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Zhao W, Guo Y. Increasing the efficiency of gene editing with CRISPR-Cas9 via concurrent expression of the Beta protein. Int J Biol Macromol 2024; 270:132431. [PMID: 38759853 DOI: 10.1016/j.ijbiomac.2024.132431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/03/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Escherichia coli has emerged as an important host for the production of biopharmaceuticals or other industrially relevant molecules. An efficient gene editing tool is indispensable for ensuring high production levels and optimal release of target products. However, in Escherichia coli, the CRISPR-Cas9 system has been shown to achieve gene modifications with relatively low frequency. Large-scale PCR screening is required, hindering the identification of positive clones. The beta protein, which weakly binds to single-stranded DNA but tightly associates with complementary strand annealing products, offers a promising solution to this issue. In the present study, we describe a targeted and continuous gene editing strategy for the Escherichia coli genome. This strategy involves the coexpression of the beta protein alongside the CRISPR-Cas9 system, enabling a variety of genome modifications such as gene deletion and insertion with an efficiency exceeding 80 %. The integrity of beta proteins is essential for the CRISPR-Cas9/Beta-based gene editing system. In this work, the deletion of either the N- or C-terminal domain significantly impaired system efficiency. Overall, our findings established the CRISPR-Cas9/Beta system as a suitable gene editing tool for various applications in Escherichia coli.
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Affiliation(s)
- Weiyu Zhao
- School of Life Sciences, Shanghai University, No. 99 Shangda Road, Shanghai 200444, China; School of Economics and Management, Tongji University, No. 1239 Siping Road, Shanghai 200092, China; Institute of Logistics Science and Engineering, Shanghai Maritime University, 1550 Haigang Avenue, Shanghai 201306, China
| | - Yanan Guo
- School of Life Sciences, Shanghai University, No. 99 Shangda Road, Shanghai 200444, China; Department of Biology, Georgia State University, Atlanta, GA 30303, United States of America.
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2
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Beardslee PC, Schmitz KR. Toxin-based screening of C-terminal tags in Escherichia coli reveals the exceptional potency of ssrA-like degrons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.576913. [PMID: 38352471 PMCID: PMC10862746 DOI: 10.1101/2024.01.29.576913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
All bacteria possess ATP-dependent proteases that destroy cytosolic proteins. These enzymes help cells mitigate proteotoxic stress, adapt to changing nutrient availability, regulate virulence phenotypes, and transition to pathogenic lifestyles. Moreover, ATP-dependent proteases have emerged as promising antibacterial and antivirulence targets in a variety of pathogens. The physiological roles of these proteases are largely defined by the complement of proteins that they degrade. Substrates are typically recognized in a highly selective manner, often via short unstructured sequences termed degrons. While a few degrons have been identified and rigorously characterized, we lack a systematic understanding of how proteases select valid degrons from the vast complexity of protein sequence space. Here, we describe a novel high-throughput screening approach in Escherichia coli that couples proteolysis of a protein toxin to cell survival. We used this method to screen a combinatorial library of C-terminal pentapeptide sequences for functionality as proteolytic degrons in wild type E. coli, and in strains lacking components of the ClpXP and ClpAP proteases. By examining the competitive enrichment of sequences over time, we found that about one percent of pentapeptide tags lead to toxin proteolysis. Interestingly, the most enriched degrons were ClpXP-dependent and highly similar to the ssrA tag, one of the most extensively characterized degrons in bacteria. Among ssrA-like sequences, we observed that specific upstream residues correlate with successful recognition. The lack of diversity among strongly enriched sequences suggests that ssrA-like tags comprise a uniquely potent class of short C-terminal degron in E. coli. Efficient proteolysis of substrates lacking such degrons likely requires adaptors or multivalent interactions. These findings broaden our understanding of the constraints that shape the bacterial proteolytic landscape. Our screening approach may be broadly applicable to probing aspects of proteolytic substrate selection in other bacterial systems.
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Affiliation(s)
- Patrick C. Beardslee
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
| | - Karl R. Schmitz
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
- Department of Biological Sciences, University of Delaware, Newark DE, 19716
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3
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Alav I, Pordelkhaki P, de Resende PE, Partington H, Gibbons S, Lord RM, Buckner MMC. Cobalt complexes modulate plasmid conjugation in Escherichia coli and Klebsiella pneumoniae. Sci Rep 2024; 14:8103. [PMID: 38582880 PMCID: PMC10998897 DOI: 10.1038/s41598-024-58895-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 04/08/2024] Open
Abstract
Antimicrobial resistance genes (ARG), such as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, are commonly carried on plasmids. Plasmids can transmit between bacteria, disseminate globally, and cause clinically important resistance. Therefore, targeting plasmids could reduce ARG prevalence, and restore the efficacy of existing antibiotics. Cobalt complexes possess diverse biological activities, including antimicrobial and anticancer properties. However, their effect on plasmid conjugation has not been explored yet. Here, we assessed the effect of four previously characterised bis(N-picolinamido)cobalt(II) complexes lacking antibacterial activity on plasmid conjugation in Escherichia coli and Klebsiella pneumoniae. Antimicrobial susceptibility testing of these cobalt complexes confirmed the lack of antibacterial activity in E. coli and K. pneumoniae. Liquid broth and solid agar conjugation assays were used to screen the activity of the complexes on four archetypical plasmids in E. coli J53. The cobalt complexes significantly reduced the conjugation of RP4, R6K, and R388 plasmids, but not pKM101, on solid agar in E. coli J53. Owing to their promising activity, the impact of cobalt complexes was tested on the conjugation of fluorescently tagged extended-spectrum β-lactamase encoding pCTgfp plasmid in E. coli and carbapenemase encoding pKpQILgfp plasmid in K. pneumoniae, using flow cytometry. The complexes significantly reduced the conjugation of pKpQILgfp in K. pneumoniae but had no impact on pCTgfp conjugation in E. coli. The cobalt complexes did not have plasmid-curing activity, suggesting that they target conjugation rather than plasmid stability. To our knowledge, this is the first study to report reduced conjugation of clinically relevant plasmids with cobalt complexes. These cobalt complexes are not cytotoxic towards mammalian cells and are not antibacterial, therefore they could be optimised and employed as inhibitors of plasmid conjugation.
