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The Phospholipid:Diacylglycerol Acyltransferase-Mediated Acyl-Coenzyme A-Independent Pathway Efficiently Diverts Fatty Acid Flux from Phospholipid into Triacylglycerol in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.00999-20. [PMID: 32680871 DOI: 10.1128/aem.00999-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 11/20/2022] Open
Abstract
Researchers have long endeavored to accumulate triacylglycerols (TAGs) or their derivatives in easily managed microbes. The attempted production of TAGs in Escherichia coli has revealed barriers to the broad applications of this technology, including low TAG productivity and slow cell growth. We have demonstrated that an acyl-CoA-independent pathway can divert phospholipid flux into TAG formation in E. coli mediated by Chlamydomonas reinhardtii phospholipid:diacylglycerol acyltransferase (CrPDAT) without interfering with membrane functions. We then showed the synergistic effect on TAG accumulation via the acyl-CoA-independent pathway mediated by PDAT and the acyl-CoA-dependent pathway mediated by wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT). Furthermore, CrPDAT led to synchronous TAG accumulation during cell growth, and this could be enhanced by supplementation of arbutin. We also showed that rationally mutated CrPDAT was capable of decreasing TAG lipase activity without impairing PDAT activity. Finally, ScPDAT from Saccharomyces cerevisiae exhibited similar activities as CrPDAT in E. coli Our results suggest that the improvement in accumulation of TAGs and their derivatives can be achieved by fine-tuning of phospholipid metabolism in E. coli Understanding the roles of PDAT in the conversion of phospholipids into TAGs during the logarithmic growth phase may enable a novel strategy for the production of microbial oils.IMPORTANCE Although phospholipid:diacylglycerol acyltransferase (PDAT) activity is presumed to exist in prokaryotic oleaginous bacteria, the corresponding gene has not been identified yet. In this article, we have demonstrated that an acyl-CoA-independent pathway can divert phospholipid flux into TAG formation in Escherichia coli mediated by exogenous CrPDAT from Chlamydomonas reinhardtii without interfering with membrane functions. In addition, the acyl-CoA-independent pathway and the acyl-CoA-dependent pathway had the synergistic effect on TAG accumulation. Overexpression of CrPDAT led to synchronous TAG accumulation during cell growth. In particular, CrPDAT possessed multiple catalytic activities, and the rational mutation of CrPDAT led to the decrease of TAG lipase activity without impairing acyltransferase activity. The present findings suggested that applying PDAT in E. coli or other prokaryotic microbes may be a promising strategy for accumulation of TAGs and their derivatives.
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152
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Sandomenico A, Sivaccumar JP, Ruvo M. Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments. Int J Mol Sci 2020; 21:ijms21176324. [PMID: 32878291 PMCID: PMC7504322 DOI: 10.3390/ijms21176324] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. While full-length antibodies require mammalian expression systems due to the occurrence of functionally and structurally important glycosylations, most antibody fragments and antibody-like molecules are non-glycosylated and can be more conveniently prepared in E. coli-based expression platforms. We propose here an updated survey of the most effective and appropriate methods of preparation of antibody fragments that exploit E. coli as an expression background and review the pros and cons of the different platforms available today. Around 250 references accompany and complete the review together with some lists of the most important new antibody-like molecules that are on the market or are being developed as new biotherapeutics or diagnostic agents.
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153
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Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
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154
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Park Y, Espah Borujeni A, Gorochowski TE, Shin J, Voigt CA. Precision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads. Mol Syst Biol 2020; 16:e9584. [PMID: 32812710 PMCID: PMC7436927 DOI: 10.15252/msb.20209584] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Genetic circuits have many applications, from guiding living therapeutics to ordering process in a bioreactor, but to be useful they have to be genetically stable and not hinder the host. Encoding circuits in the genome reduces burden, but this decreases performance and can interfere with native transcription. We have designed genomic landing pads in Escherichia coli at high-expression sites, flanked by ultrastrong double terminators. DNA payloads >8 kb are targeted to the landing pads using phage integrases. One landing pad is dedicated to carrying a sensor array, and two are used to carry genetic circuits. NOT/NOR gates based on repressors are optimized for the genome and characterized in the landing pads. These data are used, in conjunction with design automation software (Cello 2.0), to design circuits that perform quantitatively as predicted. These circuits require fourfold less RNA polymerase than when carried on a plasmid and are stable for weeks in a recA+ strain without selection. This approach enables the design of synthetic regulatory networks to guide cells in environments or for applications where plasmid use is infeasible.
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Affiliation(s)
- Yongjin Park
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Amin Espah Borujeni
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Thomas E Gorochowski
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Jonghyeon Shin
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
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155
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Newton J, Oeggl R, Janzen NH, Abad S, Reinisch D. Process adapted calibration improves fluorometric pH sensor precision in sophisticated fermentation processes. Eng Life Sci 2020; 20:331-337. [PMID: 32774205 PMCID: PMC7401234 DOI: 10.1002/elsc.201900156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/11/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022] Open
Abstract
Miniaturization and automation have become increasingly popular in bioprocess development in recent years, enabling rapid high-throughput screening and optimization of process conditions. In addition, advances in the bioprocessing industry have led to increasingly complex process designs, such as pH and temperature shifts, in microbial fed-batch fermentations for optimal soluble protein expression in a range of hosts. However, in order to develop an accurate scale-down model for bioprocess screening and optimization, small-scale bioreactors must be able to accurately reproduce these complex process designs. Monitoring methods, such as fluorometric-based pH sensors, provide elegant solutions for the miniaturization of bioreactors, however, previous research suggests that the intrinsic fluorescence of biomass alters the sigmoidal calibration curve of fluorometric pH sensors, leading to inaccurate pH control. In this article, we present results investigating the impact of biomass on the accuracy of a commercially available fluorometric pH sensor. Subsequently, we present our calibration methodology for more precise online measurement and provide recommendations for improved pH control in sophisticated fermentation processes.
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Affiliation(s)
| | | | | | - Sandra Abad
- Boehringer Ingelheim RCV GmbH & Co. KGViennaAustria
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156
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Melnikov SV, Stevens DL, Fu X, Kwok HS, Zhang JT, Shen Y, Sabina J, Lee K, Lee H, Söll D. Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations. Proc Natl Acad Sci U S A 2020; 117:17924-17931. [PMID: 32661175 PMCID: PMC7395499 DOI: 10.1073/pnas.2003132117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant Escherichia coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates that understanding molecular mechanisms of drug resistance allows us to effectively amplify even small evolutionary vulnerabilities of resistant cells to potentially enhance or enable adaptive therapies by accelerating posttreatment competition between resistant and susceptible cells.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - David L Stevens
- Department of Chemistry, Yale University, New Haven, CT 06520
| | - Xian Fu
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Hui Si Kwok
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jin-Tao Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yue Shen
- Guangdong Provincial Key Laboratory of Genome Read and Write, 518120 Shenzhen, China
- BGI-Shenzhen, 518083 Shenzhen, China
- China National Genebank, BGI-Shenzhen, 518120 Shenzhen, China
| | | | | | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
- Department of Chemistry, Yale University, New Haven, CT 06520
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157
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Gómez LA, Alvarez FI, Molina RE, Soto-Shara R, Daza-Castro C, Flores MR, León Y, Oñate AA. A Zinc-Dependent Metalloproteinase of Brucella abortus Is Required in the Intracellular Adaptation of Macrophages. Front Microbiol 2020; 11:1586. [PMID: 32765455 PMCID: PMC7379133 DOI: 10.3389/fmicb.2020.01586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 01/19/2023] Open
Abstract
Brucella abortus is a pathogen that survives in macrophages. Several virulence factors participate in this process, including the open reading frame (ORF) BAB1_0270 codifying for a zinc-dependent metalloproteinase (ZnMP). Here, its contribution in the intracellular adaptation of B. abortus was analyzed by infecting RAW264.7 macrophages with the mutant B. abortus Δ270 strain. Results showed that this ZnMP did not participated in either the adherence or the initial intracellular traffic of B. abortus in macrophages. Nevertheless, its deletion significantly increased the co-localization of B. abortus Δ270 with phagolysosomal cathepsin D and reduced its co-localization with calnexin present in endoplasmic reticulum (RE)-derived vesicles. Although B. abortus Δ270 showed an upregulated expression of genes involved in virulence (vjbR, hutC, bvrR, virB1), it was insufficient to reach a successful intracellular replication within macrophages. Furthermore, its attenuation favored in macrophages infected the production of high levels of cytokines (TNF-α and IL-6) and co-stimulatory proteins (CD80 and CD86), signals required in T cell activation. Finally, its deletion significantly reduced the ability of B. abortus Δ270 to adapt, grow and express several virulence factors under acidic conditions. Based on these results, and considering that this ZnMP has homology with ImmA/IrrE proteases, we discuss its role in the virulence of this pathogen, concluding that ZnMP is required in the intracellular adaptation of B. abortus 2308 during the infection of macrophages.
