen Francisella tularensis, which encodes multiple homologs for the ribosomal protein bS21, loss of one homolog impacts protein synthesis and virulence. Here, we explore the mechanism behind bS21-mediated changes in protein synthesis, finding that they can be linked to altered translation initiation and are dependent on specific sequences in the leaders of transcripts. Our data support a model in which ribosome composition regulates gene expression through translation, a strategy that may be conserved in diverse organisms with various sources of ribosome heterogeneity.
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Affiliation(s)
- Hannah S. Trautmann
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Sierra S. Schmidt
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Steven T. Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Kathryn M. Ramsey
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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Pivard M, Caldelari I, Brun V, Croisier D, Jaquinod M, Anzala N, Gilquin B, Teixeira C, Benito Y, Couzon F, Romby P, Moreau K, Vandenesch F. Complex Regulation of Gamma-Hemolysin Expression Impacts Staphylococcus aureus Virulence. Microbiol Spectr 2023; 11:e0107323. [PMID: 37347186 PMCID: PMC10434192 DOI: 10.1128/spectrum.01073-23] [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: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
Staphylococcus aureus gamma-hemolysin CB (HlgCB) is a core-genome-encoded pore-forming toxin that targets the C5a receptor, similar to the phage-encoded Panton-Valentine leucocidin (PVL). Absolute quantification by mass spectrometry of HlgCB in 39 community-acquired pneumonia (CAP) isolates showed considerable variations in the HlgC and HlgB yields between isolates. Moreover, although HlgC and HlgB are encoded on a single operon, their levels were dissociated in 10% of the clinical strains studied. To decipher the molecular basis for the variation in hlgCB expression and protein production among strains, different regulation levels were analyzed in representative clinical isolates and reference strains. Both the HlgCB level and the HlgC/HlgB ratio were found to depend on hlgC promoter activity and mRNA processing and translation. Strikingly, only one single nucleotide polymorphism (SNP) in the 5' untranslated region (UTR) of hlgCB mRNA strongly impaired hlgC translation in the USA300 strain, leading to a strong decrease in the level of HlgC but not in HlgB. Finally, we found that high levels of HlgCB synthesis led to mortality in a rabbit model of pneumonia, correlated with the implication of the role of HlgCB in severe S. aureus CAP. Taken together, this work illustrates the complexity of virulence factor expression in clinical strains and demonstrates a butterfly effect where subtle genomic variations have a major impact on phenotype and virulence. IMPORTANCE S. aureus virulence in pneumonia results in its ability to produce several virulence factors, including the leucocidin PVL. Here, we demonstrate that HlgCB, another leucocidin, which targets the same receptors as PVL, highly contributes to S. aureus virulence in pvl-negative strains. In addition, considerable variations in HlgCB quantities are observed among clinical isolates from patients with CAP. Biomolecular analyses have revealed that a few SNPs in the promoter sequences and only one SNP in the 5' UTR of hlgCB mRNA induce the differential expression of hlgCB, drastically impacting hlgC mRNA translation. This work illustrates the subtlety of regulatory mechanisms in bacteria, especially the sometimes major effects on phenotypes of single nucleotide variation in noncoding regions.
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Affiliation(s)
- Mariane Pivard
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Virginie Brun
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
- Université Grenoble Alpes, CEA, LETI, Clinatec, Grenoble, France
| | | | - Michel Jaquinod
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | | | - Benoît Gilquin
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
- Université Grenoble Alpes, CEA, LETI, Clinatec, Grenoble, France
| | - Chloé Teixeira
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Yvonne Benito
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
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Höllerer S, Jeschek M. Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript. Nucleic Acids Res 2023; 51:2377-2396. [PMID: 36727459 PMCID: PMC10018350 DOI: 10.1093/nar/gkad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/05/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023] Open
Abstract
Translation is a key determinant of gene expression and an important biotechnological engineering target. In bacteria, 5'-untranslated region (5'-UTR) and coding sequence (CDS) are well-known mRNA parts controlling translation and thus cellular protein levels. However, the complex interaction of 5'-UTR and CDS has so far only been studied for few sequences leading to non-generalisable and partly contradictory conclusions. Herein, we systematically assess the dynamic translation from over 1.2 million 5'-UTR-CDS pairs in Escherichia coli to investigate their collective effect using a new method for ultradeep sequence-function mapping. This allows us to disentangle and precisely quantify effects of various sequence determinants of translation. We find that 5'-UTR and CDS individually account for 53% and 20% of variance in translation, respectively, and show conclusively that, contrary to a common hypothesis, tRNA abundance does not explain expression changes between CDSs with different synonymous codons. Moreover, the obtained large-scale data provide clear experimental evidence for a base-pairing interaction between initiator tRNA and mRNA beyond the anticodon-codon interaction, an effect that is often masked for individual sequences and therefore inaccessible to low-throughput approaches. Our study highlights the indispensability of ultradeep sequence-function mapping to accurately determine the contribution of parts and phenomena involved in gene regulation.
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Affiliation(s)
- Simon Höllerer
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology – ETH Zurich, Basel CH-4058, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology – ETH Zurich, Basel CH-4058, Switzerland
- Institute of Microbiology, Synthetic Microbiology Group, University of Regensburg, Regensburg D-93053, Germany
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Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy. Mol Biol Rep 2023; 50:4105-4117. [PMID: 36877346 DOI: 10.1007/s11033-023-08314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/31/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Synonymous variations have always been ignored while studying the underlying genetic mechanisms for most of the human diseases. However, recent studies have suggested that these silent changes in the genome can alter the protein expression and folding. METHODS AND RESULTS CSRP3, which is a well-known candidate gene associated with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), was screened for 100 idiopathic DCM cases and 100 controls. Three synonymous variations were identified viz., c.96G > A, p.K32=; c.336G > A, p.A112=; c.354G > A, p.E118=. A comprehensive in silico analysis was performed using various web based widely accepted tools, Mfold, Codon Usage, HSF3.1 and RNA22. Mfold predicted structural changes in all the variants except c.96 G > A (p.K32=), however it predicted changes in the stability of mRNA due to all the synonymous variants. Codon bias was observed as evident by the Relative Synonymous Codon Usage and Log Ratio of Codon Usage Frequencies. The Human Splicing Finder also predicted remarkable changes in the regulatory elements in the variants c.336G > A and c.354 G > A. The miRNA target prediction using varied modes available in RNA22 revealed that 70.6% of the target sites of miRNAs in CSRP3 were altered due to variant c.336G > A while 29.41% sites were completely lost. CONCLUSION Findings of the present study suggest that synonymous variants revealed striking deviations in the structural conformation of mRNA, stability of mRNA, relative synonymous codon usage, splicing and miRNA binding sites from the wild type suggesting their possible role in the pathogenesis of DCM, either by destabilizing the mRNA structure, or codon usage bias or else altering the cis-acting regulatory elements during splicing.
