151
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Yang R, Santos Garcia D, Pérez Montaño F, da Silva GM, Zhao M, Jiménez Guerrero I, Rosenberg T, Chen G, Plaschkes I, Morin S, Walcott R, Burdman S. Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species. Front Microbiol 2019; 10:1400. [PMID: 31281298 PMCID: PMC6595937 DOI: 10.3389/fmicb.2019.01400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.
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Affiliation(s)
- Rongzhi Yang
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos Garcia
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco Pérez Montaño
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.,Department of Microbiology, University of Seville, Seville, Spain
| | - Gustavo Mateus da Silva
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mei Zhao
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Irene Jiménez Guerrero
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tally Rosenberg
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gong Chen
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Inbar Plaschkes
- Bioinformatics Unit, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Walcott
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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152
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Nguyen-Vo TP, Liang Y, Sankaranarayanan M, Seol E, Chun AY, Ashok S, Chauhan AS, Kim JR, Park S. Development of 3-hydroxypropionic-acid-tolerant strain of Escherichia coli W and role of minor global regulator yieP. Metab Eng 2019; 53:48-58. [DOI: 10.1016/j.ymben.2019.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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153
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Entry Exclusion of Conjugative Plasmids of the IncA, IncC, and Related Untyped Incompatibility Groups. J Bacteriol 2019; 201:JB.00731-18. [PMID: 30858294 DOI: 10.1128/jb.00731-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Conjugative plasmids of incompatibility group C (IncC), formerly known as A/C2, disseminate antibiotic resistance genes globally in diverse pathogenic species of Gammaproteobacteria. Salmonella genomic island 1 (SGI1) can be mobilized by IncC plasmids and was recently shown to reshape the conjugative type IV secretion system (T4SS) encoded by these plasmids to evade entry exclusion. Entry exclusion blocks DNA translocation between cells containing identical or highly similar plasmids. Here, we report that the protein encoded by the entry exclusion gene of IncC plasmids (eexC) mediates entry exclusion in recipient cells through recognition of the IncC-encoded TraGC protein in donor cells. Phylogenetic analyses based on EexC and TraGC homologs predicted the existence of at least three different exclusion groups among IncC-related conjugative plasmids. Mating assays using Eex proteins encoded by representative IncC and IncA (former A/C1) and related untyped plasmids confirmed these predictions and showed that the IncC and IncA plasmids belong to the C exclusion group, thereby explaining their apparent incompatibility despite their compatible replicons. Representatives of the two other exclusion groups (D and E) are untyped conjugative plasmids found in Aeromonas sp. Finally, we determined through domain swapping that the carboxyl terminus of the EexC and EexE proteins controls the specificity of these exclusion groups. Together, these results unravel the role of entry exclusion in the apparent incompatibility between IncA and IncC plasmids while shedding light on the importance of the TraG subunit substitution used by SGI1 to evade entry exclusion.IMPORTANCE IncA and IncC conjugative plasmids drive antibiotic resistance dissemination among several pathogenic species of Gammaproteobacteria due to the diversity of drug resistance genes that they carry and their ability to mobilize antibiotic resistance-conferring genomic islands such as SGI1 of Salmonella enterica While historically grouped as "IncA/C," IncA and IncC replicons were recently confirmed to be compatible and to abolish each other's entry into the cell in which they reside during conjugative transfer. The significance of our study is in identifying an entry exclusion system that is shared by IncA and IncC plasmids. It impedes DNA transfer to recipient cells bearing a plasmid of either incompatibility group. The entry exclusion protein of this system is unrelated to any other known entry exclusion proteins.
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154
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Egbert RG, Rishi HS, Adler BA, McCormick DM, Toro E, Gill RT, Arkin AP. A versatile platform strain for high-fidelity multiplex genome editing. Nucleic Acids Res 2019; 47:3244-3256. [PMID: 30788501 PMCID: PMC6451135 DOI: 10.1093/nar/gkz085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/13/2018] [Accepted: 02/09/2019] [Indexed: 12/01/2022] Open
Abstract
Precision genome editing accelerates the discovery of the genetic determinants of phenotype and the engineering of novel behaviors in organisms. Advances in DNA synthesis and recombineering have enabled high-throughput engineering of genetic circuits and biosynthetic pathways via directed mutagenesis of bacterial chromosomes. However, the highest recombination efficiencies have to date been reported in persistent mutator strains, which suffer from reduced genomic fidelity. The absence of inducible transcriptional regulators in these strains also prevents concurrent control of genome engineering tools and engineered functions. Here, we introduce a new recombineering platform strain, BioDesignER, which incorporates (i) a refactored λ-Red recombination system that reduces toxicity and accelerates multi-cycle recombination, (ii) genetic modifications that boost recombination efficiency, and (iii) four independent inducible regulators to control engineered functions. These modifications resulted in single-cycle recombineering efficiencies of up to 25% with a 7-fold increase in recombineering fidelity compared to the widely used recombineering strain EcNR2. To facilitate genome engineering in BioDesignER, we have curated eight context--neutral genomic loci, termed Safe Sites, for stable gene expression and consistent recombination efficiency. BioDesignER is a platform to develop and optimize engineered cellular functions and can serve as a model to implement comparable recombination and regulatory systems in other bacteria.
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Affiliation(s)
- Robert G Egbert
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harneet S Rishi
- Biophysics Graduate Group, University of California - Berkeley, Berkeley, CA 94720, USA
- Designated Emphasis Program in Computational and Genomic Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Benjamin A Adler
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dylan M McCormick
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Esteban Toro
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
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155
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Caldwell BJ, Bell CE. Structure and mechanism of the Red recombination system of bacteriophage λ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:33-46. [PMID: 30904699 DOI: 10.1016/j.pbiomolbio.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA; Department of Chemistry and Biochemistry, 484 West 12th Avenue, 1060 Carmack Road, Columbus, OH, 43210, USA.
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156
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Spanka DT, Konzer A, Edelmann D, Berghoff BA. High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells. Front Microbiol 2019; 10:378. [PMID: 30894840 PMCID: PMC6414554 DOI: 10.3389/fmicb.2019.00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial populations produce phenotypic variants called persisters to survive harmful conditions. Persisters are highly tolerant to antibiotics and repopulate environments after the stress has vanished. In order to resume growth, persisters have to recover from the persistent state, but the processes behind recovery remain mostly elusive. Deciphering these processes is an essential step toward understanding the persister phenomenon in its entirety. High-throughput proteomics by mass spectrometry is a valuable tool to assess persister physiology during any stage of the persister life cycle, and is expected to considerably contribute to our understanding of the recovery process. In the present study, an Escherichia coli strain, that overproduces the membrane-depolarizing toxin TisB, was established as a model for persistence by the use of high-throughput proteomics. Labeling of TisB persisters with stable isotope-containing amino acids (pulsed-SILAC) revealed an active translational response to ampicillin, including several RpoS-dependent proteins. Subsequent investigation of the persister proteome during postantibiotic recovery by label-free quantitative proteomics identified proteins with importance to the recovery process. Among them, AhpF, a component of alkyl hydroperoxide reductase, and the outer membrane porin OmpF were found to affect the persistence time of TisB persisters. Assessing the role of AhpF and OmpF in TisB-independent persisters demonstrated that the importance of a particular protein for the recovery process strongly depends on the physiological condition of a persister cell. Our study provides important insights into persister physiology and the processes behind recovery of depolarized cells.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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157
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DncV Synthesizes Cyclic GMP-AMP and Regulates Biofilm Formation and Motility in Escherichia coli ECOR31. mBio 2019; 10:mBio.02492-18. [PMID: 30837338 PMCID: PMC6401482 DOI: 10.1128/mbio.02492-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ability of bacteria to sense and respond to environmental signals is critical for survival. Bacteria use cyclic dinucleotides as second messengers to regulate a number of physiological processes, such as the fundamental life style transition between motility and sessility (biofilm formation). cGAMP, which is synthesized by a dinucleotide cyclase called DncV, is a newly discovered second messenger involved in virulence and chemotaxis in the Vibrio cholerae biovar El Tor causing the current 7th cholera pandemic. However, to what extent cGAMP exists and participates in physiological processes in other bacteria is still unknown. In this study, we found an elevated cGAMP level to possibly regulate biofilm formation and motility in the animal commensal E. coli strain ECOR31. Thus, we detected a novel role for cGAMP signaling in regulation of physiological processes other than those previously reported in proteobacterial species. Cyclic dinucleotides (cDNs) act as intracellular second messengers, modulating bacterial physiology to regulate the fundamental life style transition between motility and sessility commonly known as biofilm formation. Cyclic GMP-AMP (cGAMP), synthesized by the dinucleotide cyclase DncV, is a newly discovered cDN second messenger involved in virulence and chemotaxis in Vibrio cholerae O1 biovar El Tor. Here we report a novel role for horizontally transferred DncV in cGAMP production and regulation of biofilm formation and motility in the animal commensal strain Escherichia coli ECOR31. ECOR31 expresses a semiconstitutive temperature-independent rdar (red, dry, and rough) morphotype on Congo red agar plates characterized by the extracellular matrix components cellulose and curli fimbriae which requires activation by the major biofilm regulator CsgD and cyclic di-GMP signaling. In contrast, C-terminal His-tagged DncV negatively regulates the rdar biofilm morphotype and cell aggregation via downregulation of csgD mRNA steady-state level. Furthermore, DncV sequentially promotes and inhibits adhesion to the abiotic surface after 24 h and 48 h of growth, respectively. DncV also suppresses swimming and swarming motility posttranscriptional of the class 1 flagellum regulon gene flhD. Purified DncV produced different cDNs, cyclic di-GMP, cyclic di-AMP, an unknown product(s), and the dominant species 3′3′-cGAMP. In vivo, only the 3′3′-cGAMP concentration was elevated upon short-term overexpression of dncV, making this work a first report on cGAMP production in E. coli. Regulation of rdar biofilm formation and motility upon overexpression of untagged DncV in combination with three adjacent cotransferred gene products suggests a novel temperature-dependent cGAMP signaling module in E. coli ECOR31.