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Affiliation(s)
| | | | | | | | | | | | | | - Angel A. Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
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158
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Flicker D, Sancak Y, Mick E, Goldberger O, Mootha VK. Exploring the In Vivo Role of the Mitochondrial Calcium Uniporter in Brown Fat Bioenergetics. Cell Rep 2020; 27:1364-1375.e5. [PMID: 31042465 PMCID: PMC7231522 DOI: 10.1016/j.celrep.2019.04.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/28/2018] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
The mitochondrial calcium uniporter has been proposed to coordinate the organelle’s energetics with calcium signaling. Uniporter current has previously been reported to be extremely high in brown adipose tissue (BAT), yet it remains unknown how the uniporter contributes to BAT physiology. Here, we report the generation and characterization of a mouse model lacking Mcu, the pore forming subunit of the uniporter, specifically in BAT (BAT-Mcu-KO). BAT-Mcu-KO mice lack uniporter-based calcium uptake in BAT mitochondria but exhibit unaffected cold tolerance, diet-induced obesity, and transcriptional response to cold in BAT. Unexpectedly, we found in wild-type animals that cold powerfully activates the ATF4-dependent integrated stress response (ISR) in BAT and up-regulates circulating FGF21 and GDF15, raising the hypothesis that the ISR partly underlies the pleiotropic effects of BAT on systemic metabolism. Our study demonstrates that the uniporter is largely dispensable for BAT thermogenesis and demonstrates activation of the ISR in BAT in response to cold. Flicker et al. generate a mouse lacking mitochondrial calcium uniporter activity in brown fat. They show that the uniporter is dispensable for brown fat bioenergetics. Unexpectedly, they find that in wild type animals, cold stress induces ATF4 signaling in normal brown fat, suggesting a mechanism for cold-induced GDF15 and FGF21 elevation.
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Affiliation(s)
- Daniel Flicker
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Yasemin Sancak
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA.
| | - Eran Mick
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA.
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159
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Ma ZZ, Zhou H, Wei YL, Yan S, Shen J. A novel plasmid-Escherichia coli system produces large batch dsRNAs for insect gene silencing. PEST MANAGEMENT SCIENCE 2020; 76:2505-2512. [PMID: 32077251 DOI: 10.1002/ps.5792] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND RNA interference (RNAi)-based pest management requires efficient delivery and large-batch production of double-stranded (ds)RNA. We previously developed a nanocarrier-mediated dsRNA delivery system that could penetrate an insect's body and efficiently silence gene expression. However, there is a great need to improve the plasmid-Escherichia coli system for the mass production of dsRNA. Here, for efficient dsRNA production, we removed the rnc gene encoding endoribonuclease RNase III in E. coli BL21(DE3) and matched with the RNAi expression vector containing a single T7 promoter. RESULTS The novel pET28-BL21(DE3) RNase III-system was successfully constructed to express vestigial (vg)-dsRNA against Harmonia axyridis. dsRNA was extracted and purified from cell cultures in four E. coil systems, and the yields of dsRNA in pET28-BL21(DE3) RNase III-, pET28-HT115(DE3), L4440-BL21(DE3) RNase III- and L4440-HT115(DE3) were 4.23, 2.75, 0.88 and 1.30 μg mL-1 respectively. The dsRNA expression efficiency of our novel E. coil system was three times that of L4440-HT115(DE3), a widely used dsRNA production system. The RNAi efficiency of dsRNA produced by our system and by biochemical synthesis was comparable when injected into Harmonia axyridis. CONCLUSION Our system expressed dsRNA more efficiently than the widely used L4440-HT115(DE3) system, and the produced dsRNA showed a high gene-silencing effect. Notably, our pET28-BL21(DE3) RNase III-system provides a novel method for the mass production of dsRNA at low cost and high efficiency, which may promote gene function analysis and RNAi-based pest management. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Zhong-Zheng Ma
- Department of Entomology, MOA Key Lab of pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hang Zhou
- Department of Entomology, MOA Key Lab of pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan-Long Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shuo Yan
- Department of Entomology, MOA Key Lab of pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Entomology, MOA Key Lab of pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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160
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Nivina A, Grieb MS, Loot C, Bikard D, Cury J, Shehata L, Bernardes J, Mazel D. Structure-specific DNA recombination sites: Design, validation, and machine learning-based refinement. SCIENCE ADVANCES 2020; 6:eaay2922. [PMID: 32832653 PMCID: PMC7439510 DOI: 10.1126/sciadv.aay2922] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Recombination systems are widely used as bioengineering tools, but their sites have to be highly similar to a consensus sequence or to each other. To develop a recombination system free of these constraints, we turned toward attC sites from the bacterial integron system: single-stranded DNA hairpins specifically recombined by the integrase. Here, we present an algorithm that generates synthetic attC sites with conserved structural features and minimal sequence-level constraints. We demonstrate that all generated sites are functional, their recombination efficiency can reach 60%, and they can be embedded into protein coding sequences. To improve recombination of less efficient sites, we applied large-scale mutagenesis and library enrichment coupled to next-generation sequencing and machine learning. Our results validated the efficiency of this approach and allowed us to refine synthetic attC design principles. They can be embedded into virtually any sequence and constitute a unique example of a structure-specific DNA recombination system.
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Affiliation(s)
- Aleksandra Nivina
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
- Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maj Svea Grieb
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
| | - Céline Loot
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
| | - David Bikard
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
| | - Jean Cury
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
- Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Laila Shehata
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
| | - Juliana Bernardes
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universités, CNRS UMR 7238,75005 Paris, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Institut Pasteur, 75724 Paris, France
- CNRS UMR 3525, 75724 Paris, France
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161
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Finger-Bou M, Orsi E, van der Oost J, Staals RHJ. CRISPR with a Happy Ending: Non-Templated DNA Repair for Prokaryotic Genome Engineering. Biotechnol J 2020; 15:e1900404. [PMID: 32558098 DOI: 10.1002/biot.201900404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/04/2020] [Indexed: 12/18/2022]
Abstract
The exploration of microbial metabolism is expected to support the development of a sustainable economy and tackle several problems related to the burdens of human consumption. Microorganisms have the potential to catalyze processes that are currently unavailable, unsustainable and/or inefficient. Their metabolism can be optimized and further expanded using tools like the clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) systems. These tools have revolutionized the field of biotechnology, as they greatly streamline the genetic engineering of organisms from all domains of life. CRISPR-Cas and other nucleases mediate double-strand DNA breaks, which must be repaired to prevent cell death. In prokaryotes, these breaks can be repaired through either homologous recombination, when a DNA repair template is available, or through template-independent end joining, of which two major pathways are known. These end joining pathways depend on different sets of proteins and mediate DNA repair with different outcomes. Understanding these DNA repair pathways can be advantageous to steer the results of genome engineering experiments. In this review, we discuss different strategies for the genetic engineering of prokaryotes through either non-homologous end joining (NHEJ) or alternative end joining (AEJ), both of which are independent of exogenous DNA repair templates.
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Affiliation(s)
- Max Finger-Bou
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Enrico Orsi
- Bioprocess Engineering, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, 6708 WE, The Netherlands
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162
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Menacho‐Melgar R, Moreb EA, Efromson JP, Yang T, Hennigan JN, Wang R, Lynch MD. Improved two‐stage protein expression and purification via autoinduction of both autolysis and auto DNA/RNA hydrolysis conferred by phage lysozyme and DNA/RNA endonuclease. Biotechnol Bioeng 2020; 117:2852-2860. [DOI: 10.1002/bit.27444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/06/2020] [Accepted: 05/26/2020] [Indexed: 01/11/2023]
Affiliation(s)
| | - Eirik A. Moreb
- Department of Biomedical Engineering Duke University Durham North Carolina
| | - John P. Efromson
- Department of Biomedical Engineering Duke University Durham North Carolina
| | - Tian Yang
- Department of Biomedical Engineering Duke University Durham North Carolina
| | | | - Ruixin Wang
- Department of Biomedical Engineering Duke University Durham North Carolina
| | - Michael D. Lynch
- Department of Biomedical Engineering Duke University Durham North Carolina
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163
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Stargardt P, Feuchtenhofer L, Cserjan-Puschmann M, Striedner G, Mairhofer J. Bacteriophage Inspired Growth-Decoupled Recombinant Protein Production in Escherichia coli. ACS Synth Biol 2020; 9:1336-1348. [PMID: 32324989 DOI: 10.1021/acssynbio.0c00028] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modulating resource allocation in bacteria to redirect metabolic building blocks to the formation of recombinant proteins rather than biomass formation remains a grand challenge in biotechnology. Here, we present a novel approach for improved recombinant protein production (RPP) using Escherichia coli (E. coli) by decoupling recombinant protein synthesis from cell growth. We show that cell division and host mRNA transcription can be successfully inhibited by coexpression of a bacteriophage-derived E. coli RNA polymerase (RNAP) inhibitor peptide and that genes overtranscribed by the orthogonal T7 RNAP can finally account to >55% of cell dry mass (CDM). This RNAP inhibitor peptide binds the E. coli RNAP and therefore prevents σ-factor 70 mediated formation of transcriptional qualified open promoter complexes. Thereby, the transcription of σ-factor 70 driven host genes is inhibited, and metabolic resources can be exclusively utilized for synthesis of the protein of interest (POI). Here, we mimic the late phase of bacteriophage infection by coexpressing a phage-derived xenogeneic regulator that reprograms the host cell and thereby are able to significantly improve RPP under industrial relevant fed-batch process conditions at bioreactor scale. We have evaluated production of several different recombinant proteins at different scales (from microscale to 20 L fed-batch scale) and have been able to improve total and soluble proteins yields up to 3.4-fold in comparison to the reference expression system E. coli BL21(DE3). This novel approach for growth-decoupled RPP has profound implications for biotechnology and bioengineering and helps to establish more cost-effective and generic manufacturing processes for biologics and biomaterials.