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Jagadeesan SK, Al-gafari M, Wang J, Takallou S, Allard D, Hajikarimlou M, Kazmirchuk TDD, Moteshareie H, Said KB, Nokhbeh R, Smith M, Samanfar B, Golshani A. DBP7 and YRF1-6 Are Involved in Cell Sensitivity to LiCl by Regulating the Translation of PGM2 mRNA. Int J Mol Sci 2023; 24:ijms24021785. [PMID: 36675300 PMCID: PMC9864399 DOI: 10.3390/ijms24021785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023] Open
Abstract
Lithium chloride (LiCl) has been widely researched and utilized as a therapeutic option for bipolar disorder (BD). Several pathways, including cell signaling and signal transduction pathways in mammalian cells, are shown to be regulated by LiCl. LiCl can negatively control the expression and activity of PGM2, a phosphoglucomutase that influences sugar metabolism in yeast. In the presence of galactose, when yeast cells are challenged by LiCl, the phosphoglucomutase activity of PGM2p is decreased, causing an increase in the concentration of toxic galactose metabolism intermediates that result in cell sensitivity. Here, we report that the null yeast mutant strains DBP7∆ and YRF1-6∆ exhibit increased LiCl sensitivity on galactose-containing media. Additionally, we demonstrate that DBP7 and YRF1-6 modulate the translational level of PGM2 mRNA, and the observed alteration in translation seems to be associated with the 5'-untranslated region (UTR) of PGM2 mRNA. Furthermore, we observe that DBP7 and YRF1-6 influence, to varying degrees, the translation of other mRNAs that carry different 5'-UTR secondary structures.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Kamaledin B. Said
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Reza Nokhbeh
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Myron Smith
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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9
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Zhang M, Song J, Xiao J, Jin J, Nomura CT, Chen S, Wang Q. Engineered multiple translation initiation sites: a novel tool to enhance protein production in Bacillus licheniformis and other industrially relevant bacteria. Nucleic Acids Res 2022; 50:11979-11990. [PMID: 36382403 PMCID: PMC9723656 DOI: 10.1093/nar/gkac1039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Gram-positive bacteria are a nascent platform for synthetic biology and metabolic engineering that can provide new opportunities for the production of biomolecules. However, the lack of standardized methods and genetic parts is a major obstacle towards attaining the acceptance and widespread use of Gram-positive bacterial chassis for industrial bioproduction. In this study, we have engineered a novel mRNA leader sequence containing more than one ribosomal binding site (RBS) which could initiate translation from multiple sites, vastly enhancing the translation efficiency of the Gram-positive industrial strain Bacillus licheniformis. This is the first report elucidating the impact of more than one RBS to initiate translation and enhance protein output in B. licheniformis. We also explored the application of more than one RBS for both intracellular and extracellular protein production in B. licheniformis to demonstrate its efficiency, consistency and potential for biotechnological applications. Moreover, we applied these concepts for use in other industrially relevant Gram-positive bacteria, such as Bacillus subtilis and Corynebacterium glutamicum. In all, a highly efficient and robust broad-host expression element has been designed to strengthen and fine-tune the protein outputs for the use of bioproduction in microbial cell factories.
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Affiliation(s)
- Manyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | | | - Jun Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Christopher T Nomura
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA
| | - Shouwen Chen
- Correspondence may also be addressed to Shouwen Chen.
| | - Qin Wang
- To whom correspondence should be addressed. Tel: +86 18507140137;
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10
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Karaiyan P, Chang CCH, Chan ES, Tey BT, Ramanan RN, Ooi CW. In silico screening and heterologous expression of soluble dimethyl sulfide monooxygenases of microbial origin in Escherichia coli. Appl Microbiol Biotechnol 2022; 106:4523-4537. [PMID: 35713659 PMCID: PMC9259527 DOI: 10.1007/s00253-022-12008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
Abstract Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. Key points • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12008-8.
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Affiliation(s)
- Prasanth Karaiyan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Catherine Ching Han Chang
- Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Eng-Seng Chan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Beng Ti Tey
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia.
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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11
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Expression of the DeaD RNA helicase is regulated at multiple levels through its long mRNA 5' untranslated region. J Bacteriol 2022; 204:e0061321. [PMID: 35041499 DOI: 10.1128/jb.00613-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DEAD-box proteins (DBPs) are a prominent class of RNA remodeling proteins that alter RNA structure, a process they typically perform through an ATP-dependent RNA helicase activity. Although many DBPs have been characterized at the structural and functional level in detail, much less is known about how they are regulated. We previously showed that the messenger RNA (mRNA) for the Escherichia coli (E. coli) DeaD DBP contains an unusually long 5' untranslated region (5' UTR) of 838 nucleotides (nts) and that it is the primary RNA determinant of DeaD autoregulation. We speculated that such a long and complex 5' UTR might regulate deaD expression in additional ways. Here we show that the deaD mRNA 5' UTR regulates deaD expression at two additional levels: temperature dependent expression and through a stem-loop structure overlapping the start codon. These results support the hypothesis that a long 5' UTR can regulate gene expression through multiple mechanisms. Importance The expression of genes is frequently regulated by determinants with the 5' UTR. Although many different regulatory mechanisms that operate via the 5' UTR have been described, the functional relevance of genes with long UTRs is less clear. Here, we show that the 838 nt long 5' UTR in the deaD mRNA regulates the expression of DeaD at multiple levels. We propose that long UTRs originate to provide precise control of gene expression through multiple regulatory mechanisms, and they are indicators of the importance of their associated gene products for cellular adaptation to different environments.
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12
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Karamitros CS, Somody CM, Agnello G, Rowlinson S. Engineering of the Recombinant Expression and PEGylation Efficiency of the Therapeutic Enzyme Human Thymidine Phosphorylase. Front Bioeng Biotechnol 2021; 9:793985. [PMID: 34976980 PMCID: PMC8718881 DOI: 10.3389/fbioe.2021.793985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/12/2021] [Indexed: 12/01/2022] Open
Abstract
Human thymidine phosphorylase (HsTP) is an enzyme with important implications in the field of rare metabolic diseases. Defective mutations of HsTP lead to mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), a disease with a high unmet medical need that is associated with severe neurological and gastrointestinal complications. Current efforts focus on the development of an enzyme replacement therapy (ERT) using the Escherichia coli ortholog (EcTP). However, bacterial enzymes are counter-indicated for human therapeutic applications because they are recognized as foreign by the human immune system, thereby eliciting adverse immune responses and raising significant safety and efficacy risks. Thus, it is critical to utilize the HsTP enzyme as starting scaffold for pre-clinical drug development, thus de-risking the safety concerns associated with the use of bacterial enzymes. However, HsTP expresses very poorly in E. coli, whereas its PEGylation, a crucial chemical modification for achieving long serum persistence of therapeutic enzymes, is highly inefficient and negatively affects its catalytic activity. Here we focused on the engineering of the recombinant expression profile of HsTP in E. coli cells, as well as on the optimization of its PEGylation efficiency aiming at the development of an alternative therapeutic approach for MNGIE. We show that phylogenetic and structural analysis of proteins can provide important insights for the rational design of N’-terminus-truncation constructs which exhibit significantly improved recombinant expression levels. In addition, we developed and implemented a criteria-driven rational surface engineering strategy for the substitution of arginine-to-lysine and lysine-to-arginine residues to achieve more efficient, homogeneous and reproducible PEGylation without negatively affecting the enzymatic catalytic activity upon PEGylation. Collectively, our proposed strategies provide an effective way to optimize enzyme PEGylation and E. coli recombinant expression and are likely applicable for other proteins and enzymes.
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13
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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14
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Bharmal MHM, Gega A, Schrader JM. A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation. NAR Genom Bioinform 2021; 3:lqab081. [PMID: 34568822 PMCID: PMC8459731 DOI: 10.1093/nargab/lqab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/03/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial translation is thought to initiate by base pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA's 5' untranslated region (UTR). However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5' UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using these data, a simple computational model was built based on the combinatorial relationship of these mRNA features that can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.