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158
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Bürmann F, Lee BG, Than T, Sinn L, O'Reilly FJ, Yatskevich S, Rappsilber J, Hu B, Nasmyth K, Löwe J. A folded conformation of MukBEF and cohesin. Nat Struct Mol Biol 2019; 26:227-236. [PMID: 30833788 PMCID: PMC6433275 DOI: 10.1038/s41594-019-0196-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/25/2019] [Indexed: 11/09/2022]
Abstract
Structural maintenance of chromosomes (SMC)-kleisin complexes organize chromosomal DNAs in all domains of life, with key roles in chromosome segregation, DNA repair and regulation of gene expression. They function through the entrapment and active translocation of DNA, but the underlying conformational changes are largely unclear. Using structural biology, mass spectrometry and cross-linking, we investigated the architecture of two evolutionarily distant SMC-kleisin complexes: MukBEF from Escherichia coli, and cohesin from Saccharomyces cerevisiae. We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation. Bending at the elbow brings into proximity the hinge dimerization domain and the head-kleisin module, situated at opposite ends of the arms. Our findings favour SMC activity models that include a large conformational change in the arms, such as a relative movement between DNA contact sites during DNA loading and translocation.
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Affiliation(s)
| | | | - Thane Than
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Ludwig Sinn
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Stanislau Yatskevich
- Department of Biochemistry, University of Oxford, Oxford, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Bin Hu
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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159
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Zlatkov N, Uhlin BE. Absence of Global Stress Regulation in Escherichia coli Promotes Pathoadaptation and Novel c-di-GMP-dependent Metabolic Capability. Sci Rep 2019; 9:2600. [PMID: 30796316 PMCID: PMC6385356 DOI: 10.1038/s41598-019-39580-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/25/2019] [Indexed: 01/17/2023] Open
Abstract
Pathoadaptive mutations linked to c-di-GMP signalling were investigated in neonatal meningitis-causing Escherichia coli (NMEC). The results indicated that NMEC strains deficient in RpoS (the global stress regulator) maintained remarkably low levels of c-di-GMP, a major bacterial sessility-motility switch. Deletion of ycgG2, shown here to encode a YcgG allozyme with c-di-GMP phosphodiesterase activity, and the restoration of RpoS led to a decrease in S-fimbriae, robustly produced in artificial urine, hinting that the urinary tract could serve as a habitat for NMEC. We showed that NMEC were skilled in aerobic citrate utilization in the presence of glucose, a property that normally does not exist in E. coli. Our data suggest that this metabolic novelty is a property of extraintestinal pathogenic E. coli since we reconstituted this ability in E. coli UTI89 (a cystitis isolate) via deactivation rpoS; additionally, a set of pyelonephritis E. coli isolates were shown here to aerobically use citrate in the presence of glucose. We found that the main reason for this metabolic capability is RpoS inactivation leading to the production of the citrate transporter CitT, exploited by NMEC for ferric citrate uptake dependent on YcgG2 (an allozyme with c-di-GMP phosphodiesterase activity).
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Affiliation(s)
- Nikola Zlatkov
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umea, Sweden
| | - Bernt Eric Uhlin
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umea, Sweden.
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160
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Mitosch K, Rieckh G, Bollenbach T. Temporal order and precision of complex stress responses in individual bacteria. Mol Syst Biol 2019; 15:e8470. [PMID: 30765425 PMCID: PMC6375286 DOI: 10.15252/msb.20188470] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 12/28/2018] [Accepted: 01/22/2019] [Indexed: 01/27/2023] Open
Abstract
Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time-lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate-limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.
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Affiliation(s)
- Karin Mitosch
- IST Austria, Klosterneuburg, Austria
- EMBL Heidelberg, Heidelberg, Germany
| | - Georg Rieckh
- IST Austria, Klosterneuburg, Austria
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA
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161
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Chen W, Li Y, Wu G, Zhao L, Lu L, Wang P, Zhou J, Cao C, Li S. Simple and efficient genome recombineering using kil counter-selection in Escherichia coli. J Biotechnol 2019; 294:58-66. [PMID: 30768999 DOI: 10.1016/j.jbiotec.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 01/04/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Seamless modification of the Escherichia coli genome using positive selection / negative selection is widely used in metabolic engineering and functional genome analysis. Some excellent negative selection systems have been reported, of which tetA-sacB and inducible toxins system are prominent. To expand the existing negative selection toolkit, we constructed a new negative selection marker system based on kil gene of lambda prophage. The selection stringency of kil was measured and compared with the most widely used counter-selection gene, sacB, at the lacI, ack, and dbpa loci using different E. coli strains. At all these loci of tested strains, the selection stringency of kil significantly exceeds that of sacB by 2- to 28-fold. When dsDNA fragments were employed for recombination, the efficiency for isolating the correct recombinant of kil was significantly higher than that of sacB. This new negative selection system does not require special media or extended incubation time. However, our system cannot be used in host strains containing temperature-sensitive kil gene. A Red system providing plasmid without kil gene is recommended for use together with our system. Our counter-selection system is expected to be an addition to the engineering arsenal of E. coli.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China; Beijing Institute of Biotechnology, Beijing 100850, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guangjin Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lingfeng Zhao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Li Lu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Peng Wang
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Jianguang Zhou
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing 100850, China.
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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162
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Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R. Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol 2019; 15:e1006226. [PMID: 30716072 PMCID: PMC6375646 DOI: 10.1371/journal.pcbi.1006226] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 02/14/2019] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the central importance of transcriptional regulation in biology, it has proven difficult to determine the regulatory mechanisms of individual genes, let alone entire gene networks. It is particularly difficult to decipher the biophysical mechanisms of transcriptional regulation in living cells and determine the energetic properties of binding sites for transcription factors and RNA polymerase. In this work, we present a strategy for dissecting transcriptional regulatory sequences using in vivo methods (massively parallel reporter assays) to formulate quantitative models that map a transcription factor binding site’s DNA sequence to transcription factor-DNA binding energy. We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that our models can be used to design specific induction responses, analyze the effects of amino acid mutations on DNA sequence preference, and determine how regulatory context affects a transcription factor’s sequence specificity. It has been said that we live in the “genomic era,” a time where we can readily sequence full genomes at will. However, it remains difficult to interpret much of the information within a genome. This is especially true of non-coding sequences such as promoters, which contain a number of features such as transcription factor binding sites that determine how genes are regulated. There is no straightforward regulatory “code” that tells us how transcription factor binding sites are organized within a promoter. In this work we examine how DNA sequence determines one of the most important features of a promoter, the strength with which a transcription factor binds to its DNA binding site. We discuss an approach to modeling DNA sequence-specific transcription factor binding energies in vivo using a massively parellel reporter assay. We develop models that allow us to predict the binding energy between a transcription factor and a mutated version of its binding site. We then show that this modeling technique can be used to address a number of scientific and design questions, such as engineering the behavior of genetic circuit elements or examining how transcription factors and their binding sites co-evolve.