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Affiliation(s)
- Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Parisa Pordelkhaki
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pedro Ernesto de Resende
- School of Pharmacy, Faculty of Science, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Hannah Partington
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Simon Gibbons
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mauz, P.O. Box 33, Nizwa, 616, Oman
| | - Rianne M Lord
- School of Chemistry, Faculty of Science, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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4
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Wood WN, Rubio MA, Leiva LE, Phillips GJ, Ibba M. Methionyl-tRNA synthetase synthetic and proofreading activities are determinants of antibiotic persistence. Front Microbiol 2024; 15:1384552. [PMID: 38601944 PMCID: PMC11004401 DOI: 10.3389/fmicb.2024.1384552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Bacterial antibiotic persistence is a phenomenon where bacteria are exposed to an antibiotic and the majority of the population dies while a small subset enters a low metabolic, persistent, state and are able to survive. Once the antibiotic is removed the persistent population can resuscitate and continue growing. Several different molecular mechanisms and pathways have been implicated in this phenomenon. A common mechanism that may underly bacterial antibiotic persistence is perturbations in protein synthesis. To investigate this mechanism, we characterized four distinct metG mutants for their ability to increase antibiotic persistence. Two metG mutants encode changes near the catalytic site of MetRS and the other two mutants changes near the anticodon binding domain. Mutations in metG are of particular interest because MetRS is responsible for aminoacylation both initiator tRNAMet and elongator tRNAMet indicating that these mutants could impact translation initiation and/or translation elongation. We observed that all the metG mutants increased the level of antibiotic persistence as did reduced transcription levels of wild type metG. Although, the MetRS variants did not have an impact on MetRS activity itself, they did reduce translation rates. It was also observed that the MetRS variants affected the proofreading mechanism for homocysteine and that these mutants' growth is hypersensitive to homocysteine. Taken together with previous findings, our data indicate that both reductions in cellular Met-tRNAMet synthetic capacity and reduced proofreading of homocysteine by MetRS variants are positive determinants for bacterial antibiotic persistence.
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Affiliation(s)
- Whitney N. Wood
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Miguel Angel Rubio
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, IA, United States
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
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5
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Widney KA, Yang DD, Rusch LM, Copley SD. CRISPR-Cas9-assisted genome editing in E. coli elevates the frequency of unintended mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.584922. [PMID: 38562785 PMCID: PMC10983943 DOI: 10.1101/2024.03.19.584922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cas-assisted lambda Red recombineering techniques have rapidly become a mainstay of bacterial genome editing. Such techniques have been used to construct both individual mutants and massive libraries to assess the effects of genomic changes. We have found that a commonly used Cas9-assisted editing method results in unintended mutations elsewhere in the genome in 26% of edited clones. The unintended mutations are frequently found over 200 kb from the intended edit site and even over 10 kb from potential off-target sites. We attribute the high frequency of unintended mutations to error-prone polymerases expressed in response to dsDNA breaks introduced at the edit site. Most unintended mutations occur in regulatory or coding regions and thus may have phenotypic effects. Our findings highlight the risks associated with genome editing techniques involving dsDNA breaks in E. coli and likely other bacteria and emphasize the importance of sequencing the genomes of edited cells to ensure the absence of unintended mutations.
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Affiliation(s)
- Karl A. Widney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Dong-Dong Yang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Leo M. Rusch
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
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6
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Xiao L, Qi Z, Song K, Lv R, Chen R, Zhao H, Wu H, Li C, Xin Y, Jin Y, Li X, Xu X, Tan Y, Du Z, Cui Y, Zhang X, Yang R, Zhao X, Song Y. Interplays of mutations in waaA, cmk, and ail contribute to phage resistance in Yersinia pestis. Front Cell Infect Microbiol 2023; 13:1174510. [PMID: 37305418 PMCID: PMC10254400 DOI: 10.3389/fcimb.2023.1174510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Plague caused by Yersinia pestis remains a public health threat worldwide. Because multidrug-resistant Y. pestis strains have been found in both humans and animals, phage therapy has attracted increasing attention as an alternative strategy against plague. However, phage resistance is a potential drawback of phage therapies, and the mechanism of phage resistance in Y. pestis is yet to be investigated. In this study, we obtained a bacteriophage-resistant strain of Y. pestis (S56) by continuously challenging Y. pestis 614F with the bacteriophage Yep-phi. Genome analysis identified three mutations in strain S56: waaA* (9-bp in-frame deletion 249GTCATCGTG257), cmk* (10-bp frameshift deletion 15CCGGTGATAA24), and ail* (1-bp frameshift deletion A538). WaaA (3-deoxy-D-manno-octulosonic acid transferase) is a key enzyme in lipopolysaccharide biosynthesis. The waaA* mutation leads to decreased phage adsorption because of the failure to synthesize the lipopolysaccharide core. The mutation in cmk (encoding cytidine monophosphate kinase) increased phage resistance, independent of phage adsorption, and caused in vitro growth defects in Y. pestis. The mutation in ail inhibited phage adsorption while restoring the growth of the waaA null mutant and accelerating the growth of the cmk null mutant. Our results confirmed that mutations in the WaaA-Cmk-Ail cascade in Y. pestis contribute to resistance against bacteriophage. Our findings help in understanding the interactions between Y. pestis and its phages.
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Affiliation(s)
- Lisheng Xiao
- Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
- School of Basic Medicine, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ruichen Lv
- Hua Dong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Rong Chen
- Department of Laboratory Medicine, First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Haihong Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Hailian Wu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Cunxiang Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Youquan Xin
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Yong Jin
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xiang Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xiaoqing Xu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Xuefei Zhang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
| | - Xilin Zhao
- Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Yajun Song
- School of Basic Medicine, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- National Health Commission - Qinghai Co-construction Key Laboratory for Plague Control, Xining, China
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7
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de Mattos CD, Faith DR, Nemudryi AA, Schmidt AK, Bublitz DC, Hammond L, Kinnersley MA, Schwartzkopf CM, Robinson AJ, Joyce A, Michaels LA, Brzozowski RS, Coluccio A, Xing DD, Uchiyama J, Jennings LK, Eswara P, Wiedenheft B, Secor PR. Polyamines and linear DNA mediate bacterial threat assessment of bacteriophage infection. Proc Natl Acad Sci U S A 2023; 120:e2216430120. [PMID: 36802441 PMCID: PMC9992862 DOI: 10.1073/pnas.2216430120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/10/2023] [Indexed: 02/23/2023] Open
Abstract
Monitoring the extracellular environment for danger signals is a critical aspect of cellular survival. However, the danger signals released by dying bacteria and the mechanisms bacteria use for threat assessment remain largely unexplored. Here, we show that lysis of Pseudomonas aeruginosa cells releases polyamines that are subsequently taken up by surviving cells via a mechanism that relies on Gac/Rsm signaling. While intracellular polyamines spike in surviving cells, the duration of this spike varies according to the infection status of the cell. In bacteriophage-infected cells, intracellular polyamines are maintained at high levels, which inhibits replication of the bacteriophage genome. Many bacteriophages package linear DNA genomes and linear DNA is sufficient to trigger intracellular polyamine accumulation, suggesting that linear DNA is sensed as a second danger signal. Collectively, these results demonstrate how polyamines released by dying cells together with linear DNA allow P. aeruginosa to make threat assessments of cellular injury.