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Affiliation(s)
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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15
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Kielkopf CL, Bauer W, Urbatsch IL. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc 2021; 2021:pdb.top102129. [PMID: 33272973 DOI: 10.1101/pdb.top102129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.
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16
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Osterman IA, Chervontseva ZS, Evfratov SA, Sorokina AV, Rodin VA, Rubtsova MP, Komarova ES, Zatsepin TS, Kabilov MR, Bogdanov AA, Gelfand MS, Dontsova OA, Sergiev PV. Translation at first sight: the influence of leading codons. Nucleic Acids Res 2020; 48:6931-6942. [PMID: 32427319 PMCID: PMC7337518 DOI: 10.1093/nar/gkaa430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023] Open
Abstract
First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze >30 000 variants of the codons 2-11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame start codons enhance translation, while Shine-Dalgarno-like motifs downstream the initiation codon are inhibitory. The metabolic cost of amino acids affects the yield of protein in the poor medium. The most efficient translation was observed for variants with features resembling those of native Escherichia coli genes.
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Affiliation(s)
- Ilya A Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zoe S Chervontseva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | | | - Alena V Sorokina
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia
| | | | - Maria P Rubtsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina S Komarova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,A.A.Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Lomonosov Moscow State University, Moscow 119992, Russia
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17
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Khoobbakht D, Zare Karizi S, Motamedi MJ, Kazemi R, Roghanian P, Amani J. Immunogenicity Evaluation of Chimeric Subunit Vaccine Comprising Adhesion Coli Surface Antigens from Enterotoxigenic Escherichia coli. J Mol Microbiol Biotechnol 2020; 29:91-100. [PMID: 32645695 DOI: 10.1159/000509708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/24/2020] [Indexed: 11/19/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is the most common agent of diarrhea morbidity in developing countries. ETEC adheres to host intestinal epithelial cells via various colonization factors. The CooD and CotD proteins play a significant role in bacteria binding to the intestinal epithelial cells as adhesin tip subunits of CS1 and CS2 pili. The purpose here was to design a new construction containing cooD and cotD genes and use several types of bioinformatics software to predict the structural and immunological properties of the designed antigen. The fusion gene was synthesized with codon bias of E. coli in order to increase the expression level of the protein. The amino acid sequences, protein structure, and immunogenicity properties of potential antigens were analyzed in silico. The chimeric protein was expressed in E. coliBL21 (DE3). The antigenicity of the recombinant proteins was verified by Western blotting and ELISA. In order to assess the induced immunity, the immunized mice were challenged with wild-type ETEC by an intraperitoneal route. Immunological analyses showed the production of a high titer of IgG serum with no sign of serum-mucosal IgA antibody response. The result of the challenge assay showed that 30% of immunized mice survived. The results of this study showed that CooD-CotD recombinant protein can stimulate immunity against ETEC. The designed chimera could be a prototype for the subunit vaccine, which is worthy of further consideration.
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Affiliation(s)
- Dorna Khoobbakht
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Shohreh Zare Karizi
- Department of Genetics and Biotechnology, School of Biological Science, Varamin-Pishva, Branch of Islamic Azad University, Varamin, Iran
| | | | | | - Pooneh Roghanian
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran,
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18
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Aseev LV, Koledinskaya LS, Boni IV. Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b. RNA (NEW YORK, N.Y.) 2020; 26:814-826. [PMID: 32209634 PMCID: PMC7297116 DOI: 10.1261/rna.074237.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/22/2020] [Indexed: 06/10/2023]
Abstract
Bacterial ribosomal proteins (r-proteins) encoded by nonessential genes often carry out very important tasks in translation. In particular, this is the case of a small basic bacteria-specific r-protein L31 (bL31). Recent studies revealed a crucial role of bL31 in formation of the protein-protein intersubunit bridge B1b and hence its contribution to ribosome dynamics. Our goal was to study in vivo regulation of the rpmE operon encoding bL31. We used a previously developed approach based on chromosomally integrated fusions with the lacZ reporter. E. coli rpmE is transcribed from two promoter regions, and translation of both mRNA transcripts was shown to be feedback regulated by bL31, indicating that the autogenous operator is located within the shorter transcript. The bL31-mediated control of rpmE is gene-specific, as no regulation was found for rpmE-unrelated reporters. Thus, bL31, as many other r-proteins, possesses dual activity in living cells, acting both as an integral ribosome component and an autogenous repressor. Phylogenetic studies revealed the presence of a highly conserved stem-loop structure in the rpmE 5'UTR, a presumable translational operator targeted by bL31, which was further confirmed by site-directed mutagenesis. This stable operator stem-loop separates an AU-rich translational enhancer from a Shine-Dalgarno element, which is a rare case of a noncontiguous translation initiation region. Sequence/structure computational approaches classify bL31 as an RNA-binding protein, consistent with its repressor function discovered here. Mutational analysis of bL31 showed that its unstructured amino-terminal part enriched in lysine is necessary for the repressor activity.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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19
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Katashkina JI, Kazieva ED, Tajima Y, Mashko SV. Increased Isoprene Production by the Recombinant Pantoea ananatis Strain due to the Balanced Amplification of Mevalonate Pathway Genes. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819090023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Sterk M, Romilly C, Wagner EGH. Unstructured 5'-tails act through ribosome standby to override inhibitory structure at ribosome binding sites. Nucleic Acids Res 2019; 46:4188-4199. [PMID: 29420821 PMCID: PMC5934652 DOI: 10.1093/nar/gky073] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/26/2018] [Indexed: 11/13/2022] Open
Abstract
Initiation is the rate-limiting step in translation. It is well-known that stable structure at a ribosome binding site (RBS) impedes initiation. The ribosome standby model of de Smit and van Duin, based on studies of the MS2 phage coat cistron, proposed how high translation rates can be reconciled with stable, inhibitory structures at an RBS. Here, we revisited the coat protein system and assessed the translation efficiency from its sequestered RBS by introducing standby mutations. Further experiments with gfp reporter constructs assessed the effects of 5′-tails—as standby sites—with respect to length and sequence contributions. In particular, combining in vivo and in vitro assays, we can show that tails of CA-dinucleotide repeats—and to a lesser extent, AU-repeats—dramatically increase translation rates. Tails of increasing length reach maximal rate-enhancing effects at 16–18 nucleotides. These standby tails are single-stranded and do not exert their effect by structure changes in the neighboring RBS stem–loop. In vitro translation and toeprinting assays furthermore demonstrate that standby effects are exerted at the level of translation initiation. Finally, as expected, destabilizing mutations within the coat RBS indicate an interplay with the effects of standby tails.
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Affiliation(s)
- Maaike Sterk
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden
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21
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Normal expression of KCNJ11 is maintained by the G-quadruplex. Int J Biol Macromol 2019; 138:504-510. [PMID: 31325507 DOI: 10.1016/j.ijbiomac.2019.07.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/13/2019] [Accepted: 07/13/2019] [Indexed: 11/21/2022]
Abstract
MicroRNAs affect various pathological pathways by binding to multiple target mRNAs. Recently, it was reported that eukaryotic RNA G-quadruplexes were enriched in mRNA 3'-UTR, where microRNAs can also bind. To determine the roles of the G-quadruplex within mRNA 3'-UTR in microRNA binding sites, a bioinformatics approach was utilized to identify candidate microRNA target mRNAs with potential G-quadruplex formation. Circular dichroism spectrometry demonstrated the formation of RNA G-quadruplexes in vitro in candidate G-rich sequences. Mutated guanosines that are critical for G-quadruplex formation significantly decreased luciferase activities. Moreover, a G-quadruplex ligand TMPyP4 was used to destabilize the KCNJ11 RNA G-quadruplex in cardiomyocytes, resulting in binding of the microRNA to mRNA and subsequent suppression of KCNJ11 expression. In conclusion, our study showed that the G-quadruplex structure affects microRNA binding to its target mRNA. Thus, our study reveals a novel mechanism for G-quadruplex-dependent regulation of microRNA-mRNA interaction, which is essential to maintain normal gene expression.