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Affiliation(s)
| | | | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
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164
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Yeom H, Ryu T, Lee AC, Noh J, Lee H, Choi Y, Kim N, Kwon S. Cell-Free Bacteriophage Genome Synthesis Using Low-Cost Sequence-Verified Array-Synthesized Oligonucleotides. ACS Synth Biol 2020; 9:1376-1384. [PMID: 32383864 DOI: 10.1021/acssynbio.0c00051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthesizing engineered bacteriophages (phages) for human use has potential in various applications ranging from drug screening using a phage display to clinical use using phage therapy. However, the engineering of phages conventionally involves the use of an in vivo system that has low production efficiency because of high virulence against the host and low transformation efficiency. To circumvent these issues, de novo phage genome synthesis using chemically synthesized oligonucleotides (oligos) has increased the potential for engineering phages in a cell-free system. Here, we present a cell-free, low-cost, de novo gene synthesis technology called Sniper assembly for phage genome construction. With massively parallel sequencing of microarray-synthesized oligos, we generated and identified approximately 100 000 clonal DNA clusters in vitro and 5000 error-free ones in a cell-free environment. To demonstrate its practical application, we synthesized the Acinetobacter phage AP205 genome (4268 bp) using 65 sequence-verified DNA clones. Compared to previous reports, Sniper assembly lowered the genome synthesis cost ($0.0137/bp) by producing low-cost sequence-verified DNA.
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Affiliation(s)
- Huiran Yeom
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Taehoon Ryu
- Department of Molecular Genetic Engineering, Celemics, Inc., Seoul, 08506, Republic of Korea
| | - Amos Chungwon Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Hansaem Lee
- Department of Molecular Genetic Engineering, Celemics, Inc., Seoul, 08506, Republic of Korea
| | - Yeongjae Choi
- Nano Systems Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
- Bio-MAX institute, Seoul National University, Seoul, 08826, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul, 08826, Republic of Korea
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165
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Menacho-Melgar R, Ye Z, Moreb EA, Yang T, Efromson JP, Decker JS, Wang R, Lynch MD. Scalable, two-stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion. Biotechnol Bioeng 2020; 117:2715-2727. [PMID: 32441815 DOI: 10.1002/bit.27440] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022]
Abstract
We report the scalable production of recombinant proteins in Escherichia coli, reliant on tightly controlled autoinduction, triggered by phosphate depletion in the stationary phase. The method, reliant on engineered strains and plasmids, enables improved protein expression across scales. Expression levels using this approach have reached as high as 55% of the total cellular protein. The initial use of the method in instrumented fed-batch fermentations enables cell densities of ∼30 gCDW/L and protein titers up to 8.1 ± 0.7 g/L (∼270 mg/gCDW). The process has also been adapted to an optimized autoinduction media, enabling routine batch production at culture volumes of 20 μl (384-well plates), 100 μl (96-well plates), 20 ml, and 100 ml. In batch cultures, cell densities routinely reach ∼5-7 gCDW/L, offering protein titers above 2 g/L. The methodology has been validated with a set of diverse heterologous proteins and is of general use for the facile optimization of routine protein expression from high throughput screens to fed-batch fermentation.
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Affiliation(s)
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Tian Yang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - John P Efromson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - John S Decker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Ruixin Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
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166
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Su B, Song D, Zhu H. Homology-dependent recombination of large synthetic pathways into E. coli genome via λ-Red and CRISPR/Cas9 dependent selection methodology. Microb Cell Fact 2020; 19:108. [PMID: 32448328 PMCID: PMC7245811 DOI: 10.1186/s12934-020-01360-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Background Metabolic engineering frequently needs genomic integration of many heterologous genes for biosynthetic pathway assembly. Despite great progresses in genome editing for the model microorganism Escherichia coli, the integration of large pathway into genome for stabilized chemical production is still challenging compared with small DNA integration. Results We have developed a λ-Red assisted homology-dependent recombination for large synthetic pathway integration in E. coli. With this approach, we can integrate as large as 12 kb DNA module into the chromosome of E. coli W3110 in a single step. The efficiency of this method can reach 100%, thus markedly improve the integration efficiency and overcome the limitation of the integration size adopted the common method. Furthermore, the limiting step in the methylerythritol 4-phosphate (MEP) pathway and lycopene synthetic pathway were integrated into the W3110 genome using our system. Subsequently, the yields of the final strain were increased 106 and 4.4-fold compared to the initial strain and the reference strain, respectively. Conclusions In addition to pre-existing method, our system presents an optional strategy for avoiding using plasmids and a valuable tool for large synthetic pathway assembly in E. coli.
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Affiliation(s)
- Buli Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Dandan Song
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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167
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Choudhury A, Fankhauser RG, Freed EF, Oh EJ, Morgenthaler AB, Bassalo MC, Copley SD, Kaar JL, Gill RT. Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli. ACS Synth Biol 2020; 9:1083-1099. [PMID: 32298586 DOI: 10.1021/acssynbio.9b00440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In E. coli, editing efficiency with Cas9-mediated recombineering varies across targets due to differences in the level of Cas9:gRNA-mediated DNA double-strand break (DSB)-induced cell death. We found that editing efficiency with the same gRNA and repair template can also change with target position, cas9 promoter strength, and growth conditions. Incomplete editing, off-target activity, nontargeted mutations, and failure to cleave target DNA even if Cas9 is bound also compromise editing efficiency. These effects on editing efficiency were gRNA-specific. We propose that differences in the efficiency of Cas9:gRNA-mediated DNA DSBs, as well as possible differences in binding of Cas9:gRNA complexes to their target sites, account for the observed variations in editing efficiency between gRNAs. We show that editing behavior using the same gRNA can be modified by mutating the gRNA spacer, which changes the DNA DSB activity. Finally, we discuss how variable editing with different gRNAs could limit high-throughput applications and provide strategies to overcome these limitations.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- IAME, UMR 1137, INSERM, Universités Paris Diderot et Paris Nord, Paris, 75018, France
| | - Reilly G Fankhauser
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Emily F Freed
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Eun Joong Oh
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Andrew B Morgenthaler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Copenhagen 2800, Denmark
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168
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Simon AJ, Ellington AD, Finkelstein IJ. Retrons and their applications in genome engineering. Nucleic Acids Res 2020; 47:11007-11019. [PMID: 31598685 PMCID: PMC6868368 DOI: 10.1093/nar/gkz865] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 11/14/2022] Open
Abstract
Precision genome editing technologies have transformed modern biology. These technologies have arisen from the redirection of natural biological machinery, such as bacteriophage lambda proteins for recombineering and CRISPR nucleases for eliciting site-specific double-strand breaks. Less well-known is a widely distributed class of bacterial retroelements, retrons, that employ specialized reverse transcriptases to produce noncoding intracellular DNAs. Retrons' natural function and mechanism of genetic transmission have remained enigmatic. However, recent studies have harnessed their ability to produce DNA in situ for genome editing and evolution. This review describes retron biology and function in both natural and synthetic contexts. We also highlight areas that require further study to advance retron-based precision genome editing platforms.
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Affiliation(s)
- Anna J Simon
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J Finkelstein
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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169
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Laxhuber KS, Morrison MJ, Chure G, Belliveau NM, Strandkvist C, Naughton KL, Phillips R. Theoretical investigation of a genetic switch for metabolic adaptation. PLoS One 2020; 15:e0226453. [PMID: 32379825 PMCID: PMC7205307 DOI: 10.1371/journal.pone.0226453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
Membrane transporters carry key metabolites across the cell membrane and, from a resource standpoint, are hypothesized to be produced when necessary. The expression of membrane transporters in metabolic pathways is often upregulated by the transporter substrate. In E. coli, such systems include for example the lacY, araFGH, and xylFGH genes, which encode for lactose, arabinose, and xylose transporters, respectively. As a case study of a minimal system, we build a generalizable physical model of the xapABR genetic circuit, which features a regulatory feedback loop via membrane transport (positive feedback) and enzymatic degradation (negative feedback) of an inducer. Dynamical systems analysis and stochastic simulations show that the membrane transport makes the model system bistable in certain parameter regimes. Thus, it serves as a genetic “on-off” switch, enabling the cell to only produce a set of metabolic enzymes when the corresponding metabolite is present in large amounts. We find that the negative feedback from the degradation enzyme does not significantly disturb the positive feedback from the membrane transporter. We investigate hysteresis in the switching and discuss the role of cooperativity and multiple binding sites in the model circuit. Fundamentally, this work explores how a stable genetic switch for a set of enzymes is obtained from transcriptional auto-activation of a membrane transporter through its substrate.