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Affiliation(s)
| | - Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Artem A. Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Amelia K. Schmidt
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - DeAnna C. Bublitz
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Lauren Hammond
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL33620
| | | | | | - Autumn J. Robinson
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Alex Joyce
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Lia A. Michaels
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | | | - Alison Coluccio
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Denghui David Xing
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama700-8558, Japan
| | - Laura K. Jennings
- Division of Biological Sciences, University of Montana, Missoula, MT59812
| | - Prahathees Eswara
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL33620
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, MT59812
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8
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Arroyo-Mendoza M, Proctor A, Correa-Medina A, Brand MW, Rosas V, Wannemuehler MJ, Phillips GJ, Hinton DM. The E. coli pathobiont LF82 encodes a unique variant of σ 70 that results in specific gene expression changes and altered phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.523653. [PMID: 36798310 PMCID: PMC9934711 DOI: 10.1101/2023.02.08.523653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
LF82, an adherent invasive Escherichia coli pathobiont, is associated with ileal Crohn's disease, an inflammatory bowel disease of unknown etiology. Although LF82 contains no virulence genes, it carries several genetic differences, including single nucleotide polymorphisms (SNPs), that distinguish it from nonpathogenic E. coli. We have identified and investigated an extremely rare SNP that is within the highly conserved rpoD gene, encoding σ70, the primary sigma factor for RNA polymerase. We demonstrate that this single residue change (D445V) results in specific transcriptome and phenotypic changes that are consistent with multiple phenotypes observed in LF82, including increased antibiotic resistance and biofilm formation, modulation of motility, and increased capacity for methionine biosynthesis. Our work demonstrates that a single residue change within the bacterial primary sigma factor can lead to multiple alterations in gene expression and phenotypic changes, suggesting an underrecognized mechanism by which pathobionts and other strain variants with new phenotypes can emerge.
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Affiliation(s)
- Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Alexandra Proctor
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Abraham Correa-Medina
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
| | - Meghan Wymore Brand
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Virginia Rosas
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
| | - Michael J Wannemuehler
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Gregory J Phillips
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States, 50011
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Dr., Bethesda, MD, United States, 20892
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9
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Carranza-Saavedra D, Torres-Bacete J, Blázquez B, Sánchez Henao CP, Zapata Montoya JE, Nogales J. System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock. Front Bioeng Biotechnol 2023; 11:1176445. [PMID: 37152640 PMCID: PMC10158823 DOI: 10.3389/fbioe.2023.1176445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Replacing traditional substrates in industrial bioprocesses to advance the sustainable production of chemicals is an urgent need in the context of the circular economy. However, since the limited degradability of non-conventional carbon sources often returns lower yields, effective exploitation of such substrates requires a multi-layer optimization which includes not only the provision of a suitable feedstock but the use of highly robust and metabolically versatile microbial biocatalysts. We tackled this challenge by means of systems metabolic engineering and validated Escherichia coli W as a promising cell factory for the production of the key building block chemical 2-ketoisovalerate (2-KIV) using whey as carbon source, a widely available and low-cost agro-industrial waste. First, we assessed the growth performance of Escherichia coli W on mono and disaccharides and demonstrated that using whey as carbon source enhances it significantly. Second, we searched the available literature and used metabolic modeling approaches to scrutinize the metabolic space of E. coli and explore its potential for overproduction of 2-KIV identifying as basic strategies the block of pyruvate depletion and the modulation of NAD/NADP ratio. We then used our model predictions to construct a suitable microbial chassis capable of overproducing 2-KIV with minimal genetic perturbations, i.e., deleting the pyruvate dehydrogenase and malate dehydrogenase. Finally, we used modular cloning to construct a synthetic 2-KIV pathway that was not sensitive to negative feedback, which effectively resulted in a rerouting of pyruvate towards 2-KIV. The resulting strain shows titers of up to 3.22 ± 0.07 g/L of 2-KIV and 1.40 ± 0.04 g/L of L-valine in 24 h using whey in batch cultures. Additionally, we obtained yields of up to 0.81 g 2-KIV/g substrate. The optimal microbial chassis we present here has minimal genetic modifications and is free of nutritional autotrophies to deliver high 2-KIV production rates using whey as a non-conventional substrate.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
| | - Blas Blázquez
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Claudia Patricia Sánchez Henao
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - José Edgar Zapata Montoya
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - Juan Nogales
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- *Correspondence: Juan Nogales,
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10
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Shekhar C, Maeda T. A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli. J Basic Microbiol 2022; 62:948-962. [PMID: 35739617 DOI: 10.1002/jobm.202100636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 06/11/2022] [Indexed: 11/07/2022]
Abstract
Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.
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Affiliation(s)
- Chandra Shekhar
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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11
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Kay EJ, Mauri M, Willcocks SJ, Scott TA, Cuccui J, Wren BW. Engineering a suite of E. coli strains for enhanced expression of bacterial polysaccharides and glycoconjugate vaccines. Microb Cell Fact 2022; 21:66. [PMID: 35449016 PMCID: PMC9026721 DOI: 10.1186/s12934-022-01792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoengineering, in the biotechnology workhorse bacterium, Escherichia coli, is a rapidly evolving field, particularly for the production of glycoconjugate vaccine candidates (bioconjugation). Efficient production of glycoconjugates requires the coordinated expression within the bacterial cell of three components: a carrier protein, a glycan antigen and a coupling enzyme, in a timely fashion. Thus, the choice of a suitable E. coli host cell is of paramount importance. Microbial chassis engineering has long been used to improve yields of chemicals and biopolymers, but its application to vaccine production is sparse. RESULTS In this study we have engineered a family of 11 E. coli strains by the removal and/or addition of components rationally selected for enhanced expression of Streptococcus pneumoniae capsular polysaccharides with the scope of increasing yield of pneumococcal conjugate vaccines. Importantly, all strains express a detoxified version of endotoxin, a concerning contaminant of therapeutics produced in bacterial cells. The genomic background of each strain was altered using CRISPR in an iterative fashion to generate strains without antibiotic markers or scar sequences. CONCLUSIONS Amongst the 11 modified strains generated in this study, E. coli Falcon, Peregrine and Sparrowhawk all showed increased production of S. pneumoniae serotype 4 capsule. Eagle (a strain without enterobacterial common antigen, containing a GalNAc epimerase and PglB expressed from the chromosome) and Sparrowhawk (a strain without enterobacterial common antigen, O-antigen ligase and chain length determinant, containing a GalNAc epimerase and chain length regulators from Streptococcus pneumoniae) respectively produced an AcrA-SP4 conjugate with 4 × and 14 × more glycan than that produced in the base strain, W3110. Beyond their application to the production of pneumococcal vaccine candidates, the bank of 11 new strains will be an invaluable resource for the glycoengineering community.
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Affiliation(s)
- Emily J Kay
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marta Mauri
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sam J Willcocks
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Timothy A Scott
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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12
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Pal A, Iyer MS, Srinivasan S, Narain Seshasayee AS, Venkatesh KV. Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. Open Biol 2022; 12:210206. [PMID: 35167766 PMCID: PMC8846999 DOI: 10.1098/rsob.210206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Evolution facilitates emergence of fitter phenotypes by efficient allocation of cellular resources in conjunction with beneficial mutations. However, system-wide pleiotropic effects that redress the perturbations to the apex node of the transcriptional regulatory networks remain unclear. Here, we elucidate that absence of global transcriptional regulator CRP in Escherichia coli results in alterations in key metabolic pathways under glucose respiratory conditions, favouring stress- or hedging-related functions over growth-enhancing functions. Further, we disentangle the growth-mediated effects from the CRP regulation-specific effects on these metabolic pathways. We quantitatively illustrate that the loss of CRP perturbs proteome efficiency, as evident from metabolic as well as ribosomal proteome fractions, that corroborated with intracellular metabolite profiles. To address how E. coli copes with such systemic defect, we evolved Δcrp mutant in the presence of glucose. Besides acquiring mutations in the promoter of glucose transporter ptsG, the evolved populations recovered the metabolic pathways to their pre-perturbed state coupled with metabolite re-adjustments, which altogether enabled increased growth. By contrast to Δcrp mutant, the evolved strains remodelled their proteome efficiency towards biomass synthesis, albeit at the expense of carbon efficiency. Overall, we comprehensively illustrate the genetic and metabolic basis of pleiotropic effects, fundamental for understanding the growth physiology.
