1
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Bao Y, Cao X, Landick R. RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations. Nucleic Acids Res 2024; 52:4556-4574. [PMID: 38554114 PMCID: PMC11077087 DOI: 10.1093/nar/gkae209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024] Open
Abstract
Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). A surface-exposed domain inserted into the catalytic trigger loop (TL) of Escherichia coli RNAP, called SI3, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ΔSI3*). ΔSI3* increased transcription rate in vitro relative to ΔSI3, possibly explaining its viability, but retained both positive and negative effects of ΔSI3 on pausing. ΔSI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ΔSI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ΔSI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ΔSI3*-suppressed pauses also were associated with apparent pausing one nucleotide upstream from the consensus sequence, often generating tandem pause sites. These '-2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.
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Affiliation(s)
- Yu Bao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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2
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Rangarajan AA, Yilmaz C, Schnetz K. Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-Associated Proteins in Escherichia coli. Methods Mol Biol 2024; 2819:225-240. [PMID: 39028509 DOI: 10.1007/978-1-0716-3930-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Bacterial nucleoid-associated proteins are important factors in regulation of transcription, in nucleoid structuring, and in homeostasis of DNA supercoiling. Vice versa, transcription influences DNA supercoiling and can affect DNA binding of nucleoid-associated proteins (NAPs) such as H-NS in Escherichia coli. Here we describe genetic tools to study the interplay between transcription and nucleoid-associated proteins in E. coli. These methods include construction of genomic and plasmidic transcriptional and translational lacZ reporter gene fusions to study regulation of promoters; insertion of promoter cassettes to drive transcription into a locus of interest in the genome, for example, an H-NS-bound locus; and construction of isogenic hns and stpA mutants and precautions in doing so.
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Affiliation(s)
- Aathmaja Anandhi Rangarajan
- Institute for Genetics, University of Cologne, Cologne, Germany
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Cihan Yilmaz
- Institute for Genetics, University of Cologne, Cologne, Germany
- Qiagen, Hilden, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne, Cologne, Germany.
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3
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Wu T, Gómez-Coronado PA, Kubis A, Lindner SN, Marlière P, Erb TJ, Bar-Even A, He H. Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli. Nat Commun 2023; 14:8490. [PMID: 38123535 PMCID: PMC10733421 DOI: 10.1038/s41467-023-44247-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.
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Affiliation(s)
- Tong Wu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Armin Kubis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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4
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Masuda I, Hou YM. Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen. STAR Protoc 2023; 4:102196. [PMID: 36995932 PMCID: PMC10074243 DOI: 10.1016/j.xpro.2023.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/31/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).1.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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5
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Mund M, Weber W, Degreif D, Schiklenk C. A MAD7-based genome editing system for Escherichia coli. Microb Biotechnol 2023; 16:1000-1010. [PMID: 36929689 PMCID: PMC10128132 DOI: 10.1111/1751-7915.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 03/18/2023] Open
Abstract
A broad variety of biomolecules is industrially produced in bacteria and yeasts. These microbial expression hosts can be optimized through genetic engineering using CRISPR tools. Here, we designed and characterized such a modular genome editing system based on the Cas12a-like RNA-guided nuclease MAD7 in Escherichia coli. This system enables the efficient generation of single nucleotide polymorphisms (SNPs) or gene deletions and can directly be used with donor DNA from benchtop DNA assembly to increase throughput. We combined multiple edits to engineer an E. coli strain with reduced overflow metabolism and increased plasmid yield, highlighting the versatility and industrial applicability of this approach.
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Affiliation(s)
- Markus Mund
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Wadim Weber
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Daniel Degreif
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Christoph Schiklenk
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
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6
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Gong Z, Guo J, Li Q, Xie H. Molecular mechanism of lipopolysaccharide (LPS) in promoting biomineralization on bacterial surface. Biochim Biophys Acta Gen Subj 2023; 1867:130305. [PMID: 36621513 DOI: 10.1016/j.bbagen.2023.130305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Biomineralization on bacterial surface is affected by biomolecules of bacterial cell surface. Lipopolysaccharide (LPS) is the main and outermost component on the extracellular membrane of Gram-negative bacteria. In the present study, the molecular mechanism of LPS in affecting biomineralization of Ag+/Cl- colloids was investigated by taking advantages of two LPS structural deficient mutants of Escherichia coli. The two mutants were generated by impairing the expression of waaP or wbbH genes with CRISPR/Cas9 technology and it induced deficient polysaccharide chain of O-antigen (ΔwbbH) or phosphate groups of core oligosaccharide (ΔwaaP) in LPS structures. There were significant changes of the cell morphology and surface charge of the two mutants in comparing with that of wild type cells. LPS from ΔwaaP mutant showed increased ΔHITC upon interacting with free Ag+ ions than LPS from wild type cells or ΔwbbH mutant, implying the binding affinity of LPS to Ag+ ions is affected by the phosphate groups in core oligosaccharide. LPS from ΔwbbH mutant showed decreased endotherm (ΔQ) upon interacting with Ag+/Cl- colloids than LPS from wild type or ΔwaaP mutant cells, implying LPS polysaccharide chain structure is critical for stabilizing Ag+/Cl- colloids. Biomineralization of Ag+/Cl- colloids on ΔwbbH mutant cell surface showed distinctive morphology in comparison with that of wild type or ΔwaaP mutant cells, which confirmed the critical role of O-antigen of LPS in biomineralization. The present work provided molecular evidence of the relationship between LPS structure, ions, and ionic colloids in biomineralization on bacterial cell surface.
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Affiliation(s)
- Zechuan Gong
- Institute of Aix-marseille (AMU-WHU), Wuhan University of Technology, Wuhan 430070, China
| | - Junhui Guo
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China.
| | - Qichang Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Hao Xie
- Institute of Aix-marseille (AMU-WHU), Wuhan University of Technology, Wuhan 430070, China; School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China.