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22
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Qureshi NS, Bains JK, Sreeramulu S, Schwalbe H, Fürtig B. Conformational switch in the ribosomal protein S1 guides unfolding of structured RNAs for translation initiation. Nucleic Acids Res 2019; 46:10917-10929. [PMID: 30124944 PMCID: PMC6237739 DOI: 10.1093/nar/gky746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Initiation of bacterial translation requires that the ribosome-binding site in mRNAs adopts single-stranded conformations. In Gram-negative bacteria the ribosomal protein S1 (rS1) is a key player in resolving of structured elements in mRNAs. However, the exact mechanism of how rS1 unfolds persistent secondary structures in the translation initiation region (TIR) is still unknown. Here, we show by NMR spectroscopy that Vibrio vulnificus rS1 displays a unique architecture of its mRNA-binding domains, where domains D3 and D4 provide the mRNA-binding platform and cover the nucleotide binding length of the full-length rS1. D5 significantly increases rS1’s chaperone activity, although it displays structural heterogeneity both in isolation and in presence of the other domains, albeit to varying degrees. The heterogeneity is induced by the switch between the two equilibrium conformations and is triggered by an order-to-order transition of two mutually exclusive secondary structures (β-strand-to-α-helix) of the ‘AERERI’ sequence. The conformational switching is exploited for melting of structured 5′-UTR’s, as the conformational heterogeneity of D5 can compensate the entropic penalty of complex formation. Our data thus provides a detailed understanding of the intricate coupling of protein and RNA folding dynamics enabling translation initiation of structured mRNAs.
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Affiliation(s)
- Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
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23
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Wang Z, Zhang J, Wang X, Wei D. High level expression and characterization of the recombinant immunotoxin DAB389-4D5 scFv targeting HER2/neu-positive ovarian carcinoma cells. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Adalat R, Saleem F, Bashir A, Ahmad M, Zulfiqar S, Shakoori AR. Multiple upstream start codons (AUG) in 5' untranslated region enhance translation efficiency of cry2Ac11 without helper protein. J Cell Biochem 2019; 120:2236-2250. [PMID: 30242865 DOI: 10.1002/jcb.27534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/01/2018] [Indexed: 01/24/2023]
Abstract
Cry2Ac11, a 65 kDa insecticidal protein produced by Bacillus thuringiensis, shows toxicity against dipteran and lepidopteran larvae. It is encoded by cry2Ac11 gene ( orf3), which is part of an operon comprising orf1, orf2, and orf3. Orf2, a helper protein, helps in proper folding and prevents aberrant aggregation of newly produced molecules. In this study, we have elucidated the effect of different mutations in translation initiation region (TIR), particularly the ribosomal binding site and the start codon (RBS-ATG) on cry2Ac11 gene expression without helper protein. All recombinant constructs were expressed in acrystalliferous B. thuringiensis subsp israelensis 4Q7 under the control of strong chimeric promoter cyt1AP/STAB. Of all the mutants, mut/RBS2, with two consecutive AUGs after the spacer region in TIR, exhibited 89- and 2246-fold higher transcript levels compared with 4Q7-operSalI/RBS ( cry2Ac11 operon) and 4Q7-w-RBS ( cry2Ac11 gene), respectively. The analysis of mut/RBS2 messenger RNA (mRNA) structure in the RBS-AUG region showed the presence of RBS in the single-stranded part of the moderately stable hairpin loop. The high expression efficiency of Cry2Ac11 mutant without helper protein is a cumulative and cooperative result of chimeric promoter cyt1AP/STAB-SD with the optimal context of RBS-AUG region provided by multiple AUGs and stabilizer sequence at 3' ends.
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Affiliation(s)
- Rooma Adalat
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Faiza Saleem
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Aftab Bashir
- Department of Biological Sciences, Forman Christian College, Lahore, Pakistan
| | - Munir Ahmad
- School of Biological Sciences, Quaid-i-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Soumble Zulfiqar
- School of Biological Sciences, Quaid-i-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Abdul Rauf Shakoori
- School of Biological Sciences, Quaid-i-Azam Campus, University of the Punjab, Lahore, Pakistan.,Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
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25
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Mobasseri N, Nikzad H, Karimian M. Protective effect of oestrogen receptor α-PvuII transition against idiopathic male infertility: a case-control study and meta-analysis. Reprod Biomed Online 2019; 38:588-598. [PMID: 30738766 DOI: 10.1016/j.rbmo.2019.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/21/2022]
Abstract
RESEARCH QUESTION Is there any genetic association between oestrogen receptor alpha [ERα]-PvuII polymorphism and idiopathic male infertility? DESIGN A total of 226 infertile and 213 fertile men participated in the present case-control study. ERα-PvuII genotyping was performed using the polymerase chain reaction-restriction fragment length polymorphism [PCR-RFLP] method. Meta-analysis was also performed by pooling data collected from seven other eligible studies identified by searches of PubMed, Embase, Google Scholar, and Science Direct databases. Summary odds ratios were estimated by fixed- or random-effects models. The molecular effects of ERα-PvuII polymorphism were evaluated by bioinformatics tools. RESULTS A significant protective association was reported between ERα-PvuII and male infertility in the homozygote model [OR=0.54, 95%CI=0.3-0.98, p=0.042]. Also, a similar association was observed in asthenozoospermia subgroup [OR=0.4, 95%CI=0.18-0.9, p=0.025]. Meta-analysis also revealed that the ER-PvuII polymorphism was significantly associated with the decreased risk of male infertility in the heterozygote co-dominant model [OR=0.80, 95%CI=0.64-0.99, p=0.042]. Moreover, similar protective results were reported in stratified analyses in Caucasian subgroup in the dominant genetic model [OR=0.66, 95%CI=0.45-0.96, p=0.029] and in the heterozygote co-dominant model [OR=0.62, 95%CI=0.41-0.93, p=0.021]. A significant association was also found in studies with sample size of less than 400 subjects in heterozygote co-dominant model [OR=0.69, 95%CI=0.50-0.95, p=0.023]. The bioinformatics data indicated that ER-PvuII polymorphism could significantly affect RNA structure of ERα [p=0.004]. CONCLUSION The ERα-PvuII polymorphism could be considered as a possible protective factor against male infertility.
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Affiliation(s)
- Narges Mobasseri
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Nikzad
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran.
| | - Mohammad Karimian
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran.
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Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol 2018; 14:e1006170. [PMID: 30118473 PMCID: PMC6114898 DOI: 10.1371/journal.pcbi.1006170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/29/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.