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Affiliation(s)
- Ankita Pal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mahesh S. Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sumana Srinivasan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - K. V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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13
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Furniss RCD, Kaderabkova N, Barker D, Bernal P, Maslova E, Antwi AA, McNeil HE, Pugh HL, Dortet L, Blair JM, Larrouy-Maumus GJ, McCarthy RR, Gonzalez D, Mavridou DA. Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. eLife 2022; 11:57974. [PMID: 35025730 PMCID: PMC8863373 DOI: 10.7554/elife.57974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance in Gram-negative bacteria is one of the greatest threats to global health. New antibacterial strategies are urgently needed, and the development of antibiotic adjuvants that either neutralize resistance proteins or compromise the integrity of the cell envelope is of ever-growing interest. Most available adjuvants are only effective against specific resistance proteins. Here, we demonstrate that disruption of cell envelope protein homeostasis simultaneously compromises several classes of resistance determinants. In particular, we find that impairing DsbA-mediated disulfide bond formation incapacitates diverse β-lactamases and destabilizes mobile colistin resistance enzymes. Furthermore, we show that chemical inhibition of DsbA sensitizes multidrug-resistant clinical isolates to existing antibiotics and that the absence of DsbA, in combination with antibiotic treatment, substantially increases the survival of Galleria mellonella larvae infected with multidrug-resistant Pseudomonas aeruginosa. This work lays the foundation for the development of novel antibiotic adjuvants that function as broad-acting resistance breakers. Antibiotics, like penicillin, are the foundation of modern medicine, but bacteria are evolving to resist their effects. Some of the most harmful pathogens belong to a group called the 'Gram-negative bacteria', which have an outer layer – called the cell envelope – that acts as a drug barrier. This envelope contains antibiotic resistance proteins that can deactivate or repel antibiotics or even pump them out of the cell once they get in. One way to tackle antibiotic resistance could be to stop these proteins from working. Proteins are long chains of building blocks called amino acids that fold into specific shapes. In order for a protein to perform its role correctly, it must fold in the right way. In bacteria, a protein called DsbA helps other proteins fold correctly by holding them in place and inserting links called disulfide bonds. It was unclear whether DsbA plays a role in the folding of antibiotic resistance proteins, but if it did, it might open up new ways to treat antibiotic resistant infections. To find out more, Furniss, Kaderabkova et al. collected the genes that code for several antibiotic resistance proteins and put them into Escherichia coli bacteria, which made the bacteria resistant to antibiotics. Furniss, Kaderabkova et al. then stopped the modified E. coli from making DsbA, which led to the antibiotic resistance proteins becoming unstable and breaking down because they could not fold correctly. Further experiments showed that blocking DsbA with a chemical inhibitor in other pathogenic species of Gram-negative bacteria made these bacteria more sensitive to antibiotics that they would normally resist. To demonstrate that using this approach could work to stop infections by these bacteria, Furniss, Kaderabkova et al. used Gram-negative bacteria that produced antibiotic resistance proteins but could not make DsbA to infect insect larvae. The larvae were then treated with antibiotics, which increased their survival rate, indicating that blocking DsbA may be a good approach to tackling antibiotic resistant bacteria. According to the World Health Organization, developing new treatments against Gram-negative bacteria is of critical importance, but the discovery of new drugs has ground to a halt. One way around this is to develop ways to make existing drugs work better. Making drugs that block DsbA could offer a way to treat resistant infections using existing antibiotics in the future.
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Affiliation(s)
| | - Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Declan Barker
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Patricia Bernal
- Department of Microbiology, Universidad de Sevilla, Seville, Spain
| | - Evgenia Maslova
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Amanda Aa Antwi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Helen E McNeil
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Hannah L Pugh
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Paris-Sud University, Paris, France
| | - Jessica Ma Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | | | - Ronan R McCarthy
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Diego Gonzalez
- Department of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Despoina Ai Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
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14
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Ciusa ML, Marshall RL, Ricci V, Stone JW, Piddock LJV. Absence, loss-of-function, or inhibition of Escherichia coli AcrB does not increase expression of other efflux pump genes supporting the discovery of AcrB inhibitors as antibiotic adjuvants. J Antimicrob Chemother 2021; 77:633-640. [PMID: 34897478 PMCID: PMC8865010 DOI: 10.1093/jac/dkab452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives To determine whether expression of efflux pumps and antibiotic susceptibility are altered in Escherichia coli in response to efflux inhibition. Methods The promoter regions of nine efflux pump genes (acrAB, acrD, acrEF, emrAB, macAB, cusCFBA, mdtK, mdtABC, mdfA) were fused to gfp in pMW82 and fluorescence from each reporter construct was used as a measure of the transcriptional response to conditions in which AcrB was inhibited, absent or made non-functional. Expression was also determined by RT-qPCR. Drug susceptibility of efflux pump mutants with missense mutations known or predicted to cause loss of function of the encoded efflux pump was investigated. Results Data from the GFP reporter constructs revealed that no increased expression of the tested efflux pump genes was observed when AcrB was absent, made non-functional, or inhibited by an efflux pump inhibitor/competitive substrate, such as PAβN or chlorpromazine. This was confirmed by RT-qPCR for PAβN and chlorpromazine; however, a small but significant increase in macB gene expression was seen when acrB is deleted. Efflux inhibitors only synergized with antibiotics in the presence of a functional AcrB. When AcrB was absent or non-functional, there was no impact on MICs when other efflux pumps were also made non-functional. Conclusions Absence, loss-of-function, or inhibition of E. coli AcrB did not significantly increase expression of other efflux pump genes, which suggests there is no compensatory mechanism to overcome efflux inhibition and supports the discovery of inhibitors of AcrB as antibiotic adjuvants.