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7
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tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Rep 2022; 41:111539. [PMID: 36288695 PMCID: PMC9643105 DOI: 10.1016/j.celrep.2022.111539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/31/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3′-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival. Masuda et al. show that loss of m1G37 from the 3′ side of the tRNA anticodon renders a modified wobble nucleotide of the anticodon insufficient to decode a set of rare codons, providing a functional underpinning for the “modification circuit” between position 37 and the wobble position of the tRNA anticodon.
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8
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Giacomucci S, Mathieu-Denoncourt A, Vincent AT, Jannadi H, Duperthuy M. Experimental evolution of Vibrio cholerae identifies hypervesiculation as a way to increase motility in the presence of polymyxin B. Front Microbiol 2022; 13:932165. [PMID: 36090081 PMCID: PMC9454949 DOI: 10.3389/fmicb.2022.932165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Vibrio cholerae includes strains responsible for the cholera disease and is a natural inhabitant of aquatic environments. V. cholerae possesses a unique polar flagellum essential for motility, adhesion, and biofilm formation. In a previous study, we showed that motility and biofilm formation are altered in the presence of subinhibitory concentrations of polymyxin B in V. cholerae O1 and O139. In this study, we performed an experimental evolution to identify the genes restoring the motility in the presence of a subinhibitory concentration of polymyxin B. Mutations in five genes have been identified in three variants derived from two different parental strains A1552 and MO10: ihfA that encodes a subunit of the integration host factor (IHF), vacJ (mlaA) and mlaF, two genes belonging to the maintenance of the lipid asymmetry (Mla) pathway, dacB that encodes a penicillin-binding protein (PBP4) and involved in cell wall synthesis, and ccmH that encodes a c-type cytochrome maturation protein. We further demonstrated that the variants derived from MO10 containing mutations in vacJ, mlaF, and dacB secrete more and larger membrane vesicles that titer the polymyxin B, which increases the bacterial survival and is expected to limit its impact on the bacterial envelope and participate in the flagellum’s retention and motility.
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Affiliation(s)
- Sean Giacomucci
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | | | - Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Hanen Jannadi
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Marylise Duperthuy
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Marylise Duperthuy,
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9
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Singh AA, Pillay P, Naicker P, Alexandre K, Malatji K, Mach L, Steinkellner H, Vorster J, Chikwamba R, Tsekoa TL. Transient proteolysis reduction of Nicotiana benthamiana-produced CAP256 broadly neutralizing antibodies using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:953654. [PMID: 36061808 PMCID: PMC9433777 DOI: 10.3389/fpls.2022.953654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The hypersensitive response is elicited by Agrobacterium infiltration of Nicotiana benthamiana, including the induction and accumulation of pathogenesis-related proteins, such as proteases. This includes the induction of the expression of several cysteine proteases from the C1 (papain-like cysteine protease) and C13 (legumain-like cysteine protease) families. This study demonstrates the role of cysteine proteases: NbVPE-1a, NbVPE-1b, and NbCysP6 in the proteolytic degradation of Nicotiana benthamiana (glycosylation mutant ΔXTFT)-produced anti-human immunodeficiency virus broadly neutralizing antibody, CAP256-VRC26.25. Three putative cysteine protease cleavage sites were identified in the fragment crystallizable region. We further demonstrate the transient coexpression of CAP256-VRC26.25 with CRISPR/Cas9-mediated genome editing vectors targeting the NbVPE-1a, NbVPE-1b, and NbCysP6 genes which resulted in a decrease in CAP256-VRC26.25 degradation. No differences in structural features were observed between the human embryonic kidney 293 (HEK293)-produced and ΔXTFT broadly neutralizing antibodies produced with and without the coexpression of genome-editing vectors. Furthermore, despite the presence of proteolytically degraded fragments of plant-produced CAP256-VRC26.25 without the coexpression of genome editing vectors, no influence on the in vitro functional activity was detected. Collectively, we demonstrate an innovative in planta strategy for improving the quality of the CAP256 antibodies through the transient expression of the CRISPR/Cas9 vectors.
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Affiliation(s)
- Advaita Acarya Singh
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Priyen Pillay
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Previn Naicker
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Kabamba Alexandre
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Kanyane Malatji
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Rachel Chikwamba
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Tsepo L. Tsekoa
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
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10
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Bubnov DM, Yuzbashev TV, Khozov AA, Melkina OE, Vybornaya TV, Stan GB, Sineoky SP. Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs. Nucleic Acids Res 2022; 50:8947-8960. [PMID: 35920321 PMCID: PMC9410887 DOI: 10.1093/nar/gkac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering. We employed a counterselection strategy involving a genetic circuit based on the CI repressor of λ phage. Our design ensures elimination of most spontaneous mutants, and thus provides a counterselection stringency close to the maximum possible. We improved the efficiency of integrating long PCR-generated cassettes by exploiting the Ocr antirestriction function of T7 phage, which completely prevents degradation of unmethylated DNA by restriction endonucleases in wild-type bacteria. The employment of highly restrictive counterselection and ocr-assisted λRed recombineering allowed markerless integration of operon-sized cassettes into arbitrary genomic loci of four enterobacterial species with an efficiency of 50–100%. In the case of Escherichia coli, our strategy ensures simple combination of markerless mutations in a single strain via P1 transduction. Overall, the proposed approach can serve as a general tool for synthetic biology and metabolic engineering in a range of bacterial hosts.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
| | - Tigran V Yuzbashev
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Andrey A Khozov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills 1-12, Moscow 119234, Russia
| | - Olga E Melkina
- Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Laboratory of Bacterial Genetics, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Genomic Center, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
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11
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Wilson A, Ruiz N. The transmembrane α-helix of LptC participates in LPS extraction by the LptB 2 FGC transporter. Mol Microbiol 2022; 118:61-76. [PMID: 35678757 PMCID: PMC9544173 DOI: 10.1111/mmi.14952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022]
Abstract
Lipopolysaccharide (LPS) is an essential component of the outer membrane of most Gram‐negative bacteria that provides resistance to various toxic compounds and antibiotics. Newly synthesized LPS is extracted from the inner membrane by the ATP‐binding cassette (ABC) transporter LptB2FGC, which places the glycolipid onto a periplasmic protein bridge that connects to the outer membrane. This ABC transporter is structurally unusual in that it associates with an additional protein, LptC. The periplasmic domain of LptC is part of the transporter's bridge while its transmembrane α‐helix intercalates into the LPS‐binding cavity of the core LptB2FG transporter. LptC’s transmembrane helix affects the in vitro ATPase activity of LptB2FG, but its role in LPS transport in cells remains undefined. Here, we describe two roles of LptC’s transmembrane helix in Escherichia coli. We demonstrate that it is required to maintain proper levels of LptC and participates in coupling the activity of the ATPase LptB to that of its transmembrane partners LptF/LptG prior to loading LPS onto the periplasmic bridge. Our data support a model in which the association of LptC’s transmembrane helix with LptFG creates a nonessential step that slows down the LPS transporter.