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Affiliation(s)
- Gert Peters
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
- * E-mail:
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Function of the RNA Coliphage Qβ Proteins in Medical In Vitro Evolution. Methods Protoc 2018; 1:mps1020018. [PMID: 31164561 PMCID: PMC6526423 DOI: 10.3390/mps1020018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/16/2018] [Accepted: 05/28/2018] [Indexed: 12/14/2022] Open
Abstract
Qβ is a positive (+) single-stranded RNA bacteriophage covered by a 25 nm icosahedral shell. Qβ belongs to the family of Leviviridae and is found throughout the world (bacterial isolates and sewage). The genome of Qβ is about 4.2 kb, coding for four proteins. This genome is surrounded by 180 copies of coat proteins (capsomers) each comprised of 132 residues of amino acids. The other proteins, the subunit II (β) of a replicase, the maturation protein (A2) and the read-through or minor coat protein (A1), play a key role in phage infection. With the replicase protein, which lacks proofreading activity, as well as its short replication time, and high population size, Qβ phage has attractive features for in vitro evolution. The A1 protein gene shares the same initiation codon with the coat protein gene and is produced during translation when the coat protein’s UGA stop codon triplet (about 400 nucleotides from the initiation) is suppressed by a low level of ribosome misincorporation of tryptophan. Thus, A1 is termed the read-through protein. This RNA phage platform technology not only serves to display foreign peptides but is also exceptionally suited to address questions about in vitro evolution. The C-terminus of A1 protein confers to this RNA phage platform an exceptional feature of not only a linker for foreign peptide to be displayed also a model for evolution. This platform was used to present a peptide library of the G-H loop of the capsid region P1 of the foot-and-mouth disease virus (FMDV) called VP1 protein. The library was exposed on the exterior surface of Qβ phages, evolved and selected with the monoclonal antibodies (mAbs) SD6 of the FMDV. These hybrid phages could principally be good candidates for FMDV vaccine development. Separately, the membrane proximal external region (MPER) of human immunodeficiency virus type 1 (HIV-1) epitopes was fused with the A1 proteins and exposed on the Qβ phage exterior surface. The engineered phages with MPER epitopes were recognized by anti-MPER specific antibodies. This system could be used to overcome the challenge of effective presentation of MPER to the immune system. A key portion of this linear epitope could be randomized and evolved with the Qβ system. Overall, antigens and epitopes of RNA viruses relevant to public health can be randomized, evolved and selected in pools using the proposed Qβ model to overcome their plasticity and the challenge of vaccine development. Major epitopes of a particular virus can be engineered or displayed on the Qβ phage surface and used for vaccine efficacy evaluation, thus avoiding the use of live viruses.
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Rational design and analysis of an Escherichia coli strain for high-efficiency tryptophan production. ACTA ACUST UNITED AC 2018; 45:357-367. [DOI: 10.1007/s10295-018-2020-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/04/2018] [Indexed: 01/24/2023]
Abstract
Abstract
l-tryptophan (l-trp) is a precursor of various bioactive components and has great pharmaceutical interest. However, due to the requirement of several precursors and complex regulation of the pathways involved, the development of an efficient l-trp production strain is challenging. In this study, Escherichia coli (E. coli) strain KW001 was designed to overexpress the l-trp operator sequences (trpEDCBA) and 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (aroGfbr). To further improve the production of l-trp, pyruvate kinase (pykF) and the phosphotransferase system HPr (ptsH) were deleted after inactivation of repression (trpR) and attenuation (attenuator) to produce strain KW006. To overcome the relatively slow growth and to increase the transport rate of glucose, strain KW018 was generated by combinatorial regulation of glucokinase (galP) and galactose permease (glk) expression. To reduce the production of acetic acid, strain KW023 was created by repressive regulation of phosphate acetyltransferase (pta) expression. In conclusion, strain KW023 efficiently produced 39.7 g/L of l-trp with a conversion rate of 16.7% and a productivity of 1.6 g/L/h in a 5 L fed-batch fermentation system.
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Abstract
Cell-free synthetic biology approaches enable engineering of biomolecular systems exhibiting complex, cell-like behaviors in the absence of living entities. Often essential to these systems are user-controllable mechanisms to regulate gene expression. Here we describe synthetic RNA thermometers that enable temperature-dependent translation in the PURExpress in vitro protein synthesis system. Previously described cellular thermometers lie wholly in the 5' untranslated region and do not retain their intended function in PURExpress. By contrast, we designed hairpins between the Shine-Dalgarno sequence and complementary sequences within the gene of interest. The resulting thermometers enable high-yield, cell-free protein expression in an inducible temperature range compatible with in vitro translation systems (30-37 °C). Moreover, expression efficiency and switching behavior are tunable via small variations to the coding sequence. Our approach and resulting thermometers provide new tools for exploiting temperature as a rapid, external trigger for in vitro gene regulation.
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Affiliation(s)
- Fredrik W. Sadler
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Igor Dodevski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455
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Roy V, Roth R, Berge M, Chitta R, Vajrala S, Kuntumalla S, E Schmelzer A, Schoner R. A bicistronic vector with destabilized mRNA secondary structure yields scalable higher titer expression of human neurturin in E. coli. Biotechnol Bioeng 2017; 114:1753-1761. [PMID: 28369693 DOI: 10.1002/bit.26299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 02/22/2017] [Accepted: 03/24/2017] [Indexed: 11/10/2022]
Abstract
Human neurturin (NTN) is a cystine knot growth factor with potential therapeutic use in diseases such as Parkinson's and diabetes. Scalable high titer production of native NTN is particularly challenging because of the cystine knot structure which consists of an embedded ring comprised of at least three disulfide bonds. We sought to pursue enhanced scalable production of NTN in Escherichia coli. Our initial efforts focused on codon optimization of the first two codons following AUG, but these studies resulted in only a marginal increase in NTN expression. Therefore, we pursued an alternative strategy of using a bicistronic vector for NTN expression designed to reduce mRNA secondary structure to achieve increased ribosome binding and re-initiation. The first cistron was designed to prevent sequestration of the translation initiation region in a secondary conformation. The second cistron, which contained the NTN coding sequence itself, was engineered to disrupt double bonded base pairs and destabilize the secondary structure for ribosome re-initiation. The ensemble approach of reducing NTN's mRNA secondary structure and using the bicistronic vector had an additive effect resulting in significantly increased NTN expression. Our strain selection studies were conducted in a miniaturized bioreactor. An optimized strain was selected and scaled up to a 100 L fermentor, which yielded an inclusion body titer of 2 g/L. The inclusion bodies were refolded to yield active NTN. We believe that our strategy is applicable to other candidate proteins that are difficult-to-express due to stable mRNA secondary structures. Biotechnol. Bioeng. 2017;114: 1753-1761. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Varnika Roy
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
| | - Robert Roth
- Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Mark Berge
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
| | - Rajesh Chitta
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
| | - Sucheta Vajrala
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
| | | | - Albert E Schmelzer
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
| | - Ron Schoner
- Cell Culture and Fermentation Sciences, MedImmune, LLC, 1 MedImmune Way, Gaithersburg, Maryland, 20878
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Ghavim M, Abnous K, Arasteh F, Taghavi S, Nabavinia MS, Alibolandi M, Ramezani M. High level expression of recombinant human growth hormone in Escherichia coli: crucial role of translation initiation region. Res Pharm Sci 2017; 12:168-175. [PMID: 28515770 PMCID: PMC5385732 DOI: 10.4103/1735-5362.202462] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
For high-throughput production of recombinant protein in Escherichia coli (E. coli), besides important parameters such as efficient vector with strong promoter and compatible host, other important issues including codon usage, rare codons, and GC content specially at N-terminal region should be considered. In the current study, the effect of decreasing the percentage of GC nucleotides and optimizing codon usage at N-terminal region of human growth hormone (hGH) cDNA on the level of its expression in E. coli were investigated. Mutation in cDNA of hGH was performed through site-directed mutagenesis using PCR. Then, the mutant genes were amplified and cloned into the expression vector, pET-28a. The new constructs were transformed into the BL21(DE3) strain of E. coli and chemically induced for hGH expression. At the final stage, expressed proteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), scanning gel densitometry, and western blot. SDS-PAGE scanning gel densitometry assay and western blot analysis revealed higher expression level of hGH by using the two new expressions constructs (mutant genes vectors with decreasing GC content and optimized-codon usage at N-terminal of cDNA) in comparison with wild gene expression vector. Obtained results demonstrated that decreasing the GC nucleotide content and optimization of codon usage at N-terminal of the hGH cDNA could significantly enhance the expression of the target protein in E. coli. Our results highlight the important role of both 5´ region of the heterologous genes in terms of codon usage and also GC content on non-host protein expression in E. coli.