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Affiliation(s)
- Kathrin S Laxhuber
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Muir J Morrison
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
| | - Griffin Chure
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Nathan M Belliveau
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Charlotte Strandkvist
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
| | - Kyle L Naughton
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States of America
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
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170
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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171
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Coloma-Rivero RF, Gómez L, Alvarez F, Saitz W, Del Canto F, Céspedes S, Vidal R, Oñate AA. The Role of the Flagellar Protein FlgJ in the Virulence of Brucella abortus. Front Cell Infect Microbiol 2020; 10:178. [PMID: 32411617 PMCID: PMC7198779 DOI: 10.3389/fcimb.2020.00178] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/03/2020] [Indexed: 12/28/2022] Open
Abstract
Brucella abortus is a facultative intracellular pathogen that causes a zoonosis called brucellosis. This disease leads to abortion and infertility in cattle, and diverse complications in humans. B. abortus is a successful intracellular bacterium that has developed the ability to evade the host's immune system and it replicates in professional and non-professional phagocytic cells, persisting in the different tissues, and organs of its hosts. It has been described that Brucella expresses a polar flagellum under certain conditions, but its function is still unknown. In this study we evaluated the role of the FlgJ, a protein, presumably a peptidoglycan hydrolase involved in flagellum formation and in the virulence of B. abortus strain 2308. B. abortus 2308 ΔflgJ mutant and complemented strains were constructed to study the function of the FlgJ protein in the context of the virulence of this pathogen in in vitro and in vivo assays. The results showed that the elimination of the flgJ gene delays the growth rate of B. abortus in culture, reduces its intracellular survival capacity in professional and non-professional phagocytic cells, rendering it unable to escape from the endocytic route and not reaching the endoplasmic reticulum. It also negatively affects their persistence in BALB/c mice. Functionally, the B. abortus 2308 flgJ gene restored motility to an E. coli flgJ mutant gene. Furthermore, it was discovered that the production of FlgJ protein is associated with the bacterial adherence by B. abortus. Therefore, although the specific function of the polar flagellum for Brucella is unknown, the data indicates that the flagellar flgJ gene and its product are required for full virulence of B. abortus 2308, since its deletion significantly reduces the fitness of this pathogen in vitro and in vivo.
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Affiliation(s)
- Roberto F Coloma-Rivero
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Leonardo Gómez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Francisco Alvarez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Waleska Saitz
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.,Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Felipe Del Canto
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Sandra Céspedes
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.,Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Angel A Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
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172
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Integrating CRISPR-Enabled Trackable Genome Engineering and Transcriptomic Analysis of Global Regulators for Antibiotic Resistance Selection and Identification in Escherichia coli. mSystems 2020; 5:5/2/e00232-20. [PMID: 32317390 PMCID: PMC7174635 DOI: 10.1128/msystems.00232-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growing threat of antimicrobial resistance poses a serious threat to public health care and motivates efforts to understand the means by which resistance acquisition occurs and how this can be combatted. To address these challenges, we expedited the identification of novel mutations that enable complex phenotypic changes that result in improved tolerance to antibiotics by integrating CREATE and transcriptomic analysis of global regulators. The results give us a better understanding of the mechanisms of resistance to tetracycline antibiotics and aminoglycoside antibiotics and also indicate that the method may be used for quickly identifying resistance-related mutations. It is important to expedite our understanding of antibiotic resistance to address the increasing numbers of fatalities and environmental pollution due to the emergence of antibiotic resistance and multidrug-resistant strains. Here, we combined the CRISPR-enabled trackable genome engineering (CREATE) technology and transcriptomic analysis to investigate antibiotic tolerance in Escherichia coli. We developed rationally designed site saturation mutagenesis libraries targeting 23 global regulators to identify fitness-conferring mutations in response to diverse antibiotic stresses. We identified seven novel mutations that confer resistance to the ribosome-targeting antibiotics doxycycline, thiamphenicol, and gentamicin in E. coli. To the best of our knowledge, these mutations that we identified have not been reported previously during treatment with the indicated antibiotics. Transcriptome sequencing-based transcriptome analysis was further employed to evaluate the genome-wide changes in gene expression in E. coli for SoxR G121P and cAMP receptor protein (CRP) V140W reconstructions, and improved fitness in response to doxycycline and gentamicin was seen. In the case of doxycycline, we speculated that SoxR G121P significantly increased the expression of genes involved in carbohydrate metabolism and energy metabolism to promote cell growth for improved adaptation. In the CRP V140W mutant with improved gentamicin tolerance, the expression of several amino acid biosynthesis genes and fatty acid degradation genes was significantly changed, and these changes probably altered the cellular energy state to improve adaptation. These findings have important significance for understanding such nonspecific mechanisms of antibiotic resistance and developing new antibacterial drugs. IMPORTANCE The growing threat of antimicrobial resistance poses a serious threat to public health care and motivates efforts to understand the means by which resistance acquisition occurs and how this can be combatted. To address these challenges, we expedited the identification of novel mutations that enable complex phenotypic changes that result in improved tolerance to antibiotics by integrating CREATE and transcriptomic analysis of global regulators. The results give us a better understanding of the mechanisms of resistance to tetracycline antibiotics and aminoglycoside antibiotics and also indicate that the method may be used for quickly identifying resistance-related mutations.
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173
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Chen J, Mohammad A, Pazdernik N, Huang H, Bowman B, Tycksen E, Schedl T. GLP-1 Notch-LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1. PLoS Genet 2020; 16:e1008650. [PMID: 32196486 PMCID: PMC7153901 DOI: 10.1371/journal.pgen.1008650] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Stem cell systems are essential for the development and maintenance of polarized tissues. Intercellular signaling pathways control stem cell systems, where niche cells signal stem cells to maintain the stem cell fate/self-renewal and inhibit differentiation. In the C. elegans germline, GLP-1 Notch signaling specifies the stem cell fate, employing the sequence-specific DNA binding protein LAG-1 to implement the transcriptional response. We undertook a comprehensive genome-wide approach to identify transcriptional targets of GLP-1 signaling. We expected primary response target genes to be evident at the intersection of genes identified as directly bound by LAG-1, from ChIP-seq experiments, with genes identified as requiring GLP-1 signaling for RNA accumulation, from RNA-seq analysis. Furthermore, we performed a time-course transcriptomics analysis following auxin inducible degradation of LAG-1 to distinguish between genes whose RNA level was a primary or secondary response of GLP-1 signaling. Surprisingly, only lst-1 and sygl-1, the two known target genes of GLP-1 in the germline, fulfilled these criteria, indicating that these two genes are the primary response targets of GLP-1 Notch and may be the sole germline GLP-1 signaling protein-coding transcriptional targets for mediating the stem cell fate. In addition, three secondary response genes were identified based on their timing following loss of LAG-1, their lack of a LAG-1 ChIP-seq peak and that their glp-1 dependent mRNA accumulation could be explained by a requirement for lst-1 and sygl-1 activity. Moreover, our analysis also suggests that the function of the primary response genes lst-1 and sygl-1 can account for the glp-1 dependent peak protein accumulation of FBF-2, which promotes the stem cell fate and, in part, for the spatial restriction of elevated LAG-1 accumulation to the stem cell region. Stem cell systems are central to tissue development, homeostasis and regeneration, where niche to stem cell signaling pathways promote the stem cell fate/self-renewal and inhibit differentiation. The evolutionarily conserved GLP-1 Notch signaling pathway in the C. elegans germline is an experimentally tractable system, allowing dissection of control of the stem cell fate and inhibition of meiotic development. However, as in many systems, the primary molecular targets of the signaling pathway in stem cells is incompletely known, as are secondary molecular targets, and this knowledge is essential for a deep understanding of stem cell systems. Here we focus on the identification of the primary transcriptional targets of the GLP-1 signaling pathway that promotes the stem cell fate, employing unbiased multilevel genomic approaches. We identify only lst-1 and sygl-1, two of a number of previously reported targets, as likely the sole primary mRNA transcriptional targets of GLP-1 signaling that promote the germline stem cell fate. We also identify secondary GLP-1 signaling RNA and protein targets, whose expression shows dependence on lst-1 and sygl-1, where the protein targets reinforce the importance of posttranscriptional regulation in control of the stem cell fate.