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Affiliation(s)
- Andrew Wilson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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12
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Ellington AJ, Reisch CR. Efficient and Iterative Retron-Mediated in vivo Recombineering in E. coli. Synth Biol (Oxf) 2022; 7:ysac007. [PMID: 35673614 PMCID: PMC9165427 DOI: 10.1093/synbio/ysac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022] Open
Abstract
Recombineering is an important tool in gene editing, enabling fast, precise and highly specific in vivo modification of microbial genomes. Oligonucleotide-mediated recombineering via the in vivo production of single-stranded DNA can overcome the limitations of traditional recombineering methods that rely on the exogenous delivery of editing templates. By modifying a previously reported plasmid-based system for fully in vivo single-stranded DNA recombineering, we demonstrate iterative editing of independent loci by utilizing a temperature-sensitive origin of replication for easy curing of the editing plasmid from recombinant cells. Optimization of the promoters driving the expression of the system’s functional components, combined with targeted counterselection against unedited cells with Cas9 nuclease, enabled editing efficiencies of 90–100%. The addition of a dominant-negative mutL allele to the system allowed single-nucleotide edits that were otherwise unachievable due to mismatch repair. Finally, we tested alternative recombinases and found that efficiency significantly increased for some targets. Requiring only a single cloning step for retargeting, our system provides an easy-to-use method for rapid, efficient construction of desired mutants.
Graphical Abstract
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Affiliation(s)
- Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL 32611-7011, USA
| | - Christopher R Reisch
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL 32611-7011, USA
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13
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Hills E, Woodward TJ, Fields S, Brandsen BM. Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin. ACS Chem Biol 2022; 17:998-1010. [PMID: 35315272 PMCID: PMC9976627 DOI: 10.1021/acschembio.2c00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotic resistance is a growing threat to public health, making the development of antibiotics of critical importance. One promising class of potential new antibiotics are ribosomally synthesized and post-translationally modified peptides (RiPPs), which include klebsidin, a lasso peptide from Klebsiella pneumoniae that inhibits certain bacterial RNA polymerases. We develop a high-throughput assay based on growth inhibition of Escherichia coli to analyze the mutational tolerance of klebsidin. We transform a library of klebsidin variants into E. coli and use next-generation DNA sequencing to count the frequency of each variant before and after its expression, thereby generating functional scores for 320 of 361 single amino acid changes. We identify multiple positions in the macrocyclic ring and the C-terminal tail region of klebsidin that are intolerant to mutation, as well as positions in the loop region that are highly tolerant to mutation. Characterization of selected peptide variants scored as active reveals that each adopts a threaded lasso conformation; active loop variants applied extracellularly as peptides slow the growth of E. coli and K. pneumoniae. We generate an E. coli strain with a mutation in RNA polymerase that confers resistance to klebsidin and similarly carry out a selection with the klebsidin library. We identify a single variant, klebsidin F9Y, that maintains activity against the resistant E. coli when expressed intracellularly. This finding supports the utility of this method and suggests that comprehensive mutational analysis of lasso peptides can identify unique and potentially improved variants.
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Affiliation(s)
- Ethan Hills
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Tyler J. Woodward
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Benjamin M. Brandsen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States,Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, United States,Correspondence: Benjamin M. Brandsen, , ph. 402 280-2153
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14
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Rangarajan AA, Yilmaz C, Schnetz K. Deletion of FRT-sites by no-SCAR recombineering in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35411846 DOI: 10.1099/mic.0.001173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lambda-Red recombineering is the most commonly used method to create point mutations, insertions or deletions in Escherichia coli and other bacteria, but usually an Flp recognition target (FRT) scar-site is retained in the genome. Alternative scarless recombineering methods, including CRISPR/Cas9-assisted methods, generally require cloning steps and/or complex PCR schemes for specific targeting of the genome. Here we describe the deletion of FRT scar-sites by the scarless Cas9-assisted recombineering method no-SCAR using an FRT-specific guide RNA, sgRNAFRT, and locus-specific ssDNA oligonucleotides. We applied this method to construct a scarless E. coli strain suitable for gradual induction by l-arabinose. Genome sequencing of the resulting strain and its parent strains demonstrated that no additional mutations were introduced along with the simultaneous deletion of two FRT scar-sites. The FRT-specific no-SCAR selection by sgRNAFRT/Cas9 may be generally applicable to cure FRT scar-sites of E. coli strains constructed by classical λ-Red recombineering.