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Affiliation(s)
- Mahsa Ghavim
- Damghan Branch, Islamic Azad University, Damghan, I.R. Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
| | - Fatemeh Arasteh
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
| | - Sahar Taghavi
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
| | - Maryam Sadat Nabavinia
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran.,Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, I.R. Iran
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Hansen MMK, Ventosa Rosquelles M, Yelleswarapu M, Maas RJM, van Vugt-Jonker AJ, Heus HA, Huck WTS. Protein Synthesis in Coupled and Uncoupled Cell-Free Prokaryotic Gene Expression Systems. ACS Synth Biol 2016; 5:1433-1440. [PMID: 27306580 DOI: 10.1021/acssynbio.6b00010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Secondary structure formation of mRNA, caused by desynchronization of transcription and translation, is known to impact gene expression in vivo. Yet, inactivation of mRNA by secondary structures in cell-free protein expression is frequently overlooked. Transcription and translation rates are often not highly synchronized in cell-free expression systems, leading to a temporal mismatch between the processes and a drop in efficiency of protein production. By devising a cell-free gene expression platform in which transcriptional and translational elongation are successfully performed independently, we determine that sequence-dependent mRNA secondary structures are the main cause of mRNA inactivation in in vitro gene expression.
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Affiliation(s)
- Maike M. K. Hansen
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Marta Ventosa Rosquelles
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Maaruthy Yelleswarapu
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Aafke J. van Vugt-Jonker
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
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Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression. Microbiol Mol Biol Rev 2016; 80:1029-1057. [PMID: 27784798 DOI: 10.1128/mmbr.00026-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis.
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Gaida SM, Liedtke A, Jentges AHW, Engels B, Jennewein S. Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact 2016. [PMID: 26758196 DOI: 10.1186/s12934-12015-10406-12932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND Sustainable alternatives for the production of fuels and chemicals are needed to reduce our dependency on fossil resources and to avoid the negative impact of their excessive use on the global climate. Lignocellulosic feedstock from agricultural residues, energy crops and municipal solid waste provides an abundant and carbon-neutral alternative, but it is recalcitrant towards microbial degradation and must therefore undergo extensive pretreatment to release the monomeric sugar units used by biofuel-producing microbes. These pretreatment steps can be reduced by using microbes such as Clostridium cellulolyticum that naturally digest lignocellulose, but this limits the range of biofuels that can be produced. We therefore developed a metabolic engineering approach in C. cellulolyticum to expand its natural product spectrum and to fine tune the engineered metabolic pathways. RESULTS Here we report the metabolic engineering of C. cellulolyticum to produce n-butanol, a next-generation biofuel and important chemical feedstock, directly from crystalline cellulose. We introduced the CoA-dependent pathway for n-butanol synthesis from C. acetobutylicum and measured the expression of functional enzymes (using targeted proteomics) and the abundance of metabolic intermediates (by LC-MS/MS) to identify potential bottlenecks in the n-butanol biosynthesis pathway. We achieved yields of 40 and 120 mg/L n-butanol from cellobiose and crystalline cellulose, respectively, after cultivating the bacteria for 6 and 20 days. CONCLUSION The analysis of enzyme activities and key intracellular metabolites provides a robust framework to determine the metabolic flux through heterologous pathways in C. cellulolyticum, allowing further improvements by fine tuning individual steps to improve the yields of n-butanol.
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Affiliation(s)
- Stefan Marcus Gaida
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andrea Liedtke
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andreas Heinz Wilhelm Jentges
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Benedikt Engels
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Stefan Jennewein
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
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Gaida SM, Liedtke A, Jentges AHW, Engels B, Jennewein S. Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose. Microb Cell Fact 2016; 15:6. [PMID: 26758196 PMCID: PMC4711022 DOI: 10.1186/s12934-015-0406-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/19/2015] [Indexed: 01/13/2023] Open
Abstract
Background Sustainable alternatives for the production of fuels and chemicals are needed to reduce our dependency on fossil resources and to avoid the negative impact of their excessive use on the global climate. Lignocellulosic feedstock from agricultural residues, energy crops and municipal solid waste provides an abundant and carbon-neutral alternative, but it is recalcitrant towards microbial degradation and must therefore undergo extensive pretreatment to release the monomeric sugar units used by biofuel-producing microbes. These pretreatment steps can be reduced by using microbes such as Clostridium cellulolyticum that naturally digest lignocellulose, but this limits the range of biofuels that can be produced. We therefore developed a metabolic engineering approach in C. cellulolyticum to expand its natural product spectrum and to fine tune the engineered metabolic pathways. Results Here we report the metabolic engineering of C. cellulolyticum to produce n-butanol, a next-generation biofuel and important chemical feedstock, directly from crystalline cellulose. We introduced the CoA-dependent pathway for n-butanol synthesis from C. acetobutylicum and measured the expression of functional enzymes (using targeted proteomics) and the abundance of metabolic intermediates (by LC-MS/MS) to identify potential bottlenecks in the n-butanol biosynthesis pathway. We achieved yields of 40 and 120 mg/L n-butanol from cellobiose and crystalline cellulose, respectively, after cultivating the bacteria for 6 and 20 days. Conclusion The analysis of enzyme activities and key intracellular metabolites provides a robust framework to determine the metabolic flux through heterologous pathways in C. cellulolyticum, allowing further improvements by fine tuning individual steps to improve the yields of n-butanol. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0406-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Marcus Gaida
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andrea Liedtke
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Andreas Heinz Wilhelm Jentges
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Benedikt Engels
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
| | - Stefan Jennewein
- Department of Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
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Quantitative relationship between the mRNA secondary structure of translational initiation region and the expression level of heterologous protein in Escherichia coli. ACTA ACUST UNITED AC 2016; 43:97-102. [DOI: 10.1007/s10295-015-1699-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
Abstract
Translational efficiency in Escherichia coli is strongly influenced by mRNA secondary structure of translational initiation region (TIR). We have previously reported that the expression of heterologous protein is directly related to the minimal folding free energy (ΔG) of the local secondary structure. However, identifying biologically relevant maximum and minimum levels of expression, or exploring the optimal level between them, is a key to successful optimization of heterologous protein expression. To systematically search a large range of the ΔG of TIR, we now present a quantitative analysis of the relationship between expression level and these ΔGs. The ΔG of TIR in green fluorescent protein is found to be linearly correlated with the fluorescence intensity over a range of tenfold change. The result demonstrates that the increasing ΔG of TIR can enhance the expression level linearly with no threshold or plateau.