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Affiliation(s)
- Jian Chen
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ariz Mohammad
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Nanette Pazdernik
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Current address, Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Huiyan Huang
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Beth Bowman
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Current address, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
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174
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Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metab Eng Commun 2020; 10:e00126. [PMID: 32215253 PMCID: PMC7090339 DOI: 10.1016/j.mec.2020.e00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding β-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering. Plasmid-curing is the most time-consuming step in genome engineering approaches. We have developed a system for easy target- and self-curing of plasmid DNA. Synthetic control of replication and highly-specific in vivo DNA digestion were used. Plasmid curing with this system displays an efficiency >90% in a 24-h cultivation. Quick genome engineering facilitated genome reduction of P. putida.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Laura Friis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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175
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Dong M, Wang F, Li Q, Han R, Li A, Zhai C, Ma L. A single digestion, single-stranded oligonucleotide mediated PCR-independent site-directed mutagenesis method. Appl Microbiol Biotechnol 2020; 104:3993-4003. [PMID: 32152687 DOI: 10.1007/s00253-020-10477-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/03/2020] [Accepted: 02/14/2020] [Indexed: 12/19/2022]
Abstract
A PCR-independent in vitro site-directed mutagenesis method was established. Cas12a from Francisella novicida (FnCas12a) linearizes the plasmid with single digestion. T5 exonuclease removes the target nucleotide. A short single- or double-stranded mutagenic oligonucleotide introduces the mutation. This rapid and simple mutagenesis method is referred to as FnCas12a and T5 exonuclease mediated site-directed mutagenesis system (CT5-SDM). The platform is also suitable for the mutagenesis of plasmids larger than 10 kb. KEY POINTS: Site-directed mutagenesis mediated by single-stranded DNA. Removing target site with T5 exonuclease. Highly efficient cleavage of target DNA with FnCas12a.
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Affiliation(s)
- Mengjie Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Qingqing Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Rui Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
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176
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Schuller A, Cserjan-Puschmann M, Tauer C, Jarmer J, Wagenknecht M, Reinisch D, Grabherr R, Striedner G. Escherichia coli σ 70 promoters allow expression rate control at the cellular level in genome-integrated expression systems. Microb Cell Fact 2020; 19:58. [PMID: 32138729 PMCID: PMC7059391 DOI: 10.1186/s12934-020-01311-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/17/2020] [Indexed: 12/18/2022] Open
Abstract
Background The genome-integrated T7 expression system offers significant advantages, in terms of productivity and product quality, even when expressing the gene of interest (GOI) from a single copy. Compared to plasmid-based expression systems, this system does not incur a plasmid-mediated metabolic load, and it does not vary the dosage of the GOI during the production process. However, long-term production with T7 expression system leads to a rapidly growing non-producing population, because the T7 RNA polymerase (RNAP) is prone to mutations. The present study aimed to investigate whether two σ70 promoters, which were recognized by the Escherichia coli host RNAP, might be suitable in genome-integrated expression systems. We applied a promoter engineering strategy that allowed control of expressing the model protein, GFP, by introducing lac operators (lacO) into the constitutive T5 and A1 promoter sequences. Results We showed that, in genome-integrated E. coli expression systems that used σ70 promoters, the number of lacO sites must be well balanced. Promoters containing three and two lacO sites exhibited low basal expression, but resulted in a complete stop in recombinant protein production in partially induced cultures. In contrast, expression systems regulated by a single lacO site and the lac repressor element, lacIQ, on the same chromosome caused very low basal expression, were highly efficient in recombinant protein production, and enables fine-tuning of gene expression levels on a cellular level. Conclusions Based on our results, we hypothesized that this phenomenon was associated with the autoregulation of the lac repressor protein, LacI. We reasoned that the affinity of LacI for the lacO sites of the GOI must be lower than the affinity of LacI to the lacO sites of the endogenous lac operon; otherwise, LacI autoregulation could not take place, and the lack of LacI autoregulation would lead to a disturbance in lac repressor-mediated regulation of transcription. By exploiting the mechanism of LacI autoregulation, we created a novel E. coli expression system for use in recombinant protein production, synthetic biology, and metabolic engineering applications.
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Affiliation(s)
- Artur Schuller
- Christian Doppler Laboratory for Production of Next-level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Johanna Jarmer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Daniela Reinisch
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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177
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Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
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178
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Hao M, Wang Z, Qiao H, Yin P, Qiao J, Qi H. Dynamic Genome Editing Using In Vivo Synthesized Donor ssDNA in Escherichia coli. Cells 2020; 9:E467. [PMID: 32085579 PMCID: PMC7072734 DOI: 10.3390/cells9020467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
As a key element of genome editing, donor DNA introduces the desired exogenous sequence while working with other crucial machinery such as CRISPR-Cas or recombinases. However, current methods for the delivery of donor DNA into cells are both inefficient and complicated. Here, we developed a new methodology that utilizes rolling circle replication and Cas9 mediated (RC-Cas-mediated) in vivo single strand DNA (ssDNA) synthesis. A single-gene rolling circle DNA replication system from Gram-negative bacteria was engineered to produce circular ssDNA from a Gram-positive parent plasmid at a designed sequence in Escherichia coli. Furthermore, it was demonstrated that the desired linear ssDNA fragment could be cut out using CRISPR-associated protein 9 (CRISPR-Cas9) nuclease and combined with lambda Red recombinase as donor for precise genome engineering. Various donor ssDNA fragments from hundreds to thousands of nucleotides in length were synthesized in E. coli cells, allowing successive genome editing in growing cells. We hope that this RC-Cas-mediated in vivo ssDNA on-site synthesis system will be widely adopted as a useful new tool for dynamic genome editing.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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179
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Janesch B, Baumann L, Mark A, Thompson N, Rahmani S, Sim L, Withers SG, Wakarchuk WW. Directed evolution of bacterial polysialyltransferases. Glycobiology 2020; 29:588-598. [PMID: 30976781 DOI: 10.1093/glycob/cwz021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/15/2019] [Accepted: 03/18/2019] [Indexed: 01/30/2023] Open
Abstract
Polysialyltransferases (polySTs) are glycosyltransferases that synthesize polymers of sialic acid found in vertebrates and some bacterial pathogens. Bacterial polySTs have utility in the modification of therapeutic proteins to improve serum half-life, and the potential for tissue engineering. PolySTs are membrane-associated proteins and as recombinant proteins suffer from inherently low solubility, low expression levels and poor thermal stability. To improve their physicochemical and biochemical properties, we applied a directed evolution approach using a FACS-based ultrahigh-throughput assay as a simple, robust and reliable screening method. We were able to enrich a large mutant library and, in combination with plate-based high-throughput secondary screening, we discovered mutants with increased enzymatic activity and improved stability compared to the wildtype enzyme. This work presents a powerful strategy for the screening of directed evolution libraries of bacterial polySTs to identify better catalysts for in vitro polysialylation of therapeutics.
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Affiliation(s)
- Bettina Janesch
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Lars Baumann
- Departments of Chemistry and Biochemistry, and Michael Smith Laboratory, University of British Columbia, Vancouver, BC, Canada
| | - Alison Mark
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Nicole Thompson
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Sadia Rahmani
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Lyann Sim
- Departments of Chemistry and Biochemistry, and Michael Smith Laboratory, University of British Columbia, Vancouver, BC, Canada
| | - Stephen G Withers
- Departments of Chemistry and Biochemistry, and Michael Smith Laboratory, University of British Columbia, Vancouver, BC, Canada
| | - Warren W Wakarchuk
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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180
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Kim JM, Garcia-Alcala M, Balleza E, Cluzel P. Stochastic transcriptional pulses orchestrate flagellar biosynthesis in Escherichia coli. SCIENCE ADVANCES 2020; 6:eaax0947. [PMID: 32076637 PMCID: PMC7002133 DOI: 10.1126/sciadv.aax0947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 11/22/2019] [Indexed: 05/28/2023]
Abstract
The classic picture of flagellum biosynthesis in Escherichia coli, inferred from population measurements, depicts a deterministic program where promoters are sequentially up-regulated and are maintained steadily active throughout exponential growth. However, complex regulatory dynamics at the single-cell level can be masked by bulk measurements. Here, we discover that in individual E. coli cells, flagellar promoters are stochastically activated in pulses. These pulses are coordinated within specific classes of promoters and comprise "on" and "off" states, each of which can span multiple generations. We demonstrate that in this pulsing program, the regulatory logic of flagellar assembly dictates which promoters skip pulses. Surprisingly, pulses do not require specific transcriptional or translational regulation of the flagellar master regulator, FlhDC, but instead appears to be essentially governed by an autonomous posttranslational circuit. Our results suggest that even topologically simple transcriptional networks can generate unexpectedly rich temporal dynamics and phenotypic heterogeneities.