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Affiliation(s)
- Maria Laura Ciusa
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Robert L Marshall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Vito Ricci
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jack W Stone
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Laura J V Piddock
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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15
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Persister Escherichia coli Cells Have a Lower Intracellular pH than Susceptible Cells but Maintain Their pH in Response to Antibiotic Treatment. mBio 2021; 12:e0090921. [PMID: 34281389 PMCID: PMC8406257 DOI: 10.1128/mbio.00909-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Persister and viable but non-culturable (VBNC) cells are two clonal subpopulations that can survive multidrug exposure via a plethora of putative molecular mechanisms. Here, we combine microfluidics, time-lapse microscopy, and a plasmid-encoded fluorescent pH reporter to measure the dynamics of the intracellular pH of individual persister, VBNC, and susceptible Escherichia coli cells in response to ampicillin treatment. We found that even before antibiotic exposure, persisters have a lower intracellular pH than those of VBNC and susceptible cells. We then investigated the molecular mechanisms underlying the observed differential pH regulation in persister E. coli cells and found that this is linked to the activity of the enzyme tryptophanase, which is encoded by tnaA. In fact, in a ΔtnaA strain, we found no difference in intracellular pH between persister, VBNC, and susceptible E. coli cells. Whole-genome transcriptomic analysis revealed that, besides downregulating tryptophan metabolism, the ΔtnaA strain downregulated key pH homeostasis pathways, including the response to pH, oxidation reduction, and several carboxylic acid catabolism processes, compared to levels of expression in the parental strain. Our study sheds light on pH homeostasis, proving that the regulation of intracellular pH is not homogeneous within a clonal population, with a subset of cells displaying a differential pH regulation to perform dedicated functions, including survival after antibiotic treatment. IMPORTANCE Persister and VBNC cells can phenotypically survive environmental stressors, such as antibiotic treatment, limitation of nutrients, and acid stress, and have been linked to chronic infections and antimicrobial resistance. It has recently been suggested that pH regulation might play a role in an organism's phenotypic survival to antibiotics; however, this hypothesis remains to be tested. Here, we demonstrate that even before antibiotic treatment, cells that will become persisters have a more acidic intracellular pH than clonal cells that will be either susceptible or VBNC upon antibiotic treatment. Moreover, after antibiotic treatment, persisters become more alkaline than VBNC and susceptible E. coli cells. This newly found phenotypic feature is remarkable because it distinguishes persister and VBNC cells that have often been thought to display the same dormant phenotype. We then show that this differential pH regulation is abolished in the absence of the enzyme tryptophanase via a major remodeling of bacterial metabolism and pH homeostasis. These new whole-genome transcriptome data should be taken into account when modeling bacterial metabolism at the crucial transition from exponential to stationary phase. Overall, our findings indicate that the manipulation of the intracellular pH represents a bacterial strategy for surviving antibiotic treatment. In turn, this suggests a strategy for developing persister-targeting antibiotics by interfering with cellular components, such as tryptophanase, that play a major role in pH homeostasis.
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16
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Vaisman A, Łazowski K, Reijns MAM, Walsh E, McDonald JP, Moreno KC, Quiros DR, Schmidt M, Kranz H, Yang W, Makiela-Dzbenska K, Woodgate R. Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity. Mol Microbiol 2021; 116:909-925. [PMID: 34181784 PMCID: PMC8485763 DOI: 10.1111/mmi.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/26/2022]
Abstract
The Escherichia coli dnaE gene encodes the α‐catalytic subunit (pol IIIα) of DNA polymerase III, the cell’s main replicase. Like all high‐fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so‐called “steric gate” residue in the active site of the polymerase that physically clashes with the 2′‐OH of an incoming ribonucleotide. Our structural modeling data suggest that H760 is the steric gate residue in E.coli pol IIIα. To understand how H760 and the adjacent S759 residue help maintain genome stability, we generated DNA fragments in which the codons for H760 or S759 were systematically changed to the other nineteen naturally occurring amino acids and attempted to clone them into a plasmid expressing pol III core (α‐θ‐ε subunits). Of the possible 38 mutants, only nine were successfully sub‐cloned: three with substitutions at H760 and 6 with substitutions at S759. Three of the plasmid‐encoded alleles, S759C, S759N, and S759T, exhibited mild to moderate mutator activity and were moved onto the chromosome for further characterization. These studies revealed altered phenotypes regarding deoxyribonucleotide base selectivity and ribonucleotide discrimination. We believe that these are the first dnaE mutants with such phenotypes to be reported in the literature.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Krystian Łazowski
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Martin A M Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Erin Walsh
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kristiniana C Moreno
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dominic R Quiros
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marlen Schmidt
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Harald Kranz
- Gen-H Genetic Engineering Heidelberg GmbH, Heidelberg, Germany
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karolina Makiela-Dzbenska
- Laboratory of DNA Replication and Genome Stability, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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17
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Metabolomics Reveal Potential Natural Substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium. mBio 2021; 12:mBio.00109-21. [PMID: 33785633 PMCID: PMC8092203 DOI: 10.1128/mbio.00109-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multidrug-resistant Gram-negative bacteria pose a global threat to human health. The AcrB efflux pump confers inherent and evolved drug resistance to Enterobacterales, including Escherichia coli and Salmonella enterica serovar Typhimurium. In the fight against antibiotic resistance, drugs that target resistance mechanisms in bacteria can be used to restore the therapeutic effectiveness of antibiotics. The multidrug resistance efflux complex AcrAB-TolC is the most clinically relevant efflux pump in Enterobacterales and is a target for drug discovery. Inhibition of the pump protein AcrB allows the intracellular accumulation of a wide variety of antibiotics, effectively restoring their therapeutic potency. To facilitate the development of AcrB efflux inhibitors, it is desirable to discover the native substrates of the pump, as these could be chemically modified to become inhibitors. We analyzed the native substrate profile of AcrB in Escherichia coli MG1655 and Salmonella enterica serovar Typhimurium SL1344 using an untargeted metabolomics approach. We analyzed the endo- and exometabolome of the wild-type strain and their respective AcrB loss-of-function mutants (AcrB D408A) to determine the metabolites that are native substrates of AcrB. Although there is 95% homology between the AcrB proteins of S. Typhimurium and E. coli, we observed mostly different metabolic responses in the exometabolomes of the S. Typhimurium and E. coli AcrB D408A mutants relative to those in the wild type, potentially indicating a differential metabolic adaptation to the same mutation in these two species. Additionally, we uncovered metabolite classes that could be involved in virulence of S. Typhimurium and a potential natural substrate of AcrB common to both species.
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18
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Brewer SM, Twittenhoff C, Kortmann J, Brubaker SW, Honeycutt J, Massis LM, Pham THM, Narberhaus F, Monack DM. A Salmonella Typhi RNA thermosensor regulates virulence factors and innate immune evasion in response to host temperature. PLoS Pathog 2021; 17:e1009345. [PMID: 33651854 PMCID: PMC7954313 DOI: 10.1371/journal.ppat.1009345] [Citation(s) in RCA: 19] [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: 10/18/2020] [Revised: 03/12/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
Sensing and responding to environmental signals is critical for bacterial pathogens to successfully infect and persist within hosts. Many bacterial pathogens sense temperature as an indication they have entered a new host and must alter their virulence factor expression to evade immune detection. Using secondary structure prediction, we identified an RNA thermosensor (RNAT) in the 5' untranslated region (UTR) of tviA encoded by the typhoid fever-causing bacterium Salmonella enterica serovar Typhi (S. Typhi). Importantly, tviA is a transcriptional regulator of the critical virulence factors Vi capsule, flagellin, and type III secretion system-1 expression. By introducing point mutations to alter the mRNA secondary structure, we demonstrate that the 5' UTR of tviA contains a functional RNAT using in vitro expression, structure probing, and ribosome binding methods. Mutational inhibition of the RNAT in S. Typhi causes aberrant virulence factor expression, leading to enhanced innate immune responses during infection. In conclusion, we show that S. Typhi regulates virulence factor expression through an RNAT in the 5' UTR of tviA. Our findings demonstrate that limiting inflammation through RNAT-dependent regulation in response to host body temperature is important for S. Typhi's "stealthy" pathogenesis.