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Affiliation(s)
- Aathmaja Anandhi Rangarajan
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany.,Present address: Department of Microbiology and Molecular Genetics, 5180 Biomedical and Physical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Cihan Yilmaz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
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15
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Logel DY, Trofimova E, Jaschke PR. Codon-Restrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters. ACS Synth Biol 2022; 11:689-699. [PMID: 35043622 DOI: 10.1021/acssynbio.1c00359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters, which may constitute up to a third of the predicted Escherichia coli promoters. The promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present codon-restrained promoter silencing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ70 promoters embedded within gene coding sequences with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.
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Affiliation(s)
- Dominic Y. Logel
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Ellina Trofimova
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
| | - Paul R. Jaschke
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2109, New South Wales, Australia
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16
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Ellington AJ, Reisch CR. Generating Single Nucleotide Point Mutations in E. coli with the No-SCAR System. Methods Mol Biol 2022; 2479:119-133. [PMID: 35583736 DOI: 10.1007/978-1-0716-2233-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genetic manipulation of microbial genomes is highly relevant for studying biological systems and the development of biotechnologies. In E. coli, λ-Red recombineering is one of the most widely used gene-editing methods, enabling site-specific insertions, deletions, and point mutations of any genomic locus. The no-SCAR system combines λ-Red recombineering with CRISPR/Cas9 for programmable selection of recombinant cells. Recombineering results in the transient production of heteroduplex DNA, as only one strand of DNA is initially altered, leaving the mismatched bases susceptible to repair by the host methyl-directed mismatch repair (MMR) system and reduces the efficiency of generating single nucleotide point mutations. Here we describe a method, where expression of cas9 and the MMR-inhibiting mutLE32K variant are independently controlled by anhydrotetracycline- and cumate-inducible promoters from the pCas9CyMutL plasmid. Thus, MMR is selectively inhibited until recombinant cells have undergone replication and the desired mutation is permanently incorporated. By transiently inhibiting MMR, the accumulation of off-target mutations typically associated with MMR-deficient cell types is minimized. Methods for designing the editing template and sgRNA, cloning of the sgRNA, induction of λ-Red and MutLE32K, the transformation of editing oligo, and induction of Cas9 for mutant selection are detailed within.
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Affiliation(s)
- Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Christopher R Reisch
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA.
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17
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Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X. Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria. Nucleic Acids Res 2021; 50:e15. [PMID: 34792175 PMCID: PMC8860599 DOI: 10.1093/nar/gkab1076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
Recombineering assisted multiplex genome editing generally uses single-stranded oligonucleotides for site directed mutational changes. It has proven highly efficient for functional screens and to optimize microbial cell factories. However, this approach is limited to relatively small mutational changes. Here, we addressed the challenges involved in the use of double-stranded DNA substrates for multiplex genome engineering. Recombineering is mediated by phage single-strand annealing proteins annealing ssDNAs into the replication fork. We apply this insight to facilitate the generation of ssDNA from the dsDNA substrate and to alter the speed of replication by elevating the available deoxynucleoside triphosphate (dNTP) levels. Intracellular dNTP concentration was elevated by ribonucleotide reductase overexpression or dNTP addition to establish double-stranded DNA Recombineering-assisted Multiplex Genome Engineering (dReaMGE), which enables rapid and flexible insertional and deletional mutagenesis at multiple sites on kilobase scales in diverse bacteria without the generation of double-strand breaks or disturbance of the mismatch repair system. dReaMGE can achieve combinatorial genome engineering works, for example, alterations to multiple biosynthetic pathways, multiple promoter or gene insertions, variations of transcriptional regulator combinations, within a few days. dReaMGE adds to the repertoire of bacterial genome engineering to facilitate discovery, functional genomics, strain optimization and directed evolution of microbial cell factories.
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Affiliation(s)
- Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Wentao Zheng
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Qiang Tu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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18
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Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife 2021; 10:70619. [PMID: 34382933 PMCID: PMC8384417 DOI: 10.7554/elife.70619] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here, we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jae-Yeon Hwang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
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19
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Deacylated tRNA Accumulation Is a Trigger for Bacterial Antibiotic Persistence Independent of the Stringent Response. mBio 2021; 12:e0113221. [PMID: 34126764 PMCID: PMC8262941 DOI: 10.1128/mbio.01132-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial antibiotic persistence occurs when bacteria are treated with an antibiotic and the majority of the population rapidly dies off, but a small subpopulation enters into a dormant, persistent state and evades death. Diverse pathways leading to nucleoside triphosphate (NTP) depletion and restricted translation have been implicated in persistence, suggesting alternative redundant routes may exist to initiate persister formation. To investigate the molecular mechanism of one such pathway, functional variants of an essential component of translation (phenylalanyl-tRNA synthetase [PheRS]) were used to study the effects of quality control on antibiotic persistence. Upon amino acid limitation, elevated PheRS quality control led to significant decreases in aminoacylated tRNAPhe accumulation and increased antibiotic persistence. This increase in antibiotic persistence was most pronounced (65-fold higher) when the relA-encoded tRNA-dependent stringent response was inactivated. The increase in persistence with elevated quality control correlated with ∼2-fold increases in the levels of the RNase MazF and the NTPase MazG and a 3-fold reduction in cellular NTP pools. These data reveal a mechanism for persister formation independent of the stringent response where reduced translation capacity, as indicated by reduced levels of aminoacylated tRNA, is accompanied by active reduction of cellular NTP pools which in turn triggers antibiotic persistence. IMPORTANCE Bacterial antibiotic persistence is a transient physiological state wherein cells become dormant and thereby evade being killed by antibiotics. Once the antibiotic is removed, bacterial persisters are able to resuscitate and repopulate. It is thought that antibiotic bacterial persisters may cause reoccurring infections in the clinical setting. The molecular triggers and pathways that cause bacteria to enter into the persister state are not fully understood. Our results suggest that accumulation of deacylated tRNA is a trigger for antibiotic persistence independent of the RelA-dependent stringent response, a pathway thought to be required for persistence in many organisms. Overall, this provides a mechanism where changes in translation quality control in response to physiological cues can directly modulate bacterial persistence.