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Affiliation(s)
- Stephanie L. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nathan M. Belliveau
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - William T. Ireland
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Justin B. Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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163
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Ellis MJ, Tsai CN, Johnson JW, French S, Elhenawy W, Porwollik S, Andrews-Polymenis H, McClelland M, Magolan J, Coombes BK, Brown ED. A macrophage-based screen identifies antibacterial compounds selective for intracellular Salmonella Typhimurium. Nat Commun 2019; 10:197. [PMID: 30643129 PMCID: PMC6331611 DOI: 10.1038/s41467-018-08190-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Salmonella Typhimurium (S. Tm) establishes systemic infection in susceptible hosts by evading the innate immune response and replicating within host phagocytes. Here, we sought to identify inhibitors of intracellular S. Tm replication by conducting parallel chemical screens against S. Tm growing in macrophage-mimicking media and within macrophages. We identify several compounds that inhibit Salmonella growth in the intracellular environment and in acidic, ion-limited media. We report on the antimicrobial activity of the psychoactive drug metergoline, which is specific against intracellular S. Tm. Screening an S. Tm deletion library in the presence of metergoline reveals hypersensitization of outer membrane mutants to metergoline activity. Metergoline disrupts the proton motive force at the bacterial cytoplasmic membrane and extends animal survival during a systemic S. Tm infection. This work highlights the predictive nature of intracellular screens for in vivo efficacy, and identifies metergoline as a novel antimicrobial active against Salmonella.
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Affiliation(s)
- Michael J Ellis
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Jarrod W Johnson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697-4025, USA
| | - Helene Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, 8447 Riverside Pkwy, Bryan, TX, 77807, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697-4025, USA
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St W, Hamilton, ON, L8S 4K1, Canada.
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164
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Pines G, Oh EJ, Bassalo MC, Choudhury A, Garst AD, Fankhauser RG, Eckert CA, Gill RT. Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to the Antimalarial Drug Fosmidomycin in E. coli. ACS Synth Biol 2018; 7:2824-2832. [PMID: 30462485 DOI: 10.1021/acssynbio.8b00219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sequence to activity mapping technologies are rapidly developing, enabling the generation and isolation of mutations conferring novel phenotypes. Here we used the CRISPR enabled trackable genome engineering (CREATE) technology to investigate the inhibition of the essential ispC gene in its native genomic context in Escherichia coli. We created a full saturation library of 33 sites proximal to the ligand binding pocket and challenged this library with the antimalarial drug fosmidomycin, which targets the ispC gene product, DXR. This selection is especially challenging since it is relatively weak in E. coli, with multiple naturally occurring pathways for resistance. We identified several previously unreported mutations that confer fosmidomycin resistance, in highly conserved sites that also exist in pathogens including the malaria-inducing Plasmodium falciparum. This approach may have implications for the isolation of resistance-conferring mutations and may affect the design of future generations of fosmidomycin-based drugs.
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Affiliation(s)
- Gur Pines
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Marcelo C. Bassalo
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, 347 UCB, Boulder, Colorado 80309, United States
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Andrew D. Garst
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
| | - Reilly G. Fankhauser
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Ryan T. Gill
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, Colorado 80309, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, Colorado 80309, United States
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165
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Bassalo MC, Garst AD, Choudhury A, Grau WC, Oh EJ, Spindler E, Lipscomb T, Gill RT. Deep scanning lysine metabolism in Escherichia coli. Mol Syst Biol 2018; 14:e8371. [PMID: 30478237 PMCID: PMC6254735 DOI: 10.15252/msb.20188371] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
Our limited ability to predict genotype-phenotype relationships has called for strategies that allow testing of thousands of hypotheses in parallel. Deep scanning mutagenesis has been successfully implemented to map genotype-phenotype relationships at a single-protein scale, allowing scientists to elucidate properties that are difficult to predict. However, most phenotypes are dictated by several proteins that are interconnected through complex and robust regulatory and metabolic networks. These sophisticated networks hinder our understanding of the phenotype of interest and limit our capabilities to rewire cellular functions. Here, we leveraged CRISPR-EnAbled Trackable genome Engineering to attempt a parallel and high-resolution interrogation of complex networks, deep scanning multiple proteins associated with lysine metabolism in Escherichia coli We designed over 16,000 mutations to perturb this pathway and mapped their contribution toward resistance to an amino acid analog. By doing so, we identified different routes that can alter pathway function and flux, uncovering mechanisms that would be difficult to rationally design. This approach sets a framework for forward investigation of complex multigenic phenotypes.
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Affiliation(s)
- Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | | | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - William C Grau
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Eun J Oh
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Ryan T Gill
- Inscripta, Inc., Boulder, CO, USA
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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166
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Pu Y, Li Y, Jin X, Tian T, Ma Q, Zhao Z, Lin SY, Chen Z, Li B, Yao G, Leake MC, Lo CJ, Bai F. ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance. Mol Cell 2018; 73:143-156.e4. [PMID: 30472191 DOI: 10.1016/j.molcel.2018.10.022] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 09/07/2018] [Accepted: 10/15/2018] [Indexed: 01/06/2023]
Abstract
Cell dormancy is a widespread mechanism used by bacteria to evade environmental threats, including antibiotics. Here we monitored bacterial antibiotic tolerance and regrowth at the single-cell level and found that each individual survival cell shows different "dormancy depth," which in return regulates the lag time for cell resuscitation after removal of antibiotic. We further established that protein aggresome-a collection of endogenous protein aggregates-is an important indicator of bacterial dormancy depth, whose formation is promoted by decreased cellular ATP level. For cells to leave the dormant state and resuscitate, clearance of protein aggresome and recovery of proteostasis are required. We revealed that the ability to recruit functional DnaK-ClpB machineries, which facilitate protein disaggregation in an ATP-dependent manner, determines the lag time for bacterial regrowth. Better understanding of the key factors regulating bacterial regrowth after surviving antibiotic attack could lead to new therapeutic strategies for combating bacterial antibiotic tolerance.
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Affiliation(s)
- Yingying Pu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingxing Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Jin
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Tian Tian
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Qi Ma
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Ziyi Zhao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Ssu-Yuan Lin
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhong-Li, Taoyuan 32001, Republic of China
| | - Zhanghua Chen
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Binghui Li
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, Beijing 100069, China
| | - Guang Yao
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Mark C Leake
- Department of Physics, University of York, York YO10, UK; Department of Biology, University of York, York YO10, UK
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhong-Li, Taoyuan 32001, Republic of China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.
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167
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Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Res 2018; 46:10682-10696. [PMID: 30137486 PMCID: PMC6237786 DOI: 10.1093/nar/gky752] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/11/2018] [Accepted: 08/08/2018] [Indexed: 02/03/2023] Open
Abstract
Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been used to fully characterize only a few dozen. Identifying these remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive experimental validation of TFs using a suite of genome-wide experiments. We applied this workflow to (i) identify 16 candidate TFs from over a hundred uncharacterized genes; (ii) capture a total of 255 DNA binding peaks for ten candidate TFs resulting in six high-confidence binding motifs; (iii) reconstruct the regulons of these ten TFs by determining gene expression changes upon deletion of each TF and (iv) identify the regulatory roles of three TFs (YiaJ, YdcI, and YeiE) as regulators of l-ascorbate utilization, proton transfer and acetate metabolism, and iron homeostasis under iron-limited conditions, respectively. Together, these results demonstrate how this workflow can be used to discover, characterize, and elucidate regulatory functions of uncharacterized TFs in parallel.
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Affiliation(s)
- Ye Gao
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Yurkovich
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Ilyas Kabimoldayev
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), 72076 Tübingen, Germany
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Ke Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Xin Fang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nathan Mih
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Laurence Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Johannes Eichner
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), 72076 Tübingen, Germany
| | - Byung-Kwan Cho
- Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghyuk Kim
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, 2800 Kongens Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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168
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Liang L, Heveran C, Liu R, Gill RT, Nagarajan A, Cameron J, Hubler M, Srubar WV, Cook SM. Rational Control of Calcium Carbonate Precipitation by Engineered Escherichia coli. ACS Synth Biol 2018; 7:2497-2506. [PMID: 30384588 DOI: 10.1021/acssynbio.8b00194] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ureolytic bacteria ( e.g., Sporosarcina pasteurii) can produce calcium carbonate (CaCO3). Tailoring the size and shape of biogenic CaCO3 may increase the range of useful applications for these crystals. However, wild type Sporosarcina pasteurii is difficult to genetically engineer, limiting control of the organism and its crystal precipitates. Therefore, we designed, constructed, and compared different urease operons and expression levels for CaCO3 production in engineered Escherichia coli strains. We quantified urease expression and calcium uptake and characterized CaCO3 crystal phase and morphology for 13 engineered strains. There was a weak relationship between urease expression and crystal size, suggesting that genes surrounding the urease gene cluster affect crystal size. However, when evaluating strains with a wider range of urease expression levels, there was a negative relationship between urease activity and polycrystal size (e.g., larger crystals with lower activity). The resulting range of crystal morphologies created by the rationally designed strains demonstrates the potential for controlling biogenic CaCO3 precipitation.