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Samal J, Kandpal M, Vivekanandan P. Hepatitis B “e” antigen-mediated inhibition of HBV replication fitness and transcription efficiency in vitro. Virology 2015; 484:234-240. [DOI: 10.1016/j.virol.2015.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/25/2015] [Accepted: 06/02/2015] [Indexed: 01/04/2023]
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Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
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Wang B, Wang Y, Kennedy C. 5'-coding sequence of the nasA gene of Azotobacter vinelandii is required for efficient expression. FEMS Microbiol Lett 2014; 359:201-8. [PMID: 25110215 DOI: 10.1111/1574-6968.12570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/01/2014] [Indexed: 11/30/2022] Open
Abstract
The operon nasACBH in Azotobacter vinelandii encodes nitrate and nitrite reductases that sequentially reduce nitrate to nitrite and to ammonium for nitrogen assimilation into organic molecules. Our previous analyses showed that nasACBH expression is subject to antitermination regulation that occurs upstream of the nasA gene in response to the availability of nitrate and nitrite. In this study, we continued expression analyses of the nasA gene and observed that the nasA 5'-coding sequence plays an important role in gene expression, as demonstrated by the fact that deletions caused over sixfold reduction in the expression of the lacZ reporter gene. Further analysis suggests that the nasA 5'-coding sequence promotes gene expression in a way that is not associated with weakened transcript folding around the translational initiation region or codon usage bias. The findings from this study imply that there exists potential to improve gene expression in A. vinelandii by optimizing 5'-coding sequences.
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Affiliation(s)
- Baomin Wang
- The School of Plant Sciences, University of Arizona, Tucson, AZ, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
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Krajewski SS, Narberhaus F. Temperature-driven differential gene expression by RNA thermosensors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:978-988. [PMID: 24657524 DOI: 10.1016/j.bbagrm.2014.03.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/28/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Many prokaryotic genes are organized in operons. Genes organized in such transcription units are co-transcribed into a polycistronic mRNA. Despite being clustered in a single mRNA, individual genes can be subjected to differential regulation, which is mainly achieved at the level of translation depending on initiation and elongation. Efficiency of translation initiation is primarily determined by the structural accessibility of the ribosome binding site (RBS). Structured cis-regulatory elements like RNA thermometers (RNATs) can contribute to differential regulation of individual genes within a polycistronic mRNA. RNATs are riboregulators that mediate temperature-responsive regulation of a downstream gene by modulating the accessibility of its RBS. At low temperature, the RBS is trapped by intra-molecular base pairing prohibiting translation initiation. The secondary structure melts with increasing temperature thus liberating the RBS. Here, we present an overview of different RNAT types and specifically highlight recently discovered RNATs. The main focus of this review is on RNAT-based differential control of polycistronic operons. Finally, we discuss the influence of temperature on other riboregulators and the potential of RNATs in synthetic RNA biology. This article is part of a Special Issue entitled: Riboswitches.
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Guimaraes JC, Rocha M, Arkin AP. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res 2014; 42:4791-9. [PMID: 24510099 PMCID: PMC4005695 DOI: 10.1093/nar/gku126] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The range over which a protein is expressed, and its cell-to-cell variability, is often thought to be linked to the demand for its activity. Steady-state protein level is determined by multiple mechanisms controlling transcription and translation, many of which are limited by DNA- and RNA-encoded signals that affect initiation, elongation and termination of polymerases and ribosomes. We performed a comprehensive analysis of >100 sequence features to derive a predictive model composed of a minimal non-redundant set of factors explaining 66% of the total variation of protein abundance observed in >800 genes in Escherichia coli. The model suggests that protein abundance is primarily determined by the transcript level (53%) and by effectors of translation elongation (12%), whereas only a small fraction of the variation is explained by translational initiation (1%). Our analyses uncover a new sequence determinant, not previously described, affecting translation initiation and suggest that elongation rate is affected by both codon biases and specific amino acid composition. We also show that transcription and translation efficiency may have an effect on expression noise, which is more similar than previously assumed.
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Affiliation(s)
- Joao C Guimaraes
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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42
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Kang MS, Han SS, Kim MY, Kim BY, Huh JP, Kim HS, Lee JH. High-level expression in Corynebacterium glutamicum of nitrile hydratase from Rhodococcus rhodochrous for acrylamide production. Appl Microbiol Biotechnol 2014; 98:4379-87. [PMID: 24493572 DOI: 10.1007/s00253-014-5544-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
The nhhBAG gene of Rhodococcus rhodochrous M33 that encodes nitrile hydratase (NHase), converting acrylonitrile into acrylamide, was cloned and expressed in Corynebacterium glutamicum under the control of an ilvC promoter. The specific enzyme activity in recombinant C. glutamicum cells was about 13.6 μmol/min/mg dry cell weight (DCW). To overexpress the NHase, five types of plasmid variants were constructed by introducing mutations into 80 nucleotides near the translational initiation region (TIR) of nhhB. Of them, pNBM4 with seven mutations showed the highest NHase activity, exhibiting higher expression levels of NhhB and NhhA than wild-type pNBW33, mainly owing to decreased secondary-structure stability and an introduction of a conserved Shine-Dalgarno sequence in the translational initiation region. In a fed-batch culture of recombinant Corynebacterium cells harboring pNBM4, the cell density reached 53.4 g DCW/L within 18 h, and the specific and total enzyme activities were estimated to be 37.3 μmol/min/mg DCW and 1,992 μmol/min/mL, respectively. The use of recombinant Corynebacterium cells for the production of acrylamide from acrylonitrile resulted in a conversion yield of 93 % and a final acrylamide concentration of 42.5 % within 6 h when the total amount of fed acrylonitrile was 456 g.
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Affiliation(s)
- Mi-Suk Kang
- Department of Food Science & Biotechnology, Kyungsung University, 309, Suyeong-ro, Nam-gu, Busan, 608-736, South Korea
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Guimaraes JC, Rocha M, Arkin AP, Cambray G. D-Tailor: automated analysis and design of DNA sequences. ACTA ACUST UNITED AC 2014; 30:1087-1094. [PMID: 24398007 PMCID: PMC3982154 DOI: 10.1093/bioinformatics/btt742] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 12/17/2013] [Indexed: 11/30/2022]
Abstract
Motivation: Current advances in DNA synthesis, cloning and sequencing technologies afford high-throughput implementation of artificial sequences into living cells. However, flexible computational tools for multi-objective sequence design are lacking, limiting the potential of these technologies. Results: We developed DNA-Tailor (D-Tailor), a fully extendable software framework, for property-based design of synthetic DNA sequences. D-Tailor permits the seamless integration of multiple sequence analysis tools into a generic Monte Carlo simulation that evolves sequences toward any combination of rationally defined properties. As proof of principle, we show that D-Tailor is capable of designing sequence libraries comprising all possible combinations among three different sequence properties influencing translation efficiency in Escherichia coli. The capacity to design artificial sequences that systematically sample any given parameter space should support the implementation of more rigorous experimental designs. Availability: Source code is available for download at https://sourceforge.net/projects/dtailor/ Contact:aparkin@lbl.gov or cambray.guillaume@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online (D-Tailor Tutorial).