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Affiliation(s)
- J. Mark Kim
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Mayra Garcia-Alcala
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Enrique Balleza
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Philippe Cluzel
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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181
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Kato Y. Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production. Int J Mol Sci 2020; 21:ijms21030705. [PMID: 31973139 PMCID: PMC7037476 DOI: 10.3390/ijms21030705] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/25/2019] [Accepted: 01/19/2020] [Indexed: 02/01/2023] Open
Abstract
Expression systems for highly toxic protein genes must be conditional and suppress leakage expression to almost zero because even faint leakage expression may kill host cells, inhibit host growth, and cause loss of plasmids containing the toxic protein genes. The most widely used conditional expression systems are controlled only at the transcriptional level, and complete suppression of leakage expression is challenging. Recent progress on translational control has enabled construction of dual transcriptional-translational control systems in which leakage expression is strongly suppressed. This review summarizes the principles, features, and practical examples of dual transcriptional-translational control systems in bacteria, and provides future perspectives on these systems.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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182
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Abbasi MN, Fu J, Bian X, Wang H, Zhang Y, Li A. Recombineering for Genetic Engineering of Natural Product Biosynthetic Pathways. Trends Biotechnol 2020; 38:715-728. [PMID: 31973879 DOI: 10.1016/j.tibtech.2019.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 01/21/2023]
Abstract
Microbial genomes encode many cryptic and uncharacterized biosynthetic gene clusters (BGCs). Exploiting this unexplored genetic wealth to discover microbial novel natural products (NPs) remains a challenging issue. We review homologous recombination (HR)-based recombineering, mediated by the recombinases RecE/RecT from Rac prophage and Redα/Redβ from lambda phage, which has developed into a highly inclusive tool for direct cloning of large DNA up to 100 kb, seamless mutation, multifragment assembly, and heterologous expression of microbial NP BGCs. Its utilization in the refactoring, engineering, and functional expression of long BGCs for NP biosynthesis makes it easy to elucidate NP-producing potential in microbes. This review also highlights various applications of recombineering in NP-derived drug discovery.
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Affiliation(s)
- Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Hailong Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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183
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A continuous evolution system for contracting the host range of bacteriophage T7. Sci Rep 2020; 10:307. [PMID: 31941920 PMCID: PMC6962156 DOI: 10.1038/s41598-019-57221-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage T7 is an intracellular parasite that recognizes its host via its tail and tail fiber proteins, known as receptor-binding proteins (RBPs). The RBPs attach to specific lipopolysaccharide (LPS) features on the host. Various studies have shown expansion of the phage’s host range via mutations in the genes encoding the RBPs, whereas only a few have shown contraction of its host range. Furthermore, most experimental systems have not monitored the alteration of host range in the presence of several hosts simultaneously. Here we show that T7 phage grown in the presence of five restrictive strains and one permissive host, each with a different LPS form, gradually avoids recognition of the restrictive strains. Remarkably, avoidance of the restrictive strains was repeated in different experiments using six different permissive hosts. The evolved phages carried mutations that changed their specificity, as determined by sequencing of the genes encoding the RBPs. This system demonstrates a major role for RBPs in narrowing the range of futile infections. The system can be harnessed for host-range contraction in applications such as detection or elimination of a specific bacterial serotype by bacteriophages.
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184
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Hausjell J, Kutscha R, Gesson JD, Reinisch D, Spadiut O. The Effects of Lactose Induction on a Plasmid-Free E. coli T7 Expression System. Bioengineering (Basel) 2020; 7:E8. [PMID: 31935883 PMCID: PMC7175309 DOI: 10.3390/bioengineering7010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
Recombinant production of pharmaceutical proteins like antigen binding fragments (Fabs) in the commonly-used production host Escherichia coli presents several challenges. The predominantly-used plasmid-based expression systems exhibit the drawback of either excessive plasmid amplification or plasmid loss over prolonged cultivations. To improve production, efforts are made to establish plasmid-free expression, ensuring more stable process conditions. Another strategy to stabilize production processes is lactose induction, leading to increased soluble product formation and cell fitness, as shown in several studies performed with plasmid-based expression systems. Within this study we wanted to investigate lactose induction for a strain with a genome-integrated gene of interest for the first time. We found unusually high specific lactose uptake rates, which we could attribute to the low levels of lac-repressor protein that is usually encoded not only on the genome but additionally on pET plasmids. We further show that these unusually high lactose uptake rates are toxic to the cells, leading to increased cell leakiness and lysis. Finally, we demonstrate that in contrast to plasmid-based T7 expression systems, IPTG induction is beneficial for genome-integrated T7 expression systems concerning cell fitness and productivity.
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Affiliation(s)
- Johanna Hausjell
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
| | - Regina Kutscha
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
| | - Jeannine D. Gesson
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria; (J.D.G.); (D.R.)
| | - Daniela Reinisch
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria; (J.D.G.); (D.R.)
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, 1060 Vienna, Austria; (J.H.); (R.K.)
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185
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Kalkreuter E, Pan G, Cepeda AJ, Shen B. Targeting Bacterial Genomes for Natural Product Discovery. Trends Pharmacol Sci 2019; 41:13-26. [PMID: 31822352 DOI: 10.1016/j.tips.2019.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022]
Abstract
Bacterial natural products (NPs) and their analogs constitute more than half of the new small molecule drugs developed over the past few decades. Despite this success, interest in natural products from major pharmaceutical companies has decreased even as genomics has uncovered the large number of biosynthetic gene clusters (BGCs) that encode for novel natural products. To date, there is still a lack of universal strategies and enabling technologies to discover natural products at scale and speed. This review highlights several of the opportunities provided by genome sequencing and bioinformatics, challenges associated with translating genomes into natural products, and examples of successful strain prioritization and BGC activation strategies that have been used in the genomic era for natural product discovery from cultivatable bacteria.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alexis J Cepeda
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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186
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Negri A, Jąkalski M, Szczuka A, Pryszcz LP, Mruk I. Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor. Nucleic Acids Res 2019; 47:9542-9556. [PMID: 31372643 PMCID: PMC6765115 DOI: 10.1093/nar/gkz665] [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: 02/25/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 12/27/2022] Open
Abstract
Restriction-modification (R–M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R–M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R–M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R–M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.
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Affiliation(s)
- Alessandro Negri
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jąkalski
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Aleksandra Szczuka
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Leszek P Pryszcz
- Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology, Warsaw, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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187
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Toll-like receptor 2 expression on c-kit + cells tracks the emergence of embryonic definitive hematopoietic progenitors. Nat Commun 2019; 10:5176. [PMID: 31729371 PMCID: PMC6858454 DOI: 10.1038/s41467-019-13150-0] [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: 02/14/2019] [Accepted: 10/21/2019] [Indexed: 12/27/2022] Open
Abstract
Hematopoiesis in mammalian embryos proceeds through three successive waves of hematopoietic progenitors. Since their emergence spatially and temporally overlap and phenotypic markers are often shared, the specifics regarding their origin, development, lineage restriction and mutual relationships have not been fully determined. The identification of wave-specific markers would aid to resolve these uncertainties. Here, we show that toll-like receptors (TLRs) are expressed during early mouse embryogenesis. We provide phenotypic and functional evidence that the expression of TLR2 on E7.5 c-kit+ cells marks the emergence of precursors of erythro-myeloid progenitors (EMPs) and provides resolution for separate tracking of EMPs from primitive progenitors. Using in vivo fate mapping, we show that at E8.5 the Tlr2 locus is already active in emerging EMPs and in progenitors of adult hematopoietic stem cells (HSC). Together, this data demonstrates that the activation of the Tlr2 locus tracks the earliest events in the process of EMP and HSC specification. There is limited knowledge of markers to identify various waves of murine embryonic hematopoiesis. Here, the authors show that the expression of toll-like receptor 2 (TLR2) on E7.5 c-kit+ cells marks the emergence of erythro-myeloid progenitor precursors and that the Tlr2 locus is active in E8.5 precursors of adult HSCs.
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188
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Chen W, Chen R, Wang H, Li Y, Zhang Y, Li S. Tuning chromosomal gene expression in Escherichia coli by combining single-stranded oligonucleotides mediated recombination and kil counter selection system. J Biotechnol 2019; 307:63-68. [PMID: 31678458 DOI: 10.1016/j.jbiotec.2019.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/03/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
Extensively modulating gene expression to achieve optimal flux is a critical step in metabolic engineering. Gene expression is usually modulated at the transcriptional level by controlling the strength of a promoter. However, this type of modulation is often hampered by its inability to fully sample the complete continuum of transcriptional control. In Escherichia coli, this limitation can be solved by constructing promoters with a wide range of strengths. In this study, a highly efficient method was developed to modulate a particular chromosomal gene of E. coli at a wide range of expression levels. This was achieved by combining highly efficient single-stranded oligonucleotide-mediated recombination and a stringent counter selection system kil. Using this strategy, a chromosomal library, with a range from 0.3% to 388% relative to the wild lac promoter, was easily obtained. The strength of our chromosomal promoter library was approximately 5-60 times wider in range than those of libraries reported before.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui Wang
- School of Biological Medicine, Beijing City University, Beijing, 10084, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yunyi Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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189
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Lustyk D, Kinský S, Ullrich KK, Yancoskie M, Kašíková L, Gergelits V, Sedlacek R, Chan YF, Odenthal-Hesse L, Forejt J, Jansa P. Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice. Genetics 2019; 213:1047-1063. [PMID: 31562180 PMCID: PMC6827376 DOI: 10.1534/genetics.119.302554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023] Open
Abstract
F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus domesticus autosomes, and the X-linked Hstx2 locus. Hstx2 modulates the extent of Prdm9-dependent meiotic arrest and harbors two additional factors responsible for intersubspecific introgression-induced oligospermia (Hstx1) and meiotic recombination rate (Meir1). To facilitate positional cloning and to overcome the recombination suppression within the 4.3 Mb encompassing the Hstx2 locus, we designed Hstx2-CRISPR and SPO11/Cas9 transgenes aimed to induce DNA double-strand breaks specifically within the Hstx2 locus. The resulting recombinant reduced the Hstx2 locus to 2.70 Mb (chromosome X: 66.51-69.21 Mb). The newly defined Hstx2 locus still operates as the major X-linked factor of the F1 hybrid sterility, and controls meiotic chromosome synapsis and meiotic recombination rate. Despite extensive further crosses, the 2.70 Mb Hstx2 interval behaved as a recombination cold spot with reduced PRDM9-mediated H3K4me3 hotspots and absence of DMC1-defined DNA double-strand-break hotspots. To search for structural anomalies as a possible cause of recombination suppression, we used optical mapping and observed high incidence of subspecies-specific structural variants along the X chromosome, with a striking copy number polymorphism of the microRNA Mir465 cluster. This observation together with the absence of a strong sterility phenotype in Fmr1 neighbor (Fmr1nb) null mutants support the role of microRNA as a likely candidate for Hstx2.