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20
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Wahlig TA, Stanton E, Godfrey JJ, Stasic AJ, Wong ACL, Kaspar CW. A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40. Front Microbiol 2021; 12:671453. [PMID: 34149657 PMCID: PMC8208086 DOI: 10.3389/fmicb.2021.671453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
The outer membrane of Salmonella enterica plays an important role in combating stress encountered in the environment and hosts. The transport and insertion of lipopolysaccharides (LPS) into the outer membrane involves lipopolysaccharide transport proteins (LptA-F) and mutations in the genes encoding for these proteins are often lethal or result in the transport of atypical LPS that can alter stress tolerance in bacteria. During studies of heterogeneity in bile salts tolerance, S. enterica serovar Typhimurium E40 was segregated into bile salts tolerant and sensitive cells by screening for growth in TSB with 10% bile salts. An isolate (E40V) with a bile salts MIC >20% was selected for further characterization. Whole-genome sequencing of E40 and E40V using Illumina and PacBio SMRT technologies revealed a non-synonymous single nucleotide polymorphism (SNP) in lptG. Leucine at residue 26 in E40 was substituted with proline in E40V. In addition to growth in the presence of 10% bile salts, E40V was susceptible to novobiocin while E40 was not. Transcriptional analysis of E40 and E40V, in the absence of bile salts, revealed significantly greater (p < 0.05) levels of transcript in three genes in E40V; yjbE (encoding for an extracellular polymeric substance production protein), yciE (encoding for a putative stress response protein), and an uncharacterized gene annotated as an acid shock protein precursor (ASPP). No transcripts of genes were present at a greater level in E40 compared to E40V. Corresponding with the greater level of these transcripts, E40V had greater survival at pH 3.35 and staining of Calcofluor-binding polysaccharide (CBPS). To confirm the SNP in lptG was associated with these phenotypes, strain E40E was engineered from E40 to encode for the variant form of LptG (L26P). E40E exhibited the same differences in gene transcripts and phenotypes as E40V, including susceptibility to novobiocin, confirming the SNP was responsible for these differences.
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Affiliation(s)
- Taylor A Wahlig
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Eliot Stanton
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Jared J Godfrey
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Andrew J Stasic
- U. S. Food and Drug Administration, Center for Biologics Evaluation and Research, Washington, DC, United States
| | - Amy C L Wong
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Charles W Kaspar
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
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21
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- 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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22
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Wilkens D, Meusinger R, Hein S, Simon J. Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea. Environ Microbiol 2020; 23:1407-1421. [PMID: 33264482 DOI: 10.1111/1462-2920.15344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Reinhard Meusinger
- Department of Chemistry, Macromolecular Chemistry, Technical University of Darmstadt, Alarich-Weiss-Str. 4, Darmstadt, 64287, Germany
| | - Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, 64283, Germany
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23
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Yilmaz C, Rangarajan AA, Schnetz K. The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli. J Bacteriol 2020; 203:JB.00427-20. [PMID: 33318048 PMCID: PMC8095459 DOI: 10.1128/jb.00427-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
PdeL is a transcription regulator and catalytically active c-di-GMP phosphodiesterases (PDE) in Escherichia coli PdeL has been shown to be a transcription autoregulator, while no other target genes have been identified so far. Here, we show that PdeL represses transcription of the flagella class II operon, fliFGHIJK, and activates sslE encoding an extracellular anchored metalloprotease, among additional loci. DNA-binding studies and expression analyses using plasmidic reporters suggest that regulation of the fliF and sslE promoters by PdeL is direct. Transcription repression of the fliFGHIJK operon, encoding protein required for assembly of the flagellar basal body, results in inhibition of motility on soft agar plates and reduction of flagella assembly, as shown by fluorescence staining of the flagella hook protein FlgE. PdeL-mediated repression of motility is independent of its phosphodiesterase activity. Thus, in motility control the transcription regulator function of PdeL reducing the number of assembled flagella is apparently epistatic to its phosphodiesterase function, which can indirectly promote the activity of the flagellar motor by lowering the c-di-GMP concentration.Bacteria adopt different lifestyles depending on their environment and physiological condition. In Escherichia coli and other enteric bacteria the transition between the motile and the sessile state is controlled at multiple levels from the regulation of gene expression to the modulation of various processes by the second messenger c-di-GMP as signaling molecule. The significance of our research is in identifying PdeL, a protein of dual function that hydrolyzes c-di-GMP and that regulates transcription of genes, as a repressor of Flagella gene expression and an inhibitor of motility, which adds an additional regulatory switch to the control of motility.
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Affiliation(s)
- Cihan Yilmaz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
| | | | - Karin Schnetz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
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24
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Kelly P, Kavoor A, Ibba M. Fine-Tuning of Alanyl-tRNA Synthetase Quality Control Alleviates Global Dysregulation of the Proteome. Genes (Basel) 2020; 11:genes11101222. [PMID: 33081015 PMCID: PMC7603204 DOI: 10.3390/genes11101222] [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: 09/25/2020] [Revised: 10/10/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022] Open
Abstract
One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have evolved mechanisms to prevent erroneous aa-tRNA formation with non-cognate amino acid substrates. Of particular interest is the post-transfer proofreading activity of alanyl-tRNA synthetase (AlaRS) which prevents the accumulation of Ser-tRNAAla and Gly-tRNAAla in the cell. We have previously shown that defects in AlaRS proofreading of Ser-tRNAAla lead to global dysregulation of the E. coli proteome, subsequently causing defects in growth, motility, and antibiotic sensitivity. Here we report second-site AlaRS suppressor mutations that alleviate the aforementioned phenotypes, revealing previously uncharacterized residues within the AlaRS proofreading domain that function in quality control.