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Affiliation(s)
| | | | | | | | | | - Jeffrey Cameron
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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169
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Nishikawa M, Shen L, Ogawa K. Taurine dioxygenase (tauD)-independent taurine assimilation in Escherichia coli. Microbiology (Reading) 2018; 164:1446-1456. [DOI: 10.1099/mic.0.000723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Masanobu Nishikawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
| | - Lianhua Shen
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
| | - Ken’ichi Ogawa
- Research Institute for Biological Sciences Okayama (RIBS Okayama), Japan
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170
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Single-Homology-Arm Linear DNA Recombination by the Nonhomologous End Joining Pathway as a Novel and Simple Gene Inactivation Method: a Proof-of-Concept Study in Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2018; 84:AEM.00795-18. [PMID: 30030230 DOI: 10.1128/aem.00795-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023] Open
Abstract
Nonhomologous end joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo Here, we established a proof-of-concept single-homology-arm linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate nonreplicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. strain DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA single homolog to the sequence in the chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% of prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, an Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for nonmodel microorganisms.IMPORTANCE Many nonmodel Gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knock out 11 genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the single-homology-arm linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse nonmodel prokaryotic organisms.
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171
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Anderson MT, Mitchell LA, Zhao L, Mobley HLT. Citrobacter freundii fitness during bloodstream infection. Sci Rep 2018; 8:11792. [PMID: 30087402 PMCID: PMC6081441 DOI: 10.1038/s41598-018-30196-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/24/2018] [Indexed: 12/16/2022] Open
Abstract
Sepsis resulting from microbial colonization of the bloodstream is a serious health concern associated with high mortality rates. The objective of this study was to define the physiologic requirements of Citrobacter freundii in the bloodstream as a model for bacteremia caused by opportunistic Gram-negative pathogens. A genetic screen in a murine host identified 177 genes that contributed significantly to fitness, the majority of which were broadly classified as having metabolic or cellular maintenance functions. Among the pathways examined, the Tat protein secretion system conferred the single largest fitness contribution during competition infections and a putative Tat-secreted protein, SufI, was also identified as a fitness factor. Additional work was focused on identifying relevant metabolic pathways for bacteria in the bloodstream environment. Mutations that eliminated the use of glucose or mannitol as carbon sources in vitro resulted in loss of fitness in the murine model and similar results were obtained upon disruption of the cysteine biosynthetic pathway. Finally, the conservation of identified fitness factors was compared within a cohort of Citrobacter bloodstream isolates and between Citrobacter and Serratia marcescens, the results of which suggest the presence of conserved strategies for bacterial survival and replication in the bloodstream environment.
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Affiliation(s)
- Mark T Anderson
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, MI, USA
| | - Lindsay A Mitchell
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, MI, USA
| | - Lili Zhao
- University of Michigan School of Public Health, Biostatistics Department, Ann Arbor, MI, USA
| | - Harry L T Mobley
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, MI, USA.
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172
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Murine cytomegalovirus M72 promotes acute virus replication in vivo and is a substrate of the TRiC/CCT complex. Virology 2018; 522:92-105. [PMID: 30029015 DOI: 10.1016/j.virol.2018.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/07/2018] [Indexed: 01/30/2023]
Abstract
Betaherpesvirus dUTPase homologs are core herpesvirus proteins, but little is known about their role during infection. Human cytomegalovirus (HCMV) UL72 and murine cytomegalovirus (MCMV) M72 have been designated dUTPase homologs, and previous studies indicate UL72 is dispensable for replication and enzymatically inactive. Here, we report the initial characterization of MCMV M72. M72 does not possess dUTPase activity, and is expressed as a leaky-late gene product with multiple protein isoforms. Importantly, M72 augments MCMV replication in vitro and during the early stage of acute infection in vivo. We identify and confirm interaction of M72 with the eukaryotic chaperonin tailless complex protein -1 (TCP-1) ring complex (TRiC) or chaperonin containing tailless complex polypeptide 1 (CCT). Accumulating biochemical evidence indicates M72 forms homo-oligomers and is a substrate of TRiC/CCT. Taken together, we provide the first evidence of M72's contribution to viral pathogenesis, and identify a novel interaction with the TRiC/CCT complex.
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173
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Hua M, Guo J, Li M, Chen C, Zhang Y, Song C, Jiang D, Du P, Zeng H. A Dual-Replicon Shuttle Vector System for Heterologous Gene Expression in a Broad Range of Gram-Positive and Gram-Negative Bacteria. Curr Microbiol 2018; 75:1391-1400. [PMID: 29987521 DOI: 10.1007/s00284-018-1535-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022]
Abstract
Origin of replication (ori in theta-replicating plasmids or dso in rolling circle replicating plasmids) initiates plasmid replication in a broad range of bacteria. These two kinds of plasmids were both identified in Streptococcus, a genus composed of both human commensal bacteria and pathogens with the ability to cause severe community-acquired infections, including meningitides, septicemia, and respiratory tract diseases. Given the important roles of Streptococcus in the exchange of genetic elements with other symbiotic microbes, the genotypes and phenotypes of both Streptococcus spp. and other symbiotic species could be changed during colonization of the host. Therefore, an improved plasmid system is required to study the functional, complicated, and changeable genomes of Streptococcus. In this study, a dual-replicon shuttle vector system named pDRE was constructed to achieve heterologous gene expression. The vector system contained theta replicon for Escherichia coli. The origin of rolling circle replicon was synthesized according to pMV158 in Gram-positive bacteria. By measuring the products of inserted genes at multiple cloning sites, the ability of this vector system in the replication and expression of heterologous genes was assessed in four Streptococcus and three other Gram-positive bacteria: Bacillus subtilis, Lactococcus lactis, and Staphylococcus aureus. The results showed that the newly constructed vector could simultaneously replicate and express heterologous genes in a broad range of Gram-positive and Gram-negative bacteria, thus providing a potentially powerful genetic tool for further functional analysis.
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Affiliation(s)
- Mingxi Hua
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Jingjing Guo
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Min Li
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Dong Jiang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
| | - Hui Zeng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
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174
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Deletion of pyruvate decarboxylase gene in Zymomonas mobilis by recombineering through bacteriophage lambda red genes. J Microbiol Methods 2018; 151:111-117. [PMID: 29958909 DOI: 10.1016/j.mimet.2018.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 11/22/2022]
Abstract
Zymomonas mobilis ZM4 is a gram negative ethanologenic bacterium used in several biotechnological applications. Metabolic engineering in this bacterium is limited because of the available genome engineering tools. In the present study, we report genome engineering in this bacterium using bacteriophage lambda Red genes. Stability of plasmid replicons RK2 (pSIM9) and pBBR1 (pSIM7) containing the lambda Red genes was found to be 78% and 74%, respectively. We demonstrate successful deletion of pyruvate decarboxylase gene by recombineering in Z. mobilis. The deletion was confirmed by PCR and by estimating the metabolites formed. Ethanol, which was the main product in wild type cells, was formed in almost negligible amount in the pdc-deleted mutant. The developed Δpdc Z. mobilis cells can be exploited for production of desired bioproducts by expression of suitable enzymes that can regenerate NAD+.
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175
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An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Commun Biol 2018; 1:66. [PMID: 30271948 PMCID: PMC6123781 DOI: 10.1038/s42003-018-0076-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/10/2018] [Indexed: 12/15/2022] Open
Abstract
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful production of a growing catalog of natural products and high-value chemicals. However, development at industrial levels has been hindered by the large resource investments required. Here we present an integrated Design–Build-Test–Learn (DBTL) pipeline for the discovery and optimization of biosynthetic pathways, which is designed to be compound agnostic and automated throughout. We initially applied the pipeline for the production of the flavonoid (2S)-pinocembrin in Escherichia coli, to demonstrate rapid iterative DBTL cycling with automation at every stage. In this case, application of two DBTL cycles successfully established a production pathway improved by 500-fold, with competitive titers up to 88 mg L−1. The further application of the pipeline to optimize an alkaloids pathway demonstrates how it could facilitate the rapid optimization of microbial strains for production of any chemical compound of interest. Pablo Carbonell et al. present an automated pipeline for the discovery and optimization of biosynthetic pathways for microbial production of fine chemicals. They apply their pipeline to the production of the flavonoid (2S)-pinocembrin in Escherichia coli and show improvement of the pathway by 500-fold.