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Affiliation(s)
- Susan M. Brewer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Jens Kortmann
- Genentech, Inc., South San Francisco, California, United States of America
| | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jared Honeycutt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Liliana Moura Massis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trung H. M. Pham
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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19
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Fast and antibiotic free genome integration into Escherichia coli chromosome. Sci Rep 2020; 10:16510. [PMID: 33020519 PMCID: PMC7536200 DOI: 10.1038/s41598-020-73348-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022] Open
Abstract
Genome-based Escherichia coli expression systems are superior to conventional plasmid-based systems as the metabolic load triggered by recombinant compounds is significantly reduced. The efficiency of T7-based transcription compensates for low gene dosage (single copy) and facilitates high product formation rates. While common Gene Bridges' λ-red mediated recombination technique for site directed integration of genes into the host genome is very efficient, selection for positive clones is based on antibiotic resistance markers and removal thereof is often time consuming. For the generation of industrial production strains, flexibility in terms of integration site is not required, yet time from gene design to a stable clone is a quite relevant parameter. In this study, we developed a fast, efficient and antibiotic-free integration method for E. coli as production strain. We combined the λ-red recombination system with the site-directed homing endonuclease I from Saccharaomyces cerevisiae (I-SceI) for selection. In a first step, λ-red proteins are performing genome integration of a linear, antibiotic marker-free integration cassette. The engineered host strain carries the I-SceI restriction sequence at the attTn7 site, where the integration event happens. After homologous recombination and integration at the target site, site-specific genome cleavage by endonuclease I-SceI is induced, thereby killing all cells still containing an intact I-SceI site. In case of positive recombination events, the genomic I-SceI site is deleted and cleavage is no longer possible. Since plasmids are designed to contain another I-SceI restriction site they are destroyed by self-cleavage, a procedure replacing the time-consuming plasmid curing. The new plasmid-based "All-In-One" genome integration method facilitates significantly accelerated generation of genome-integrated production strains in 4 steps.
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20
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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21
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Cianfanelli FR, Cunrath O, Bumann D. Efficient dual-negative selection for bacterial genome editing. BMC Microbiol 2020; 20:129. [PMID: 32448155 PMCID: PMC7245781 DOI: 10.1186/s12866-020-01819-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Gene editing is key for elucidating gene function. Traditional methods, such as consecutive single-crossovers, have been widely used to modify bacterial genomes. However, cumbersome cloning and limited efficiency of negative selection often make this method slower than other methods such as recombineering. Results Here, we established a time-effective variant of consecutive single-crossovers. This method exploits rapid plasmid construction using Gibson assembly, a convenient E. coli donor strain, and efficient dual-negative selection for improved suicide vector resolution. We used this method to generate in-frame deletions, insertions and point mutations in Salmonella enterica with limited hands-on time. Adapted versions enabled efficient gene editing also in Pseudomonas aeruginosa and multi-drug resistant (MDR) Escherichia coli clinical isolates. Conclusions Our method is time-effective and allows facile manipulation of multiple bacterial species including MDR clinical isolates. We anticipate that this method might be broadly applicable to additional bacterial species, including those for which recombineering has been difficult to implement.
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Affiliation(s)
| | - Olivier Cunrath
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland.
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22
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Buckner MMC, Ciusa ML, Meek RW, Moorey AR, McCallum GE, Prentice EL, Reid JP, Alderwick LJ, Di Maio A, Piddock LJV. HIV Drugs Inhibit Transfer of Plasmids Carrying Extended-Spectrum β-Lactamase and Carbapenemase Genes. mBio 2020; 11:e03355-19. [PMID: 32098822 PMCID: PMC7042701 DOI: 10.1128/mbio.03355-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial-resistant (AMR) infections pose a serious risk to human and animal health. A major factor contributing to this global crisis is the sharing of resistance genes between different bacteria via plasmids. The WHO lists Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae, producing extended-spectrum β-lactamases (ESBL) and carbapenemases as "critical" priorities for new drug development. These resistance genes are most often shared via plasmid transfer. However, finding methods to prevent resistance gene sharing has been hampered by the lack of screening systems for medium-/high-throughput approaches. Here, we have used an ESBL-producing plasmid, pCT, and a carbapenemase-producing plasmid, pKpQIL, in two different Gram-negative bacteria, E. coli and K. pneumoniae Using these critical resistance-pathogen combinations, we developed an assay using fluorescent proteins, flow cytometry, and confocal microscopy to assess plasmid transmission inhibition within bacterial populations in a medium-throughput manner. Three compounds with some reports of antiplasmid properties were tested; chlorpromazine reduced transmission of both plasmids and linoleic acid reduced transmission of pCT. We screened the Prestwick library of over 1,200 FDA-approved drugs/compounds. From this, we found two nucleoside analogue drugs used to treat HIV, abacavir and azidothymidine (AZT), which reduced plasmid transmission (AZT, e.g., at 0.25 μg/ml reduced pCT transmission in E. coli by 83.3% and pKpQIL transmission in K. pneumoniae by 80.8% compared to untreated controls). Plasmid transmission was reduced by concentrations of the drugs which are below peak serum concentrations and are achievable in the gastrointestinal tract. These drugs could be used to decolonize humans, animals, or the environment from AMR plasmids.IMPORTANCE More and more bacterial infections are becoming resistant to antibiotics. This has made treatment of many infections very difficult. One of the reasons this is such a large problem is that bacteria are able to share their genetic material with other bacteria, and these shared genes often include resistance to a variety of antibiotics, including some of our drugs of last resort. We are addressing this problem by using a fluorescence-based system to search for drugs that will stop bacteria from sharing resistance genes. We uncovered a new role for two drugs used to treat HIV and show that they are able to prevent the sharing of two different types of resistance genes in two unique bacterial strains. This work lays the foundation for future work to reduce the prevalence of resistant infections.