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Affiliation(s)
- Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
| | - Arundhati Kavoor
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; (P.K.); (A.K.)
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Correspondence: ; Tel.: +1-714-516-5235
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25
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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26
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Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. J Bacteriol 2020; 202:JB.00133-20. [PMID: 32341074 DOI: 10.1128/jb.00133-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/21/2020] [Indexed: 01/24/2023] Open
Abstract
Bacteria synthesize inorganic polyphosphate (polyP) in response to a variety of different stress conditions. polyP protects bacteria by acting as a protein-stabilizing chaperone, metal chelator, or regulator of protein function, among other mechanisms. However, little is known about how stress signals are transmitted in the cell to lead to increased polyP accumulation. Previous work in the model enterobacterium Escherichia coli has indicated that the RNA polymerase-binding regulatory protein DksA is required for polyP synthesis in response to nutrient limitation stress. In this work, I set out to characterize the role of DksA in polyP regulation in more detail. I found that overexpression of DksA increases cellular polyP content (explaining the long-mysterious phenotype of dksA overexpression rescuing growth of a dnaK mutant at high temperatures) and characterized the roles of known functional residues of DksA in this process, finding that binding to RNA polymerase is required but that none of the other functions of DksA appear to be necessary. Transcriptomics revealed genome-wide transcriptional changes upon nutrient limitation, many of which were affected by DksA, and follow-up experiments identified complex interactions between DksA and the stress-sensing alternative sigma factors FliA, RpoN, and RpoE that impact polyP production, indicating that regulation of polyP synthesis is deeply entwined in the multifactorial stress response network of E. coli IMPORTANCE Inorganic polyphosphate (polyP) is an evolutionarily ancient, widely conserved biopolymer required for stress resistance and pathogenesis in diverse bacteria, but we do not understand how its synthesis is regulated. In this work, I gained new insights into this process by characterizing the role of the transcriptional regulator DksA in polyP regulation in Escherichia coli and identifying previously unknown links between polyP synthesis and the stress-responsive alternative sigma factors FliA, RpoN, and RpoE.
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27
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Valderrama JA, Kulkarni SS, Nizet V, Bier E. A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus. Nat Commun 2019; 10:5726. [PMID: 31844051 PMCID: PMC6915771 DOI: 10.1038/s41467-019-13649-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Gene-drive systems in diploid organisms bias the inheritance of one allele over another. CRISPR-based gene-drive expresses a guide RNA (gRNA) into the genome at the site where the gRNA directs Cas9-mediated cleavage. In the presence of Cas9, the gRNA cassette and any linked cargo sequences are copied via homology-directed repair (HDR) onto the homologous chromosome. Here, we develop an analogous CRISPR-based gene-drive system for the bacterium Escherichia coli that efficiently copies a gRNA cassette and adjacent cargo flanked with sequences homologous to the targeted gRNA/Cas9 cleavage site. This "pro-active" genetic system (Pro-AG) functionally inactivates an antibiotic resistance marker on a high copy number plasmid with ~ 100-fold greater efficiency than control CRISPR-based methods, suggesting an amplifying positive feedback loop due to increasing gRNA dosage. Pro-AG can likewise effectively edit large plasmids or single-copy genomic targets or introduce functional genes, foreshadowing potential applications to biotechnology or biomedicine.
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Affiliation(s)
- J Andrés Valderrama
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
- Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Surashree S Kulkarni
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA.
- Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.
| | - Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA.
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA.
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28
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Kopp J, Slouka C, Spadiut O, Herwig C. The Rocky Road From Fed-Batch to Continuous Processing With E. coli. Front Bioeng Biotechnol 2019; 7:328. [PMID: 31824931 PMCID: PMC6880763 DOI: 10.3389/fbioe.2019.00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli still serves as a beloved workhorse for the production of many biopharmaceuticals as it fulfills essential criteria, such as having fast doubling times, exhibiting a low risk of contamination, and being easy to upscale. Most industrial processes in E. coli are carried out in fed-batch mode. However, recent trends show that the biotech industry is moving toward time-independent processing, trying to improve the space-time yield, and especially targeting constant quality attributes. In the 1950s, the term "chemostat" was introduced for the first time by Novick and Szilard, who followed up on the previous work performed by Monod. Chemostat processing resulted in a major hype 10 years after its official introduction. However, enthusiasm decreased as experiments suffered from genetic instabilities and physiology issues. Major improvements in strain engineering and the usage of tunable promotor systems facilitated chemostat processes. In addition, critical process parameters have been identified, and the effects they have on diverse quality attributes are understood in much more depth, thereby easing process control. By pooling the knowledge gained throughout the recent years, new applications, such as parallelization, cascade processing, and population controls, are applied nowadays. However, to control the highly heterogeneous cultivation broth to achieve stable productivity throughout long-term cultivations is still tricky. Within this review, we discuss the current state of E. coli fed-batch process understanding and its tech transfer potential within continuous processing. Furthermore, the achievements in the continuous upstream applications of E. coli and the continuous downstream processing of intracellular proteins will be discussed.