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176
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Bubnov DM, Yuzbashev TV, Vybornaya TV, Netrusov AI, Sineoky SP. Development of new versatile plasmid-based systems for λRed-mediated Escherichia coli genome engineering. J Microbiol Methods 2018; 151:48-56. [PMID: 29885886 DOI: 10.1016/j.mimet.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/06/2018] [Accepted: 06/06/2018] [Indexed: 10/14/2022]
Abstract
Plasmid-based systems are the most appropriate for multistep lambda Red (λRed)-mediated recombineering, such as the assembly of strains for biotechnological applications. Currently, the widely used λRed-expressing plasmids use a temperature-sensitive origin of replication or temperature shift control of λRed expression. In this work, we have constructed a new, conditionally replicating vector that can be efficiently eliminated from the host strain through passaging in medium containing isopropyl-β-d-thiogalactopyranoside. Using the new vector, we have developed two improved helper plasmids (viz., pDL17 and pDL14) for dsDNA and oligonucleotide-mediated recombineering, respectively. The plasmid pDL14 contains a dominant negative mutSK622A allele that suppresses methyl-directed mismatch repair (MMR). The coexpression of λRed and mutSK622A provides efficient oligonucleotide-mediated recombineering in the presence of active host MMR. The expression of λRed was placed under the control of the tightly regulated PrhaB promoter. Because of their low expression level under uninduced conditions, both plasmids could be maintained without elimination for multiple recombineering steps. The temperature-independent replication of the plasmids and control of λRed expression by l-rhamnose allow for all procedures to be performed at 37 °C. Thus, the new plasmids are robust, convenient, and versatile tools for Escherichia coli genome editing.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia; Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills, 1-12, Moscow 119234, Russia.
| | - Tigran V Yuzbashev
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia.
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Alexander I Netrusov
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills, 1-12, Moscow 119234, Russia
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRCVKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia.
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177
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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178
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Abstract
Antibiotic-resistant bacteria represent a major threat to our ability to treat bacterial infections. Two factors that determine the evolutionary success of antibiotic resistance mutations are their impact on resistance level and the fitness cost. Recent studies suggest that resistance mutations commonly show epistatic interactions, which would complicate predictions of their stability in bacterial populations. We analyzed 13 different chromosomal resistance mutations and 10 host strains of Salmonella enterica and Escherichia coli to address two main questions. (i) Are there epistatic interactions between different chromosomal resistance mutations? (ii) How does the strain background and genetic distance influence the effect of chromosomal resistance mutations on resistance and fitness? Our results show that the effects of combined resistance mutations on resistance and fitness are largely predictable and that epistasis remains rare even when up to four mutations were combined. Furthermore, a majority of the mutations, especially target alteration mutations, demonstrate strain-independent phenotypes across different species. This study extends our understanding of epistasis among resistance mutations and shows that interactions between different resistance mutations are often predictable from the characteristics of the individual mutations. The spread of antibiotic-resistant bacteria imposes an urgent threat to public health. The ability to forecast the evolutionary success of resistant mutants would help to combat dissemination of antibiotic resistance. Previous studies have shown that the phenotypic effects (fitness and resistance level) of resistance mutations can vary substantially depending on the genetic context in which they occur. We conducted a broad screen using many different resistance mutations and host strains to identify potential epistatic interactions between various types of resistance mutations and to determine the effect of strain background on resistance phenotypes. Combinations of several different mutations showed a large amount of phenotypic predictability, and the majority of the mutations displayed strain-independent phenotypes. However, we also identified a few outliers from these patterns, illustrating that the choice of host organism can be critically important when studying antibiotic resistance mutations.
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179
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Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Metab Eng 2018; 47:463-474. [PMID: 29751103 DOI: 10.1016/j.ymben.2018.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 11/22/2022]
Abstract
Pseudomonas putida has gained much interest among metabolic engineers as a workhorse for producing valuable natural products. While a few gene knockout tools for P. putida have been reported, integration of heterologous genes into the chromosome of P. putida, an essential strategy to develop stable industrial strains producing heterologous bioproducts, requires development of a more efficient method. Current methods rely on time-consuming homologous recombination techniques and transposon-mediated random insertions. Here we report a RecET recombineering system for markerless integration of heterologous genes into the P. putida chromosome. The efficiency and capacity of the recombineering system were first demonstrated by knocking out various genetic loci on the P. putida chromosome with knockout lengths widely spanning 0.6-101.7 kb. The RecET recombineering system developed here allowed successful integration of biosynthetic gene clusters for four proof-of-concept bioproducts, including protein, polyketide, isoprenoid, and amino acid derivative, into the target genetic locus of P. putida chromosome. The markerless recombineering system was completed by combining Cre/lox system and developing efficient plasmid curing systems, generating final strains free of antibiotic markers and plasmids. This markerless recombineering system for efficient gene knockout and integration will expedite metabolic engineering of P. putida, a bacterial host strain of increasing academic and industrial interest.
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180
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Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages. Sci Rep 2018; 8:6961. [PMID: 29725068 PMCID: PMC5934437 DOI: 10.1038/s41598-018-25201-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/04/2018] [Indexed: 11/15/2022] Open
Abstract
Adaptive laboratory evolution is an important tool to evolve organisms to increased tolerance towards different physical and chemical stress. It is applied to study the evolution of antibiotic resistance as well as genetic mechanisms underlying improvements in production strains. Adaptive evolution experiments can be automated in a high-throughput fashion. However, the characterization of the resulting lineages can become a time consuming task, when the performance of each lineage is evaluated individually. Here, we present a novel method for the markerless insertion of randomized genetic barcodes into the genome of Escherichia coli using a novel dual-auxotrophic selection approach. The barcoded E. coli library allows multiplexed phenotyping of evolved strains in pooled competition experiments. We use the barcoded library in an adaptive evolution experiment; evolving resistance towards three common antibiotics. Comparing this multiplexed phenotyping with conventional susceptibility testing and growth-rate measurements we can show a significant positive correlation between the two approaches. Use of barcoded bacterial strain libraries for individual adaptive evolution experiments drastically reduces the workload of characterizing the resulting phenotypes and enables prioritization of lineages for in-depth characterization. In addition, barcoded clones open up new ways to profile community dynamics or to track lineages in vivo or situ.
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181
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Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production. Metab Eng 2018; 47:303-313. [DOI: 10.1016/j.ymben.2018.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
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182
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Hutinet G, Besle A, Son O, McGovern S, Guerois R, Petit MA, Ochsenbein F, Lecointe F. Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein. Front Microbiol 2018; 9:743. [PMID: 29740405 PMCID: PMC5928155 DOI: 10.3389/fmicb.2018.00743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo, but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro, Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo, though Sak4 and its SSB are unable to promote strand exchange in vitro. Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves.
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Affiliation(s)
- Geoffrey Hutinet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Arthur Besle
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Son
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stephen McGovern
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François Lecointe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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183
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Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Res 2018; 46:2901-2917. [PMID: 29394395 PMCID: PMC5888115 DOI: 10.1093/nar/gky069] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/21/2018] [Accepted: 01/24/2018] [Indexed: 12/18/2022] Open
Abstract
Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator of catabolite repression. Unlike for CRP, in vivo DNA binding information of Cra is scarce. Here we generate and integrate ChIP-exo and RNA-seq data to identify 39 binding sites for Cra and 97 regulon genes that are regulated by Cra in Escherichia coli. An integrated metabolic-regulatory network was formed by including experimentally-derived regulatory information and a genome-scale metabolic network reconstruction. Applying analysis methods of systems biology to this integrated network showed that Cra enables optimal bacterial growth on poor carbon sources by redirecting and repressing glycolysis flux, by activating the glyoxylate shunt pathway, and by activating the respiratory pathway. In these regulatory mechanisms, the overriding regulatory activity of Cra over CRP is fundamental. Thus, elucidation of interacting transcriptional regulation of core carbon metabolism in bacteria by two key transcription factors was possible by combining genome-wide experimental measurement and simulation with a genome-scale metabolic model.