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Affiliation(s)
- Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Faculty of Science, Charles University, Prague CZ-12000, Czech Republic
| | - Slavomír Kinský
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Kristian Karsten Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Michelle Yancoskie
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Lenka Kašíková
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Radislav Sedlacek
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Yingguang Frank Chan
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
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190
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Garoff L, Huseby DL, Praski Alzrigat L, Hughes D. Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli. J Antimicrob Chemother 2019; 73:3285-3292. [PMID: 30239743 DOI: 10.1093/jac/dky356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background Chromosomal mutations that reduce ciprofloxacin susceptibility in Escherichia coli characteristically map to drug target genes (gyrAB and parCE), and genes encoding regulators of the AcrAB-TolC efflux pump. Mutations in RNA polymerase can also reduce susceptibility, by up-regulating the MdtK efflux pump. Objectives We asked whether mutations in additional chromosomal gene classes could reduce susceptibility to ciprofloxacin. Methods Experimental evolution, complemented by WGS analysis, was used to select and identify mutations that reduce susceptibility to ciprofloxacin. Transcriptome analysis, genetic reconstructions, susceptibility measurements and competition assays were used to identify significant genes and explore the mechanism of resistance. Results Mutations in three different aminoacyl-tRNA synthetase genes (leuS, aspS and thrS) were shown to reduce susceptibility to ciprofloxacin. For two of the genes (leuS and aspS) the mechanism was partially dependent on RelA activity. Two independently selected mutations in leuS (Asp162Asn and Ser496Pro) were studied in most detail, revealing that they induce transcriptome changes similar to a stringent response, including up-regulation of three efflux-associated loci (mdtK, acrZ and ydhIJK). Genetic analysis showed that reduced susceptibility depended on the activity of these loci. Broader antimicrobial susceptibility testing showed that the leuS mutations also reduce susceptibility to additional classes of antibiotics (chloramphenicol, rifampicin, mecillinam, ampicillin and trimethoprim). Conclusions The identification of mutations in multiple tRNA synthetase genes that reduce susceptibility to ciprofloxacin and other antibiotics reveals the existence of a large mutational target that could contribute to resistance development by up-regulation of an array of efflux pumps.
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Affiliation(s)
- Linnéa Garoff
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Douglas L Huseby
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Lisa Praski Alzrigat
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
| | - Diarmaid Hughes
- Uppsala University, Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala, Sweden
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191
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Fosmidomycin, an inhibitor of isoprenoid synthesis, induces persistence in Chlamydia by inhibiting peptidoglycan assembly. PLoS Pathog 2019; 15:e1008078. [PMID: 31622442 PMCID: PMC6818789 DOI: 10.1371/journal.ppat.1008078] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/29/2019] [Accepted: 09/12/2019] [Indexed: 11/19/2022] Open
Abstract
The antibiotic, fosmidomycin (FSM) targets the methylerythritol phosphate (MEP) pathway of isoprenoid synthesis by inhibiting the essential enzyme, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (Dxr) and is lethal to intracellular parasites and bacteria. The obligate intracellular bacterial pathogen, Chlamydia trachomatis, alternates between two developmental forms: the extracellular, infectious elementary body (EB), and the intracellular, replicative form called the reticulate body (RB). Several stressful growth conditions including iron deprivation halt chlamydial cell division and cause development of a morphologically enlarged, but viable form termed an aberrant body (AB). This phenotype constitutes the chlamydial developmental state known as persistence. This state is reversible as removal of the stressor allows the chlamydiae to re-enter and complete the normal developmental cycle. Bioinformatic analysis indicates that C. trachomatis encodes a homolog of Dxr, but its function and the requirement for isoprenoid synthesis in chlamydial development is not fully understood. We hypothesized that chlamydial Dxr (DxrCT) is functional and that the methylerythritol phosphate (MEP) pathway is required for normal chlamydial development. Thus, FSM exposure should be lethal to C. trachomatis. Overexpression of chlamydial Dxr (DxrCT) in Escherichia coli under FSM exposure and in a conditionally lethal dxr mutant demonstrated that DxrCT functions similarly to E. coli Dxr. When Chlamydia-infected cultures were exposed to FSM, EB production was significantly reduced. However, titer recovery assays, electron microscopy, and peptidoglycan labeling revealed that FSM inhibition of isoprenoid synthesis is not lethal to C. trachomatis, but instead induces persistence. Bactoprenol is a critical isoprenoid required for peptidoglycan precursor assembly. We therefore conclude that FSM induces persistence in Chlamydia by preventing bactoprenol production necessary for peptidoglycan precursor assembly and subsequent cell division.
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192
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Hu Z, Ghosh A, Stolze SC, Horváth M, Bai B, Schaefer S, Zündorf S, Liu S, Harzen A, Hajheidari M, Sarnowski TJ, Nakagami H, Koncz Z, Koncz C. Gene modification by fast-track recombineering for cellular localization and isolation of components of plant protein complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:411-429. [PMID: 31276249 PMCID: PMC6852550 DOI: 10.1111/tpj.14450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 05/04/2023]
Abstract
To accelerate the isolation of plant protein complexes and study cellular localization and interaction of their components, an improved recombineering protocol is described for simple and fast site-directed modification of plant genes in bacterial artificial chromosomes (BACs). Coding sequences of fluorescent and affinity tags were inserted into genes and transferred together with flanking genomic sequences of desired size by recombination into Agrobacterium plant transformation vectors using three steps of E. coli transformation with PCR-amplified DNA fragments. Application of fast-track recombineering is illustrated by the simultaneous labelling of CYCLIN-DEPENDENT KINASE D (CDKD) and CYCLIN H (CYCH) subunits of kinase module of TFIIH general transcription factor and the CDKD-activating CDKF;1 kinase with green fluorescent protein (GFP) and mCherry (green and red fluorescent protein) tags, and a PIPL (His18 -StrepII-HA) epitope. Functionality of modified CDKF;1 gene constructs is verified by complementation of corresponding T-DNA insertion mutation. Interaction of CYCH with all three known CDKD homologues is confirmed by their co-localization and co-immunoprecipitation. Affinity purification and mass spectrometry analyses of CDKD;2, CYCH, and DNA-replication-coupled HISTONE H3.1 validate their association with conserved TFIIH subunits and components of CHROMATIN ASSEMBLY FACTOR 1, respectively. The results document that simple modification of plant gene products with suitable tags by fast-track recombineering is well suited to promote a wide range of protein interaction and proteomics studies.