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Affiliation(s)
- Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
| | - Christoph Slouka
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
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29
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Psonis JJ, Chahales P, Henderson NS, Rigel NW, Hoffman PS, Thanassi DG. The small molecule nitazoxanide selectively disrupts BAM-mediated folding of the outer membrane usher protein. J Biol Chem 2019; 294:14357-14369. [PMID: 31391254 PMCID: PMC6768635 DOI: 10.1074/jbc.ra119.009616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial pathogens assemble adhesive surface structures termed pili or fimbriae to initiate and sustain infection of host tissues. Uropathogenic Escherichia coli, the primary causative agent of urinary tract infections, expresses type 1 and P pili required for colonization of the bladder and kidney, respectively. These pili are assembled by the conserved chaperone-usher (CU) pathway, in which a periplasmic chaperone works together with an outer membrane (OM) usher protein to build and secrete the pilus fiber. Previously, we found that the small molecule and antiparasitic drug nitazoxanide (NTZ) inhibits CU pathway-mediated pilus biogenesis in E. coli by specifically interfering with proper maturation of the usher protein in the OM. The usher is folded and inserted into the OM by the β-barrel assembly machine (BAM) complex, which in E. coli comprises five proteins, BamA-E. Here, we show that sensitivity of the usher to NTZ is modulated by BAM expression levels and requires the BamB and BamE lipoproteins. Furthermore, a genetic screen for NTZ-resistant bacterial mutants isolated a mutation in the essential BamD lipoprotein. These findings suggest that NTZ selectively interferes with an usher-specific arm of the BAM complex, revealing new details of the usher folding pathway and BAM complex function. Evaluation of a set of NTZ derivatives identified compounds with increased potency and disclosed that NTZ's nitrothiazole ring is critical for usher inhibition. In summary, our findings indicate highly specific effects of NTZ on the usher folding pathway and have uncovered NTZ analogs that specifically decrease usher levels in the OM.
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Affiliation(s)
- John J Psonis
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Peter Chahales
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Nadine S Henderson
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
| | - Nathan W Rigel
- Department of Biology, Hofstra University, Hempstead, New York 11549
| | - Paul S Hoffman
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia 22908
| | - David G Thanassi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794
- Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794
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30
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Srinivas S, Hu Z, Cronan JE. Escherichia coli vectors having stringently repressible replication origins allow a streamlining of Crispr/Cas9 gene editing. Plasmid 2019; 103:53-62. [PMID: 31047915 PMCID: PMC7260698 DOI: 10.1016/j.plasmid.2019.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 02/05/2023]
Abstract
Readily curable plasmids facilitate the construction of plasmid-free bacterial strains after the plasmid encoded genes are no longer needed. The most popular of these plasmids features a temperature-sensitive (Ts) pSC101 origin of replication which can readily revert during usage and cannot be used to construct Ts mutations in essential genes. Plasmid pAM34 which contains an IPTG-dependent origin of replication largely overcomes this issue but is limited by carrying the most commonly utilized antibiotic selection and replication origin. This study describes the construction of an expanded series of plasmid vectors having replication origins of p15a, RSF1030 or RSF1031 that like pAM34 have IPTG-dependent replication. Surprisingly, these plasmids can be cured in fewer generations than pAM34. Derivatives of pAM34 with alternative antibiotic selection markers were also constructed. The utility of these vectors is demonstrated in the construction of a CRISPR-Cas9 system consisting of an IPTG-dependent Cas9 plasmid and a curable guide RNA plasmid having a streptomycin counterselection marker. This system was successfully demonstrated by construction of point mutations, deletions and insertions in the E. coli genome with a very high efficiency and in a shorter timescale than extant methods. The plasmids themselves were readily cured either together or singly from the resultant strains with minimal effort.
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Affiliation(s)
- Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Zhe Hu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America.
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31
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Li P, Lin H, Mi Z, Xing S, Tong Y, Wang J. Screening of Polyvalent Phage-Resistant Escherichia coli Strains Based on Phage Receptor Analysis. Front Microbiol 2019; 10:850. [PMID: 31105661 PMCID: PMC6499177 DOI: 10.3389/fmicb.2019.00850] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/02/2019] [Indexed: 01/21/2023] Open
Abstract
Bacteria-based biotechnology processes are constantly under threat from bacteriophage infection, with phage contamination being a non-neglectable problem for microbial fermentation. The essence of this problem is the complex co-evolutionary relationship between phages and bacteria. The development of phage control strategies requires further knowledge about phage-host interactions, while the widespread use of Escherichia coli strain BL21 (DE3) in biotechnological processes makes the study of phage receptors in this strain particularly important. Here, eight phages infecting E. coli BL21 (DE3) via different receptors were isolated and subsequently identified as members of the genera T4virus, Js98virus, Felix01virus, T1virus, and Rtpvirus. Phage receptors were identified by whole-genome sequencing of phage-resistant E. coli strains and sequence comparison with wild-type BL21 (DE3). Results showed that the receptors for the isolated phages, designated vB_EcoS_IME18, vB_EcoS_IME253, vB_EcoM_IME281, vB_EcoM_IME338, vB_EcoM_IME339, vB_EcoM_IME340, vB_EcoM_IME341, and vB_EcoS_IME347 were FhuA, FepA, OmpF, lipopolysaccharide, Tsx, OmpA, FadL, and YncD, respectively. A polyvalent phage-resistant BL21 (DE3)-derived strain, designated PR8, was then identified by screening with a phage cocktail consisting of the eight phages. Strain PR8 is resistant to 23 of 32 tested phages including Myoviridae and Siphoviridae phages. Strains BL21 (DE3) and PR8 showed similar expression levels of enhanced green fluorescent protein. Thus, PR8 may be used as a phage resistant strain for fermentation processes. The findings of this study contribute significantly to our knowledge of phage-host interactions and may help prevent phage contamination in fermentation.