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Affiliation(s)
- Donghyuk Kim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin 446–701, Republic of Korea
| | - Sang Woo Seo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- School of Chemical and Biological Engineering, Institute of Chemical Prcocess, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ye Gao
- Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hojung Nam
- School of Information and Communication, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, Republic of Korea
| | - Gabriela I Guzman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- The Novo Nordisk Foundation Center for Biosustainabiliy, Danish Technical University, 6 Kogle Alle, Hørsholm, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- The Novo Nordisk Foundation Center for Biosustainabiliy, Danish Technical University, 6 Kogle Alle, Hørsholm, Denmark
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184
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Freed EF, Pines G, Eckert CA, Gill RT. Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies: Modifying Gene Expression inE. coliby Inserting Synthetic DNA Cassettes and Molecular Barcodes. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Affiliation(s)
- Emily F. Freed
- Biosciences Center, National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401 USA
| | - Gur Pines
- University of Colorado; Chemical and Biological Engineering; 3415 Colorado Ave Boulder CO 80303 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
| | - Carrie A. Eckert
- Biosciences Center, National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
| | - Ryan T. Gill
- University of Colorado; Chemical and Biological Engineering; 3415 Colorado Ave Boulder CO 80303 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
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185
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Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella. Proc Natl Acad Sci U S A 2018; 115:E2614-E2623. [PMID: 29487214 PMCID: PMC5856525 DOI: 10.1073/pnas.1714718115] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Invasive nontyphoidal Salmonella disease is a major and previously neglected tropical disease responsible for an estimated ∼390,000 deaths per year in Africa, largely caused by a variant of Salmonella Typhimurium called ST313. Despite the availability of >100,000 Salmonella genomes, it has proven challenging to associate individual SNPs with pathogenic traits of this dangerous bacterium. Here, we used a transcriptomic strategy to identify a single-nucleotide change in a promoter region responsible for crucial phenotypic differences of African S. Typhimurium. Our findings show that a noncoding nucleotide of the bacterial genome can have a profound effect upon the pathogenesis of infectious disease. Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely related to the ST19 group of S. Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by only ∼1,000 SNPs. We hypothesized that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes. Here we identified 3,597 transcriptional start sites of the ST313 strain D23580, and searched for a gene-expression signature linked to pathogenesis of Salmonella. We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance, and modulated virulence in the chicken infection model. We propose that high levels of PgtE expression by African S. Typhimurium ST313 promote bacterial survival and dissemination during human infection. Our finding of a functional role for an extragenic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on noncoding regions of the genome.
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186
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Diverse genetic error modes constrain large-scale bio-based production. Nat Commun 2018; 9:787. [PMID: 29463788 PMCID: PMC5820350 DOI: 10.1038/s41467-018-03232-w] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/26/2018] [Indexed: 11/18/2022] Open
Abstract
A transition toward sustainable bio-based chemical production is important for green growth. However, productivity and yield frequently decrease as large-scale microbial fermentation progresses, commonly ascribed to phenotypic variation. Yet, given the high metabolic burden and toxicities, evolutionary processes may also constrain bio-based production. We experimentally simulate large-scale fermentation with mevalonic acid-producing Escherichia coli. By tracking growth rate and production, we uncover how populations fully sacrifice production to gain fitness within 70 generations. Using ultra-deep (>1000×) time-lapse sequencing of the pathway populations, we identify multiple recurring intra-pathway genetic error modes. This genetic heterogeneity is only detected using deep-sequencing and new population-level bioinformatics, suggesting that the problem is underestimated. A quantitative model explains the population dynamics based on enrichment of spontaneous mutant cells. We validate our model by tuning production load and escape rate of the production host and apply multiple orthogonal strategies for postponing genetically driven production declines. The declining performance of scale-up bioreactor cultures is commonly attributed to phenotypic and physical heterogeneities. Here, the authors reveal multiple recurring intra-pathway error modes that limit engineered E. coli mevalonic acid production over time- and industrial-scale fermentations.
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187
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Clarke BR, Ovchinnikova OG, Kelly SD, Williamson ML, Butler JE, Liu B, Wang L, Gou X, Follador R, Lowary TL, Whitfield C. Molecular basis for the structural diversity in serogroup O2-antigen polysaccharides in Klebsiella pneumoniae. J Biol Chem 2018; 293:4666-4679. [PMID: 29602878 DOI: 10.1074/jbc.ra117.000646] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/23/2018] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae is a major health threat. Vaccination and passive immunization are considered as alternative therapeutic strategies for managing Klebsiella infections. Lipopolysaccharide O antigens are attractive candidates because of the relatively small range of known O-antigen polysaccharide structures, but immunotherapeutic applications require a complete understanding of the structures found in clinical settings. Currently, the precise number of Klebsiella O antigens is unknown because available serological tests have limited resolution, and their association with defined chemical structures is sometimes uncertain. Molecular serotyping methods can evaluate clinical prevalence of O serotypes but require a full understanding of the genetic determinants for each O-antigen structure. This is problematic with Klebsiella pneumoniae because genes outside the main rfb (O-antigen biosynthesis) locus can have profound effects on the final structure. Here, we report two new loci encoding enzymes that modify a conserved polysaccharide backbone comprising disaccharide repeat units [→3)-α-d-Galp-(1→3)-β-d-Galf-(1→] (O2a antigen). We identified in serotype O2aeh a three-component system that modifies completed O2a glycan in the periplasm by adding 1,2-linked α-Galp side-group residues. In serotype O2ac, a polysaccharide comprising disaccharide repeat units [→5)-β-d-Galf-(1→3)-β-d-GlcpNAc-(1→] (O2c antigen) is attached to the non-reducing termini of O2a-antigen chains. O2c-polysaccharide synthesis is dependent on a locus encoding three glycosyltransferase enzymes. The authentic O2aeh and O2c antigens were recapitulated in recombinant Escherichia coli hosts to establish the essential gene set for their synthesis. These findings now provide a complete understanding of the molecular genetic basis for the known variations in Klebsiella O-antigen carbohydrate structures based on the O2a backbone.
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Affiliation(s)
- Bradley R Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Olga G Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Monica L Williamson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jennifer E Butler
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda St. TEDA, Tianjin 300457, China
| | - Lu Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda St. TEDA, Tianjin 300457, China
| | - Xi Gou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda St. TEDA, Tianjin 300457, China
| | | | - Todd L Lowary
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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188
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Pontes MH, Groisman EA. Protein synthesis controls phosphate homeostasis. Genes Dev 2018; 32:79-92. [PMID: 29437726 PMCID: PMC5828397 DOI: 10.1101/gad.309245.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
Abstract
In this study, Pontes et al. show that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu in yeast and bacteria. Their findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature. Phosphorus is an essential element assimilated largely as orthophosphate (Pi). Cells respond to Pi starvation by importing Pi from their surroundings. We now report that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu. In the bacterium Salmonella enterica serovar Typhimurium, this response entails phosphorylation of the regulatory protein PhoB and transcription of PhoB-dependent Pi transporter genes and is eliminated upon stimulation of adenosine triphosphate (ATP) hydrolysis. When protein synthesis is impaired due to low cytoplasmic magnesium (Mg2+), Salmonella triggers the Pi starvation response because ribosomes are destabilized, which reduces ATP consumption and thus free cytoplasmic Pi. This response is transient because low cytoplasmic Mg2+ promotes an uptake in Mg2+ and a decrease in ATP levels, which stabilizes ribosomes, resulting in ATP consumption and Pi increase, thus ending the response. Notably, pharmacological inhibition of protein synthesis also elicited a Pi starvation response in the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae. Our findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature.
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Affiliation(s)
- Mauricio H Pontes
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA.,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA.,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
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189
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Rhinoscleroma pathogenesis: The type K3 capsule of Klebsiella rhinoscleromatis is a virulence factor not involved in Mikulicz cells formation. PLoS Negl Trop Dis 2018; 12:e0006201. [PMID: 29381692 PMCID: PMC5806929 DOI: 10.1371/journal.pntd.0006201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/09/2018] [Accepted: 12/31/2017] [Indexed: 12/16/2022] Open
Abstract
Rhinoscleroma is a human specific chronic granulomatous infection of the nose and upper airways caused by the Gram-negative bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. Although considered a rare disease, it is endemic in low-income countries where hygienic conditions are poor. A hallmark of this pathology is the appearance of atypical foamy monocytes called Mikulicz cells. However, the pathogenesis of rhinoscleroma remains poorly investigated. Capsule polysaccharide (CPS) is a prominent virulence factor in bacteria. All K. rhinoscleromatis strains are of K3 serotype, suggesting that CPS can be an important driver of rhinoscleroma disease. In this study, we describe the creation of the first mutant of K. rhinoscleromatis, inactivated in its capsule export machinery. Using a murine model recapitulating the formation of Mikulicz cells in lungs, we observed that a K. rhinoscleromatis CPS mutant (KR cps-) is strongly attenuated and that mice infected with a high dose of KR cps- are still able to induce Mikulicz cells formation, unlike a K. pneumoniae capsule mutant, and to partially recapitulate the characteristic strong production of IL-10. Altogether, the results of this study show that CPS is a virulence factor of K. rhinoscleromatis not involved in the specific appearance of Mikulicz cells.