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Affiliation(s)
- Zhoubo Hu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Ajit Ghosh
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Department of Biochemistry and Molecular BiologyShahjalal University of Science and TechnologySylhet3114, Bangladesh
| | - Sara C. Stolze
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mihály Horváth
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Bing Bai
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Sabine Schaefer
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Simone Zündorf
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Shanda Liu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Anne Harzen
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mohsen Hajheidari
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Botanical InstituteCologne Biocenter, Cluster of Excellence on Plant Sciences, University of CologneD‐50674CologneGermany
| | - Tomasz J. Sarnowski
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5A02‐106WarsawPoland
| | - Hirofumi Nakagami
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Zsuzsa Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Csaba Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Plant BiologyBiological Research Center of Hungarian Academy of SciencesTemesvári krt. 62H‐6726SzegedHungary
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193
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RNase G controls tpiA mRNA abundance in response to oxygen availability in Escherichia coli. J Microbiol 2019; 57:910-917. [DOI: 10.1007/s12275-019-9354-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 01/25/2023]
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194
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Nair RR, Vasse M, Wielgoss S, Sun L, Yu YTN, Velicer GJ. Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences. Nat Commun 2019; 10:4301. [PMID: 31541093 PMCID: PMC6754418 DOI: 10.1038/s41467-019-12140-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/22/2019] [Indexed: 01/08/2023] Open
Abstract
Generalist bacterial predators are likely to strongly shape many important ecological and evolutionary features of microbial communities, for example by altering the character and pace of molecular evolution, but investigations of such effects are scarce. Here we report how predator-prey interactions alter the evolution of fitness, genomes and phenotypic diversity in coevolving bacterial communities composed of Myxococcus xanthus as predator and Escherichia coli as prey, relative to single-species controls. We show evidence of reciprocal adaptation and demonstrate accelerated genomic evolution specific to coevolving communities, including the rapid appearance of mutator genotypes. Strong parallel evolution unique to the predator-prey communities occurs in both parties, with predators driving adaptation at two prey traits associated with virulence in bacterial pathogens-mucoidy and the outer-membrane protease OmpT. Our results suggest that generalist predatory bacteria are important determinants of how complex microbial communities and their interaction networks evolve in natural habitats.
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Affiliation(s)
- Ramith R Nair
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland.
| | - Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland.
| | - Sébastien Wielgoss
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
| | - Lei Sun
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
- Department of Systems Biology, Harvard Medical School, 02115, Boston, MA, USA
| | - Yuen-Tsu N Yu
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
| | - Gregory J Velicer
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
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195
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Watson JF, García-Nafría J. In vivo DNA assembly using common laboratory bacteria: A re-emerging tool to simplify molecular cloning. J Biol Chem 2019; 294:15271-15281. [PMID: 31522138 DOI: 10.1074/jbc.rev119.009109] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular cloning is a cornerstone of biomedical, biotechnological, and synthetic biology research. As such, improved cloning methodologies can significantly advance the speed and cost of research projects. Whereas current popular cloning approaches use in vitro assembly of DNA fragments, in vivo cloning offers potential for greater simplification. It is generally assumed that bacterial in vivo cloning requires Escherichia coli strains with enhanced recombination ability; however, this is incorrect. A widely present, bacterial RecA-independent recombination pathway is re-emerging as a powerful tool for molecular cloning and DNA assembly. This poorly understood pathway offers optimal cloning properties (i.e. seamless, directional, and sequence-independent) without requiring in vitro DNA assembly or specialized bacteria, therefore vastly simplifying cloning procedures. Although the use of this pathway to perform DNA assembly was first reported over 25 years ago, it failed to gain popularity, possibly due to both technical and circumstantial reasons. Technical limitations have now been overcome, and recent reports have demonstrated its versatility for DNA manipulation. Here, we summarize the historical trajectory of this approach and collate recent reports to provide a roadmap for its optimal use. Given the simplified protocols and minimal requirements, cloning using in vivo DNA assembly in E. coli has the potential to become widely employed across the molecular biology community.
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Affiliation(s)
- Jake F Watson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
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196
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Chure G, Razo-Mejia M, Belliveau NM, Einav T, Kaczmarek ZA, Barnes SL, Lewis M, Phillips R. Predictive shifts in free energy couple mutations to their phenotypic consequences. Proc Natl Acad Sci U S A 2019; 116:18275-18284. [PMID: 31451655 PMCID: PMC6744869 DOI: 10.1073/pnas.1907869116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, we present a framework centered on measuring changes in the free energy of the system to link individual mutations in an allosteric transcriptional repressor to the parameters which govern its response. We find that the energetic effects of the mutations can be categorized into several classes which have characteristic curves as a function of the inducer concentration. We experimentally test these diagnostic predictions using the well-characterized LacI repressor of Escherichia coli, probing several mutations in the DNA binding and inducer binding domains. We find that the change in gene expression due to a point mutation can be captured by modifying only the model parameters that describe the respective domain of the wild-type protein. These parameters appear to be insulated, with mutations in the DNA binding domain altering only the DNA affinity and those in the inducer binding domain altering only the allosteric parameters. Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations. Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing an avenue for identifying and quantifying epistatic interactions.
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Affiliation(s)
- Griffin Chure
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Manuel Razo-Mejia
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Nathan M Belliveau
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Tal Einav
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
| | - Zofii A Kaczmarek
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Stephanie L Barnes
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Mitchell Lewis
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Rob Phillips
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
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197
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Atkinson SP. Previews. Stem Cells Transl Med 2019. [PMCID: PMC6766597 DOI: 10.1002/sctm.19-0270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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198
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Gou Y, Liu W, Wang JJ, Tan L, Hong B, Guo L, Liu H, Pan Y, Zhao Y. CRISPR-Cas9 knockout of qseB induced asynchrony between motility and biofilm formation in Escherichia coli. Can J Microbiol 2019; 65:691-702. [DOI: 10.1139/cjm-2019-0100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Generally, cell motility and biofilm formation are tightly regulated. The QseBC two-component system (TCS) serves as a bridge for bacterial signal transmission, in which the protein QseB acts as a response regulator bacterial motility, biofilm formation, and virulence. The mechanisms that govern the interaction between QseBC and their functions have been studied in general, but the regulatory role of QseB on bacterial motility and biofilm formation is unknown. In this study, the CRISPR-Cas9 system was used to construct the Escherichia coli MG1655ΔqseB strain (strain ΔqseB), and the effects of the qseB gene on changes in motility and biofilm formation in the wild type (WT) were determined. The motility assay results showed that the ΔqseB strain had higher (p < 0.05) motility than the WT strain. However, there was no difference in the formation of biofilm between the ΔqseB and WT strains. Real-time quantitative PCR illustrated that deletion of qseB in the WT strain downregulated expression of the type I pili gene fimA. Therefore, we might conclude that the ΔqseB induced the downregulation of fimA, which led to asynchrony between motility and biofilm formation in E. coli, providing new insight into the functional importance of QseB in regulating cell motility and biofilm formation.
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Affiliation(s)
- Yi Gou
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Weiqi Liu
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jing Jing Wang
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Ling Tan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Bin Hong
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Linxia Guo
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
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Fink M, Vazulka S, Egger E, Jarmer J, Grabherr R, Cserjan‐Puschmann M, Striedner G. Microbioreactor Cultivations of Fab‐ProducingEscherichia coliReveal Genome‐Integrated Systems as Suitable for Prospective Studies on Direct Fab Expression Effects. Biotechnol J 2019; 14:e1800637. [DOI: 10.1002/biot.201800637] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/11/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Mathias Fink
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
| | - Sophie Vazulka
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
| | - Esther Egger
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
| | - Johanna Jarmer
- Boehringer Ingelheim RCV GmbH & Co KGDr. Boehringer‐Gasse 5‐11 A‐1120 Vienna Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
| | - Monika Cserjan‐Puschmann
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next‐Level Biopharmaceuticals in E. coli, Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 18 A‐1190 Vienna Austria
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Grimwade JE, Rozgaja TA, Gupta R, Dyson K, Rao P, Leonard AC. Origin recognition is the predominant role for DnaA-ATP in initiation of chromosome replication. Nucleic Acids Res 2019; 46:6140-6151. [PMID: 29800247 PMCID: PMC6158602 DOI: 10.1093/nar/gky457] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 05/11/2018] [Indexed: 01/06/2023] Open
Abstract
In all cells, initiation of chromosome replication depends on the activity of AAA+ initiator proteins that form complexes with replication origin DNA. In bacteria, the conserved, adenosine triphosphate (ATP)-regulated initiator protein, DnaA, forms a complex with the origin, oriC, that mediates DNA strand separation and recruitment of replication machinery. Complex assembly and origin activation requires DnaA-ATP, which differs from DnaA-ADP in its ability to cooperatively bind specific low affinity sites and also to oligomerize into helical filaments. The degree to which each of these activities contributes to the DnaA-ATP requirement for initiation is not known. In this study, we compared the DnaA-ATP dependence of initiation from wild-type Escherichia coli oriC and a synthetic origin (oriCallADP), whose multiple low affinity DnaA sites bind DnaA-ATP and DnaA-ADP similarly. OriCallADP was fully occupied and unwound by DnaA-ADP in vitro, and, in vivo, oriCallADP suppressed lethality of DnaA mutants defective in ATP binding and ATP-specific oligomerization. However, loss of preferential DnaA-ATP binding caused over-initiation and increased sensitivity to replicative stress. The findings indicate both DnaA-ATP and DnaA-ADP can perform most of the mechanical functions needed for origin activation, and suggest that a key reason for ATP-regulation of DnaA is to control replication initiation frequency.
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Affiliation(s)
- Julia E Grimwade
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
| | - Tania A Rozgaja
- AREVA Inc North America, 6100 Southwest Blvd #400, Benbrook, TX 76109, USA
| | - Rajat Gupta
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
| | - Kyle Dyson
- University of Florida College of Medicine, P.O. Box 100215, Gainesville, FL 32610, USA
| | - Prassanna Rao
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
| | - Alan C Leonard
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
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