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Affiliation(s)
- Ping Li
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China.,State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hong Lin
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaozhen Xing
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,Department of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jingxue Wang
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China
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32
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Erian AM, Gibisch M, Pflügl S. Engineered E. coli W enables efficient 2,3-butanediol production from glucose and sugar beet molasses using defined minimal medium as economic basis. Microb Cell Fact 2018; 17:190. [PMID: 30501633 PMCID: PMC6267845 DOI: 10.1186/s12934-018-1038-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 12/03/2022] Open
Abstract
Background Efficient microbial production of chemicals is often hindered by the cytotoxicity of the products or by the pathogenicity of the host strains. Hence 2,3-butanediol, an important drop-in chemical, is an interesting alternative target molecule for microbial synthesis since it is non-cytotoxic. Metabolic engineering of non-pathogenic and industrially relevant microorganisms, such as Escherichia coli, have already yielded in promising 2,3-butanediol titers showing the potential of microbial synthesis of 2,3-butanediol. However, current microbial 2,3-butanediol production processes often rely on yeast extract as expensive additive, rendering these processes infeasible for industrial production. Results The aim of this study was to develop an efficient 2,3-butanediol production process with E. coli operating on the premise of using cost-effective medium without complex supplements, considering second generation feedstocks. Different gene donors and promoter fine-tuning allowed for construction of a potent E. coli strain for the production of 2,3-butanediol as important drop-in chemical. Pulsed fed-batch cultivations of E. coli W using microaerobic conditions showed high diol productivity of 4.5 g l−1 h−1. Optimizing oxygen supply and elimination of acetoin and by-product formation improved the 2,3-butanediol titer to 68 g l−1, 76% of the theoretical maximum yield, however, at the expense of productivity. Sugar beet molasses was tested as a potential substrate for industrial production of chemicals. Pulsed fed-batch cultivations produced 56 g l−1 2,3-butanediol, underlining the great potential of E. coli W as production organism for high value-added chemicals. Conclusion A potent 2,3-butanediol producing E. coli strain was generated by considering promoter fine-tuning to balance cell fitness and production capacity. For the first time, 2,3-butanediol production was achieved with promising titer, rate and yield and no acetoin formation from glucose in pulsed fed-batch cultivations using chemically defined medium without complex hydrolysates. Furthermore, versatility of E. coli W as production host was demonstrated by efficiently converting sucrose from sugar beet molasses into 2,3-butanediol. Electronic supplementary material The online version of this article (10.1186/s12934-018-1038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Maria Erian
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Martin Gibisch
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria.
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33
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Li P, Lin H, Mi Z, Tong Y, Wang J. vB_EcoS_IME347 a novel T1-like Escherichia coli bacteriophage. J Basic Microbiol 2018; 58:968-976. [PMID: 30146706 DOI: 10.1002/jobm.201800271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 01/21/2023]
Abstract
Advances in phage therapy and its application require more information on phage genome characteristics and host-phage interaction mechanisms. In this study, a so far unknown T1-like Escherichia coli phage was identified and named vB_EcoS_IME347 (IME347). The genome length of phage IME347 is 50,048 bp with a G + C content of 49.7%. BLASTn alignment showed that the phage has its highest homology (identity 78%, query cover 72%) with phage SRT8 (GenBank: MF996376). Electron microscopy showed that phage IME347 has an icosahedral head and a long non-contractiled tail, features of the family Siphoviridae. Phylogenetic analysis of the large subunit of the terminal enzyme and tail fiber protein revealed that phage IME347 is a novel member of the T1 virus. Furthermore, through comparative genomics, silencing mutation, phage spotting assay, and phage adsorption assay, an E. coli BL21 TonB-dependent receptor YncD was identified to be responsible for phage IME347 adsorption and entry. The identification of the phage receptor YncD enriches the phage receptor database and provides a theoretical basis for bacteriophage therapy.
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Affiliation(s)
- Ping Li
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hong Lin
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingxue Wang
- Food Safety Laboratory, Department of Food Science and Engineering, Ocean University of China, Qingdao, China
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34
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Pellock S, Creekmore BC, Walton WG, Mehta N, Biernat KA, Cesmat AP, Ariyarathna Y, Dunn ZD, Li B, Jin J, James LI, Redinbo MR. Gut Microbial β-Glucuronidase Inhibition via Catalytic Cycle Interception. ACS CENTRAL SCIENCE 2018; 4:868-879. [PMID: 30062115 PMCID: PMC6062831 DOI: 10.1021/acscentsci.8b00239] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 05/10/2023]
Abstract
Microbial β-glucuronidases (GUSs) cause severe gut toxicities that limit the efficacy of cancer drugs and other therapeutics. Selective inhibitors of bacterial GUS have been shown to alleviate these side effects. Using structural and chemical biology, mass spectrometry, and cell-based assays, we establish that piperazine-containing GUS inhibitors intercept the glycosyl-enzyme catalytic intermediate of these retaining glycosyl hydrolases. We demonstrate that piperazine-based compounds are substrate-dependent GUS inhibitors that bind to the GUS-GlcA catalytic intermediate as a piperazine-linked glucuronide (GlcA, glucuronic acid). We confirm the GUS-dependent formation of inhibitor-glucuronide conjugates by LC-MS and show that methylated piperazine analogs display significantly reduced potencies. We further demonstrate that a range of approved piperazine- and piperidine-containing drugs from many classes, including those for the treatment of depression, infection, and cancer, function by the same mechanism, and we confirm through gene editing that these compounds selectively inhibit GUS in living bacterial cells. Together, these data reveal a unique mechanism of GUS inhibition and show that a range of therapeutics may impact GUS activities in the human gut.
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Affiliation(s)
- Samuel
J. Pellock
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Benjamin C. Creekmore
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William G. Walton
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Naimee Mehta
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kristen A. Biernat
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew P. Cesmat
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yamuna Ariyarathna
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Zachary D. Dunn
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jian Jin
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mt. Sinai, New York, New York 10029, United States
| | - Lindsey I. James
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew R. Redinbo
- Department
of Chemistry, Center for Integrated Chemical Biology and Drug Discovery,
Eshelman School of Pharmacy, and Integrated Program for Biological and Genome
Sciences, and Departments of Biochemistry and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- E-mail:
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35
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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