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190
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König E, Zerbini F, Zanella I, Fraccascia D, Grandi G. Multiple Stepwise Gene Knockout Using CRISPR/Cas9 in Escherichia coli. Bio Protoc 2018; 8:e2688. [PMID: 34179238 PMCID: PMC8203979 DOI: 10.21769/bioprotoc.2688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Accepted: 12/25/2017] [Indexed: 11/02/2022] Open
Abstract
With the recent implementation of the CRISPR/Cas9 technology as a standard tool for genome editing, laboratories all over the world are undergoing one of the biggest advancements in molecular biology since PCR. The key advantage of this method is its simplicity and universal applicability for species of any phylum. Of particular interest is the extensively studied Gram-negative bacterium Escherichia coli, as it is considered as the workhorse for both research and industrial purposes. Here, we present a simple, robust and effective protocol using the CRISPR/Cas9 system in combination with the λ Red machinery for gene knockout in E. coli. Crucial in our procedure is the use of a double-stranded donor DNA and a curing strategy for removal of the guide RNA encoding plasmid that allows starting a new mutation after only two working days. Our protocol allows multiple, stepwise gene knockout strains with high mutagenesis efficiencies applicable for high-throughput approaches.
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Affiliation(s)
- Enrico König
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Francesca Zerbini
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Ilaria Zanella
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Davide Fraccascia
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Guido Grandi
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
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191
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Hao N, Shearwin KE, Dodd IB. Programmable DNA looping using engineered bivalent dCas9 complexes. Nat Commun 2017; 8:1628. [PMID: 29158476 PMCID: PMC5696343 DOI: 10.1038/s41467-017-01873-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022] Open
Abstract
DNA looping is a ubiquitous and critical feature of gene regulation. Although DNA looping can be efficiently detected, tools to readily manipulate DNA looping are limited. Here we develop CRISPR-based DNA looping reagents for creation of programmable DNA loops. Cleavage-defective Cas9 proteins of different specificity are linked by heterodimerization or translational fusion to create bivalent complexes able to link two separate DNA regions. After model-directed optimization, the reagents are validated using a quantitative DNA looping assay in E. coli. Looping efficiency is ~15% for a 4.7 kb loop, but is significantly improved by loop multiplexing with additional guides. Bivalent dCas9 complexes are also used to activate endogenous norVW genes by rewiring chromosomal DNA to bring distal enhancer elements to the gene promoters. Such reagents should allow manipulation of DNA looping in a variety of cell types, aiding understanding of endogenous loops and enabling creation of new regulatory connections. DNA loops are a ubiquitious feature of gene regulation across the kingdoms of life. Here the authors design a Cas9-based dimerization system for inducing DNA loops in E. coli, allowing activation and rewiring of gene expression.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Keith E Shearwin
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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192
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Ekandjo LK, Ruppel S, Remus R, Witzel K, Patz S, Becker Y. Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656 T. Can J Microbiol 2017; 64:97-106. [PMID: 29059532 DOI: 10.1139/cjm-2017-0532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological nitrogen fixation (BNF) is considered one of the key plant-growth-promoting (PGP) factors for diazotrophic organisms. Whether the iron and iron-molybdenum nitrogenases of Kosakonia radicincitans contribute to its PGP effect is yet to be proven. Hence, for the first time, we conducted site-directed mutagenesis in K. radicincitans to knock out anfH and (or) nifH as a mean to deactivate BNF in this strain. We used 15N2-labeled air to trace BNF activities in ΔanfH, ΔnifH, and ΔanfHΔnifH mutants. Assessing bacterial growth, nitrogen content, and 15N incorporation revealed that BNF is impaired in K. radicincitans DSM16656T ΔnifH and ΔanfHΔnifH. However, we detected no significant contribution of the Fe nitrogenase to biological dinitrogen assimilation under our pure bacterial culture experimental conditions. Such nondiazotrophic K. radicincitans DSM16656T mutants represent excellent tools for investigating nitrogen nutrition in K. radicincitans-inoculated plants.
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Affiliation(s)
- Lempie K Ekandjo
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Silke Ruppel
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Rainer Remus
- b Leibniz Centre for Agricultural Landscape Research, Eberswalder Straβe 84, 15374 Müncheberg, Germany
| | - Katja Witzel
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Sascha Patz
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Yvonne Becker
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
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193
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Slininger Lee MF, Jakobson CM, Tullman-Ercek D. Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering. ACS Synth Biol 2017; 6:1880-1891. [PMID: 28585808 DOI: 10.1021/acssynbio.7b00042] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments are a class of proteinaceous organelles comprising a characteristic protein shell enclosing a set of enzymes. Compartmentalization can prevent escape of volatile or toxic intermediates, prevent off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment organelles will enhance the function of heterologous pathways, but to do so, it is critical to understand how to control diffusion in and out of the microcompartment organelle. To this end, we explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. We found that the ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. Finally, we show that the hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations will affect growth on 1,2-propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the use of two strategies to engineer microcompartments to control metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores.
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Affiliation(s)
- Marilyn F. Slininger Lee
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Christopher M. Jakobson
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Systems Biology, Stanford University, Stanford, California, 94305, United States
| | - Danielle Tullman-Ercek
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208-3120, United States
- Chemistry
of Life Processes Institute, Northwestern University, 2170 Campus
Drive, Evanston, Illinois 60208-3120, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, Illinois 60208-3120, United States
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194
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Jones DL, Leroy P, Unoson C, Fange D, Ćurić V, Lawson MJ, Elf J. Kinetics of dCas9 target search in Escherichia coli. Science 2017; 357:1420-1424. [PMID: 28963258 PMCID: PMC6150439 DOI: 10.1126/science.aah7084] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 06/09/2017] [Accepted: 08/24/2017] [Indexed: 12/12/2022]
Abstract
How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living Escherichia coli by combining single-molecule fluorescence microscopy and bulk restriction-protection assays. We find that it takes a single fluorescently labeled dCas9 6 hours to find the correct target sequence, which implies that each potential target is bound for less than 30 milliseconds. Once bound, dCas9 remains associated until replication. To achieve fast targeting, both Cas9 and its guide RNA have to be present at high concentrations.
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Affiliation(s)
- Daniel Lawson Jones
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Prune Leroy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Unoson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Fange
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Vladimir Ćurić
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Michael J Lawson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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195
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Tse H, Gu Q, Sze KH, Chu IK, Kao RYT, Lee KC, Lam CW, Yang D, Tai SSC, Ke Y, Chan E, Chan WM, Dai J, Leung SP, Leung SY, Yuen KY. A tricyclic pyrrolobenzodiazepine produced by Klebsiella oxytoca is associated with cytotoxicity in antibiotic-associated hemorrhagic colitis. J Biol Chem 2017; 292:19503-19520. [PMID: 28972161 DOI: 10.1074/jbc.m117.791558] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/19/2017] [Indexed: 12/12/2022] Open
Abstract
Cytotoxin-producing Klebsiella oxytoca is the causative agent of antibiotic-associated hemorrhagic colitis (AAHC). Recently, the cytotoxin associated with AAHC was identified as tilivalline, a known pentacyclic pyrrolobenzodiazepine (PBD) metabolite produced by K. oxytoca Although this assertion of tilivalline's role in AAHC is supported by evidence from animal experiments, some key aspects of this finding appear to be incompatible with toxicity mechanisms of known PBD toxins. We therefore hypothesized that K. oxytoca may produce some other uncharacterized cytotoxins. To address this question, we investigated whether tilivalline alone is indeed necessary and sufficient to induce cytotoxicity or whether K. oxytoca also produces other cytotoxins. LC-MS- and NMR-based metabolomic analyses revealed the presence of an abundant tricyclic PBD, provisionally designated kleboxymycin, in the supernatant of toxigenic K. oxytoca strains. Moreover, by generating multiple mutants with gene deletions affecting tilivalline biosynthesis, we show that a tryptophanase-deficient, tilivalline-negative K. oxytoca mutant induced cytotoxicity in vitro similar to tilivalline-positive K. oxytoca strains. Furthermore, synthetic kleboxymycin exhibited greater than 9-fold higher cytotoxicity than tilivalline in TC50 cell culture assays. We also found that the biosynthetic pathways for kleboxymycin and tilivalline appear to overlap, as tilivalline is an indole derivative of kleboxymycin. In summary, our results indicate that tilivalline is not essential for inducing cytotoxicity observed in K. oxytoca-associated AAHC and that kleboxymycin is a tilivalline-related bacterial metabolite with even higher cytotoxicity.