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Affiliation(s)
- Joao C Guimaraes
- Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Miguel Rocha
- Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Guillaume Cambray
- Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res 2013; 42:2646-59. [PMID: 24234441 PMCID: PMC3936740 DOI: 10.1093/nar/gkt1139] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ribosome's interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5' untranslated regions (5' UTRs) are commonly found in bacterial mRNAs, though the physical mechanisms that determine how the ribosome binds these upstream regions remain poorly defined. Here, we systematically investigate the ribosome's interactions with structured standby sites, upstream of Shine-Dalgarno sequences, and show that these interactions can modulate translation initiation rates by over 100-fold. We find that an mRNA's translation initiation rate is controlled by the amount of single-stranded surface area, the partial unfolding of RNA structures to minimize the ribosome's binding free energy penalty, the absence of cooperative binding and the potential for ribosomal sliding. We develop a biophysical model employing thermodynamic first principles and a four-parameter free energy model to accurately predict the ribosome's translation initiation rates for 136 synthetic 5' UTRs with large structures, diverse shapes and multiple standby site modules. The model predicts and experiments confirm that the ribosome can readily bind distant standby site modules that support high translation rates, providing a physical mechanism for observed context effects and long-range post-transcriptional regulation.
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Affiliation(s)
- Amin Espah Borujeni
- Department of Chemical Engineering, Penn State University, University Park, PA 16802, USA and Department of Agricultural and Biological Engineering, Penn State University, University Park, PA 16802, USA
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Synthetic regulatory RNAs as tools for engineering biological systems: Design and applications. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Seo SW, Yang J, Min BE, Jang S, Lim JH, Lim HG, Kim SC, Kim SY, Jeong JH, Jung GY. Synthetic biology: Tools to design microbes for the production of chemicals and fuels. Biotechnol Adv 2013; 31:811-7. [DOI: 10.1016/j.biotechadv.2013.03.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/14/2013] [Accepted: 03/28/2013] [Indexed: 10/27/2022]
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Mitarai N, Pedersen S. Control of ribosome traffic by position-dependent choice of synonymous codons. Phys Biol 2013; 10:056011. [PMID: 24104350 DOI: 10.1088/1478-3975/10/5/056011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species.
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Affiliation(s)
- Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark
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Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans. J Bacteriol 2013; 195:5092-101. [PMID: 24013626 DOI: 10.1128/jb.00663-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spirochete Leptospira interrogans causes a systemic infection that provokes a febrile illness. The putative lipoproteins LigA and LigB promote adhesion of Leptospira to host proteins, interfere with coagulation, and capture complement regulators. In this study, we demonstrate that the expression level of the LigA and LigB proteins was substantially higher when L. interrogans proliferated at 37°C instead of the standard culture temperature of 30°C. The RNA comprising the 175-nucleotide 5' untranslated region (UTR) and first six lig codons, whose sequence is identical in ligA and ligB, is predicted to fold into two distinct stem-loop structures separated by a single-stranded region. The ribosome-binding site is partially sequestered in double-stranded RNA within the second structure. Toeprint analysis revealed that in vitro formation of a 30S-tRNA(fMet)-mRNA ternary complex was inhibited unless a 5' deletion mutation disrupted the second stem-loop structure. To determine whether the lig sequence could mediate temperature-regulated gene expression in vivo, the 5' UTR and the first six codons were inserted between the Escherichia coli l-arabinose promoter and bgaB (β-galactosidase from Bacillus stearothermophilus) to create a translational fusion. The lig fragment successfully conferred thermoregulation upon the β-galactosidase reporter in E. coli. The second stem-loop structure was sufficient to confer thermoregulation on the reporter, while sequences further upstream in the 5' UTR slightly diminished expression at each temperature tested. Finally, the expression level of β-galactosidase was significantly higher when point mutations predicted to disrupt base pairs in the second structure were introduced into the stem. Compensatory mutations that maintained base pairing of the stem without restoring the wild-type sequence reinstated the inhibitory effect of the 5' UTR on expression. These results indicate that ligA and ligB expression is limited by double-stranded RNA that occludes the ribosome-binding site. At elevated temperatures, the ribosome-binding site is exposed to promote translation initiation.
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Sharma R, Ahlawat S, Maitra A, Roy M, Mandakmale S, Tantia MS. Polymorphism of BMP4 gene in Indian goat breeds differing in prolificacy. Gene 2013; 532:140-5. [PMID: 24013084 DOI: 10.1016/j.gene.2013.08.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/22/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
Bone morphogenetic proteins (BMPs) are members of the TGF-β (transforming growth factor-beta) superfamily, of which BMP4 is the most important due to its crucial role in follicular growth and differentiation, cumulus expansion and ovulation. Reproduction is a crucial trait in goat breeding and based on the important role of BMP4 gene in reproduction it was considered as a possible candidate gene for the prolificacy of goats. The objective of the present study was to detect polymorphism in intronic, exonic and 3' un-translated regions of BMP4 gene in Indian goats. Nine different goat breeds (Barbari, Beetal, Black Bengal, Malabari, Jakhrana (Twinning>40%), Osmanabadi, Sangamneri (Twinning 20-30%), Sirohi and Ganjam (Twinning<10%)) differing in prolificacy and geographic distribution were employed for polymorphism scanning. Cattle sequence (AC_000167.1) was used to design primers for the amplification of a targeted region followed by direct DNA sequencing to identify the genetic variations. Single nucleotide polymorphisms (SNPs) were not detected in exon 3, the intronic region and the 3' flanking region. A SNP (G1534A) was identified in exon 2. It was a non-synonymous mutation resulting in an arginine to lysine change in a corresponding protein sequence. G to A transition at the 1534 locus revealed two genotypes GG and GA in the nine investigated goat breeds. The GG genotype was predominant with a genotype frequency of 0.98. The GA genotype was present in the Black Bengal as well as Jakhrana breed with a genotype frequency of 0.02. A microsatellite was identified in the 3' flanking region, only 20 nucleotides downstream from the termination site of the coding region, as a short sequence with more than nineteen continuous and repeated CA dinucleotides. Since the gene is highly evolutionarily conserved, identification of a non-synonymous SNP (G1534A) in the coding region gains further importance. To our knowledge, this is the first report of a mutation in the coding region of the caprine BMP4 gene. But whether the reproduction trait of goat is associated with the BMP4 polymorphism, needs to be further defined by association studies in more populations so as to delineate an effect on it.
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Affiliation(s)
- Rekha Sharma
- National Bureau of Animal Genetic Resources, Karnal 132001, India.
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Reconstitution of active mycobacterial binuclear iron monooxygenase complex in Escherichia coli. Appl Environ Microbiol 2013; 79:6033-9. [PMID: 23892738 DOI: 10.1128/aem.01856-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial binuclear iron monooxygenases play numerous physiological roles in oxidative metabolism. Monooxygenases of this type found in actinomycetes also catalyze various useful reactions and have attracted much attention as oxidation biocatalysts. However, difficulties in expressing these multicomponent monooxygenases in heterologous hosts, particularly in Escherichia coli, have hampered the development of engineered oxidation biocatalysts. Here, we describe a strategy to functionally express the mycobacterial binuclear iron monooxygenase MimABCD in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of the mimABCD gene expression in E. coli revealed that the oxygenase components MimA and MimC were insoluble. Furthermore, although the reductase MimB was expressed at a low level in the soluble fraction of E. coli cells, a band corresponding to the coupling protein MimD was not evident. This situation rendered the transformed E. coli cells inactive. We found that the following factors are important for functional expression of MimABCD in E. coli: coexpression of the specific chaperonin MimG, which caused MimA and MimC to be soluble in E. coli cells, and the optimization of the mimD nucleotide sequence, which led to efficient expression of this gene product. These two remedies enabled this multicomponent monooxygenase to be actively expressed in E. coli. The strategy described here should be generally applicable to the E. coli expression of other actinomycetous binuclear iron monooxygenases and related enzymes and will accelerate the development of engineered oxidation biocatalysts for industrial processes.
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