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Affiliation(s)
- Michelle M C Buckner
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - M Laura Ciusa
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Richard W Meek
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alice R Moorey
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Gregory E McCallum
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Emma L Prentice
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Jeremy P Reid
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alessandro Di Maio
- Birmingham Advanced Light Microscopy, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Laura J V Piddock
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
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23
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Ricci V, Zhang D, Teale C, Piddock LJV. The O-Antigen Epitope Governs Susceptibility to Colistin in Salmonella enterica. mBio 2020; 11:e02831-19. [PMID: 31992619 PMCID: PMC6989106 DOI: 10.1128/mbio.02831-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/09/2019] [Indexed: 12/15/2022] Open
Abstract
Group D and group B Salmonella enterica serovars differ in their susceptibility to colistin with the former frequently intrinsically resistant (MIC > 2 μg/ml); however, the mechanism has not been described. Here, we show that the O-antigen epitope in group D Salmonella governs the levels of colistin susceptibility. Substitution of the rfbJ gene in a group B Salmonella with the rfbSE genes from a group D Salmonella conferred a decrease in susceptibility to colistin. The presence of dideoxyhexose, abequose, and the deoxymannose, tyvelose, differentiate the Salmonella group B and group D O antigens, respectively. We hypothesize that the subtle difference between abequose and tyvelose hinders the colistin molecule from reaching its target. Whole-genome sequencing also revealed that increased colistin susceptibility in a group D Salmonella veterinary isolate was due to a defect in the O-antigen polymerase protein, Rfc. This study shows that two different mechanisms that influence the presence and composition of O antigens affect colistin susceptibility in Salmonella entericaIMPORTANCE Some serovars of Salmonella, namely, those belonging to group D, appear to show a degree of intrinsic resistance to colistin. This observed intrinsic colistin resistance is of concern since this last-resort drug might no longer be effective for treating severe human infections with the most common Salmonella serovar, Salmonella enterica serovar Enteritidis. Here, we show that the O-antigen epitope in group D Salmonella governs the levels of colistin susceptibility. Using whole-genome sequencing, we also revealed that increased colistin susceptibility in a group D Salmonella veterinary isolate was due to a defect in the O-antigen polymerase protein, Rfc. In summary, we show that two different mechanisms that influence the presence and composition of O antigens affect colistin susceptibility in Salmonella enterica.
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Affiliation(s)
- Vito Ricci
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
| | - Dexian Zhang
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Husbandry and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Christopher Teale
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, United Kingdom
| | - Laura J V Piddock
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
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24
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Salmonella enterica Requires Lipid Metabolism Genes To Replicate in Proinflammatory Macrophages and Mice. Infect Immun 2019; 88:IAI.00776-19. [PMID: 31611277 DOI: 10.1128/iai.00776-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 12/28/2022] Open
Abstract
To survive and replicate during infection, pathogens utilize different carbon and energy sources depending on the nutritional landscape of their host microenvironment. Salmonella enterica serovar Typhimurium is an intracellular bacterial pathogen that occupies diverse cellular niches. While it is clear that Salmonella Typhimurium requires access to glucose during systemic infection, data on the need for lipid metabolism are mixed. We report that Salmonella Typhimurium strains lacking lipid metabolism genes were defective for systemic infection of mice. Bacterial lipid import, β-oxidation, and glyoxylate shunt genes were required for tissue colonization upon oral or intraperitoneal inoculation. In cultured macrophages, lipid import and β-oxidation genes were required for bacterial replication and/or survival only when the cell culture medium was supplemented with nonessential amino acids. Removal of glucose from tissue culture medium further enhanced these phenotypes and, in addition, conferred a requirement for glyoxylate shunt genes. We also observed that Salmonella Typhimurium needs lipid metabolism genes in proinflammatory but not anti-inflammatory macrophages. These results suggest that during systemic infection, the Salmonella Typhimurium that relies upon host lipids to replicate is within proinflammatory macrophages that have access to amino acids but not glucose. An improved understanding of the host microenvironments in which pathogens have specific metabolic requirements may facilitate the development of targeted approaches to treatment.
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25
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Alanyl-tRNA Synthetase Quality Control Prevents Global Dysregulation of the Escherichia coli Proteome. mBio 2019; 10:mBio.02921-19. [PMID: 31848288 PMCID: PMC6918089 DOI: 10.1128/mbio.02921-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mechanisms have evolved to prevent errors in replication, transcription, and translation of genetic material, with translational errors occurring most frequently. Errors in protein synthesis can occur at two steps, during tRNA aminoacylation and ribosome decoding. Recent advances in protein mass spectrometry have indicated that previous reports of translational errors have potentially underestimated the frequency of these events, but also that the majority of translational errors occur during ribosomal decoding, suggesting that aminoacylation errors are evolutionarily less tolerated. Despite that interpretation, there is evidence that some aminoacylation errors may be regulated, and thus provide a benefit to the cell, while others are clearly detrimental. Here, we show that while it has been suggested that regulated Thr-to-Ser substitutions may be beneficial, there is a threshold beyond which these errors are detrimental. In contrast, we show that errors mediated by alanyl-tRNA synthetase (AlaRS) are not well tolerated and induce a global stress response that leads to gross perturbation of the Escherichia coli proteome, with potentially catastrophic effects on fitness and viability. Tolerance for Ala mistranslation appears to be much lower than with other translational errors, consistent with previous reports of multiple proofreading mechanisms targeting mischarged tRNAAla These results demonstrate the essential role of aminoacyl-tRNA proofreading in optimizing cellular fitness and suggest that any potentially beneficial effects of mistranslation may be confined to specific amino acid substitutions.IMPORTANCE Errors in protein synthesis have historically been assumed to be detrimental to the cell. While there are many reports that translational errors are consequential, there is a growing body of evidence that some mistranslation events may be tolerated or even beneficial. Using two models of mistranslation, we compare the direct phenotypic effects of these events in Escherichia coli This work provides insight into the threshold for tolerance of specific mistranslation events that were previously predicted to be broadly neutral to proteome integrity. Furthermore, these data reveal the effects of mistranslation beyond the general unfolded stress response, leading to global translational reprogramming.
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26
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Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. eLife 2019; 8:53535. [PMID: 31815667 PMCID: PMC6941894 DOI: 10.7554/elife.53535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited by an evolving gene. We have evolved a strain of Escherichia coli in which a secondary promiscuous activity has been recruited to serve an essential function. The gene encoding the ‘weak-link’ enzyme amplified in all eight populations, but mutations improving the newly needed activity occurred in only one. Most adaptive mutations occurred elsewhere in the genome. Some mutations increase expression of the enzyme upstream of the weak-link enzyme, pushing material through the dysfunctional metabolic pathway. Others enhance production of a co-substrate for a downstream enzyme, thereby pulling material through the pathway. Most of these latter mutations are detrimental in wild-type E. coli, and thus would require reversion or compensation once a sufficient new activity has evolved.