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Affiliation(s)
- Herman Tse
- From the Department of Microbiology.,Research Centre of Infection and Immunity, and.,the State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR, Hong Kong, China.,the Carol Yu Centre for Infection
| | | | - Kong-Hung Sze
- From the Department of Microbiology.,Research Centre of Infection and Immunity, and.,the State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR, Hong Kong, China.,the Carol Yu Centre for Infection
| | | | - Richard Y-T Kao
- From the Department of Microbiology.,Research Centre of Infection and Immunity, and.,the State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR, Hong Kong, China.,the Carol Yu Centre for Infection
| | - Kam-Chung Lee
- From the Department of Microbiology.,Research Centre of Infection and Immunity, and.,the State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR, Hong Kong, China.,the Carol Yu Centre for Infection
| | | | | | | | | | | | | | - Jun Dai
- From the Department of Microbiology
| | | | | | - Kwok-Yung Yuen
- From the Department of Microbiology, .,Research Centre of Infection and Immunity, and.,the State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR, Hong Kong, China.,the Carol Yu Centre for Infection
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196
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Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J. Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Mol Cell 2017; 67:826-836.e5. [PMID: 28781237 PMCID: PMC5591071 DOI: 10.1016/j.molcel.2017.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022]
Abstract
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically identical population and facilitates its adaptation to changing environments.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Codon, Terminator
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Genetic Fitness
- Genotype
- Kinetics
- Luminescent Proteins/biosynthesis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- One-Carbon Group Transferases
- Phenotype
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Transcription, Genetic
- Red Fluorescent Protein
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Karl W Barber
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Kalyn J Weiss
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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197
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Umenhoffer K, Draskovits G, Nyerges Á, Karcagi I, Bogos B, Tímár E, Csörgő B, Herczeg R, Nagy I, Fehér T, Pál C, Pósfai G. Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis. ACS Synth Biol 2017; 6:1471-1483. [PMID: 28426191 DOI: 10.1021/acssynbio.6b00378] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, nonessential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization. Here, we sought to establish a rapid methodology to improve the stability of microbial hosts. The novel workflow involves genome shuffling between a mobile genetic element-free strain and the target cell, and subsequent rounds of CRISPR/Cas-assisted MAGE on multiplex targets. The power and speed of the procedure was demonstrated on E. coli BL21(DE3), a host routinely used for plasmid-based heterologous protein expression. All 9 prophages and 50 insertion elements were efficiently deleted or inactivated. Together with additional targeted manipulations (e.g., inactivation of error-prone DNA-polymerases), the changes resulted in an improved bacterial host with a hybrid (harboring segments of K-12 DNA), 9%-downsized and clean genome. The combined capacity of phage-mediated generalized transduction and CRISPR/Cas-selected MAGE offers a way for rapid, large scale editing of bacterial genomes.
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Affiliation(s)
- Kinga Umenhoffer
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Gábor Draskovits
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ákos Nyerges
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ildikó Karcagi
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Balázs Bogos
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Edit Tímár
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Bálint Csörgő
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd, 6782 Mórahalom, Hungary
- Institute
of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Tamás Fehér
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Csaba Pál
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - György Pósfai
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
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198
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Anderson MT, Mitchell LA, Mobley HLT. Cysteine Biosynthesis Controls Serratia marcescens Phospholipase Activity. J Bacteriol 2017; 199:e00159-17. [PMID: 28559296 PMCID: PMC5527384 DOI: 10.1128/jb.00159-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/22/2017] [Indexed: 01/01/2023] Open
Abstract
Serratia marcescens causes health care-associated opportunistic infections that can be difficult to treat due to a high incidence of antibiotic resistance. One of the many secreted proteins of S. marcescens is the PhlA phospholipase enzyme. Genes involved in the production and secretion of PhlA were identified by screening a transposon insertion library for phospholipase-deficient mutants on phosphatidylcholine-containing medium. Mutations were identified in four genes (cyaA, crp, fliJ, and fliP) that are involved in the flagellum-dependent PhlA secretion pathway. An additional phospholipase-deficient isolate harbored a transposon insertion in the cysE gene encoding a predicted serine O-acetyltransferase required for cysteine biosynthesis. The cysE requirement for extracellular phospholipase activity was confirmed using a fluorogenic phospholipase substrate. Phospholipase activity was restored to the cysE mutant by the addition of exogenous l-cysteine or O-acetylserine to the culture medium and by genetic complementation. Additionally, phlA transcript levels were decreased 6-fold in bacteria lacking cysE and were restored with added cysteine, indicating a role for cysteine-dependent transcriptional regulation of S. marcescens phospholipase activity. S. marcescenscysE mutants also exhibited a defect in swarming motility that was correlated with reduced levels of flhD and fliA flagellar regulator gene transcription. Together, these findings suggest a model in which cysteine is required for the regulation of both extracellular phospholipase activity and surface motility in S. marcescensIMPORTANCESerratia marcescens is known to secrete multiple extracellular enzymes, but PhlA is unusual in that this protein is thought to be exported by the flagellar transport apparatus. In this study, we demonstrate that both extracellular phospholipase activity and flagellar function are dependent on the cysteine biosynthesis pathway. Furthermore, a disruption of cysteine biosynthesis results in decreased phlA and flagellar gene transcription, which can be restored by supplying bacteria with exogenous cysteine. These results identify a previously unrecognized role for CysE and cysteine in the secretion of S. marcescens phospholipase and in bacterial motility.
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Affiliation(s)
- Mark T Anderson
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, Michigan, USA
| | - Lindsay A Mitchell
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, Michigan, USA
| | - Harry L T Mobley
- University of Michigan Medical School, Department of Microbiology and Immunology, Ann Arbor, Michigan, USA
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Lauritsen I, Porse A, Sommer MOA, Nørholm MHH. A versatile one-step CRISPR-Cas9 based approach to plasmid-curing. Microb Cell Fact 2017; 16:135. [PMID: 28764701 PMCID: PMC5540278 DOI: 10.1186/s12934-017-0748-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/22/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Plasmids are widely used and essential tools in molecular biology. However, plasmids often impose a metabolic burden and are only temporarily useful for genetic engineering, bio-sensing and characterization purposes. While numerous techniques for genetic manipulation exist, a universal tool enabling rapid removal of plasmids from bacterial cells is lacking. RESULTS Based on replicon abundance and sequence conservation analysis, we show that the vast majority of bacterial cloning and expression vectors share sequence similarities that allow for broad CRISPR-Cas9 targeting. We have constructed a universal plasmid-curing system (pFREE) and developed a one-step protocol and PCR procedure that allow for identification of plasmid-free clones within 24 h. While the context of the targeted replicons affects efficiency, we obtained curing efficiencies between 40 and 100% for the plasmids most widely used for expression and engineering purposes. By virtue of the CRISPR-Cas9 targeting, our platform is highly expandable and can be applied in a broad host context. We exemplify the wide applicability of our system in Gram-negative bacteria by demonstrating the successful application in both Escherichia coli and the promising cell factory chassis Pseudomonas putida. CONCLUSION As a fast and freely available plasmid-curing system, targeting virtually all vectors used for cloning and expression purposes, we believe that pFREE has the potential to eliminate the need for individualized vector suicide solutions in molecular biology. We envision the application of pFREE to be especially useful in methodologies involving multiple plasmids, used sequentially or simultaneously, which are becoming increasingly popular for genome editing or combinatorial pathway engineering.
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Affiliation(s)
- Ida Lauritsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Morten O. A. Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Näsvall J, Knöppel A, Andersson DI. Duplication-Insertion Recombineering: a fast and scar-free method for efficient transfer of multiple mutations in bacteria. Nucleic Acids Res 2017; 45:e33. [PMID: 27899661 PMCID: PMC5389514 DOI: 10.1093/nar/gkw1078] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/25/2016] [Indexed: 11/18/2022] Open
Abstract
We have developed a new λ Red recombineering methodology for generating transient selection markers that can be used to transfer mutations between bacterial strains of both Escherichia coli and Salmonella enterica. The method is fast, simple and allows for the construction of strains with several mutations without any unwanted sequence changes (scar-free). The method uses λ Red recombineering to generate a marker-held tandem duplication, termed Duplication-Insertion (Dup-In). The Dup-Ins can easily be transferred between strains by generalized transduction and are subsequently rapidly lost by homologous recombination between the two copies of the duplicated sequence, leaving no scar sequence or antibiotic resistance cassette behind. We demonstrate the utility of the method by generating several Dup-Ins in E. coli and S. enterica to transfer genetically linked mutations in both essential and non-essential genes. We have successfully used this methodology to re-construct mutants found after various types of selections, and to introduce foreign genes into the two species. Furthermore, recombineering with two overlapping fragments was as efficient as recombineering with the corresponding single large fragment, allowing more complicated constructions without the need for overlap extension PCR.
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Affiliation(s)
- Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Anna Knöppel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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