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Affiliation(s)
- Andrew B Morgenthaler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Wallis R Kinney
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Christopher C Ebmeier
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Corinne M Walsh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, United States
| | - Daniel J Snyder
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Vaughn S Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - William M Old
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Shelley D Copley
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
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27
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Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet 2018; 14:e1007615. [PMID: 30148850 PMCID: PMC6128649 DOI: 10.1371/journal.pgen.1007615] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/07/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023] Open
Abstract
Synonymous mutations do not alter the specified amino acid but may alter the structure or function of an mRNA in ways that impact fitness. There are few examples in the literature, however, in which the effects of synonymous mutations on microbial growth rates have been measured, and even fewer for which the underlying mechanism is understood. We evolved four populations of a strain of Salmonella enterica in which a promiscuous enzyme has been recruited to replace an essential enzyme. A previously identified point mutation increases the enzyme’s ability to catalyze the newly needed reaction (required for arginine biosynthesis) but decreases its ability to catalyze its native reaction (required for proline biosynthesis). The poor performance of this enzyme limits growth rate on glucose. After 260 generations, we identified two synonymous mutations in the first six codons of the gene encoding the weak-link enzyme that increase growth rate by 41 and 67%. We introduced all possible synonymous mutations into the first six codons and found substantial effects on growth rate; one doubles growth rate, and another completely abolishes growth. Computational analyses suggest that these mutations affect either the stability of a stem-loop structure that sequesters the start codon or the accessibility of the region between the Shine-Dalgarno sequence and the start codon. Thus, these mutations would be predicted to affect translational efficiency and thereby indirectly affect mRNA stability because translating ribosomes protect mRNA from degradation. Experimental data support these hypotheses. We conclude that the effects of the synonymous mutations are due to a combination of effects on mRNA stability and translation efficiency that alter levels of the weak-link enzyme. These findings suggest that synonymous mutations can have profound effects on fitness under strong selection and that their importance in evolution may be under-appreciated. When a new enzyme is needed, microbes often recruit a pre-existing enzyme with a promiscuous activity corresponding to the newly needed activity. Such enzymes are often the “weak-link” in metabolism because they have not evolved to efficiently catalyze the new reaction. Under these circumstances, increasing the level of the weak-link enzyme can improve fitness. We evolved a strain of S. enterica in which a weak-link enzyme–E383A ProA–serves essential functions in synthesis of proline and arginine for 260 generations and then sequenced the genomes of several evolved strains. A mutation in the promoter of the operon encoding E383A ProA increased growth rate 9-fold. More surprisingly, a mutation upstream of the start codon and two synonymous mutations within the first six codons also increased growth rate by up to 68%. Introduction of all possible synonymous mutations in the first six codons showed that some doubled growth rate, while others slowed or even prevented growth. Computational and experimental data suggest that these effects were due to enhanced translational efficiency of the weak-link enzyme. These results show that synonymous mutations, once assumed to be selectively neutral, can have strong impacts on fitness when growth rate is limited by a weak-link enzyme.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Andrew B. Morgenthaler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Wallis R. Kinney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Christopher C. Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Daniel J. Snyder
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - William M. Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Vaughn S. Cooper
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
- * E-mail:
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28
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Reens AL, Crooks AL, Su CC, Nagy TA, Reens DL, Podoll JD, Edwards ME, Yu EW, Detweiler CS. A cell-based infection assay identifies efflux pump modulators that reduce bacterial intracellular load. PLoS Pathog 2018; 14:e1007115. [PMID: 29879224 PMCID: PMC6007937 DOI: 10.1371/journal.ppat.1007115] [Citation(s) in RCA: 29] [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: 02/06/2018] [Revised: 06/19/2018] [Accepted: 05/21/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial efflux pumps transport small molecules from the cytoplasm or periplasm outside the cell. Efflux pump activity is typically increased in multi-drug resistant (MDR) pathogens; chemicals that inhibit efflux pumps may have potential for antibiotic development. Using an in-cell screen, we identified three efflux pump modulators (EPMs) from a drug diversity library. The screening platform uses macrophages infected with the human Gram-negative pathogen Salmonella enterica (Salmonella) to identify small molecules that prevent bacterial replication or survival within the host environment. A secondary screen for hit compounds that increase the accumulation of an efflux pump substrate, Hoechst 33342, identified three small molecules with activity comparable to the known efflux pump inhibitor PAβN (Phe-Arg β-naphthylamide). The three putative EPMs demonstrated significant antibacterial activity against Salmonella within primary and cell culture macrophages and within a human epithelial cell line. Unlike traditional antibiotics, the three compounds did not inhibit bacterial growth in standard microbiological media. The three compounds prevented energy-dependent efflux pump activity in Salmonella and bound the AcrB subunit of the AcrAB-TolC efflux system with KDs in the micromolar range. Moreover, the EPMs display antibacterial synergy with antimicrobial peptides, a class of host innate immune defense molecules present in body fluids and cells. The EPMs also had synergistic activity with antibiotics exported by AcrAB-TolC in broth and in macrophages and inhibited efflux pump activity in MDR Gram-negative ESKAPE clinical isolates. Thus, an in-cell screening approach identified EPMs that synergize with innate immunity to kill bacteria and have potential for development as adjuvants to antibiotics.
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Affiliation(s)
- Abigail L. Reens
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Amy L. Crooks
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve, Cleveland OH, United States of America
| | - Toni A. Nagy
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - David L. Reens
- Department of Physics, University of Colorado Boulder, Boulder, CO, United States of America
- JILA, National Institutes of Standards and Technology and University of Colorado Boulder, Boulder, CO, United States of America
| | - Jessica D. Podoll
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Madeline E. Edwards
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve, Cleveland OH, United States of America
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
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29
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Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Scherer S, Neuhaus K. The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai. Front Microbiol 2018; 9:931. [PMID: 29867840 PMCID: PMC5960689 DOI: 10.3389/fmicb.2018.00931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/23/2018] [Indexed: 12/26/2022] Open
Abstract
Current notion presumes that only one protein is encoded at a given bacterial genetic locus. However, transcription and translation of an overlapping open reading frame (ORF) of 186 bp length were discovered by RNAseq and RIBOseq experiments. This ORF is almost completely embedded in the annotated L,D-transpeptidase gene ECs2385 of Escherichia coli O157:H7 Sakai in the antisense reading frame -3. The ORF is transcribed as part of a bicistronic mRNA, which includes the annotated upstream gene ECs2384, encoding a murein lipoprotein. The transcriptional start site of the operon resides 38 bp upstream of the ECs2384 start codon and is driven by a predicted σ70 promoter, which is constitutively active under different growth conditions. The bicistronic operon contains a ρ-independent terminator just upstream of the novel gene, significantly decreasing its transcription. The novel gene can be stably expressed as an EGFP-fusion protein and a translationally arrested mutant of ano, unable to produce the protein, shows a growth advantage in competitive growth experiments compared to the wild type under anaerobiosis. Therefore, the novel antisense overlapping gene is named ano (anaerobiosis responsive overlapping gene). A phylostratigraphic analysis indicates that ano originated very recently de novo by overprinting after the Escherichia/Shigella clade separated from other enterobacteria. Therefore, ano is one of the very rare cases of overlapping genes known in the genus Escherichia.
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Affiliation(s)
- Sarah M Hücker
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | - Sonja Vanderhaeghen
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany
| | | | - Siegfried Scherer
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.,Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Technical University of Munich, Freising, Germany.,Core Facility Microbiome/NGS, Institute for Food & Health, Technical University of Munich, Freising, Germany
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30
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Tenthorey JL, Haloupek N, López-Blanco JR, Grob P, Adamson E, Hartenian E, Lind NA, Bourgeois NM, Chacón P, Nogales E, Vance RE. The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion. Science 2018; 358:888-893. [PMID: 29146805 PMCID: PMC5842810 DOI: 10.1126/science.aao1140] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022]
Abstract
Robust innate immune detection of rapidly evolving pathogens is critical for host defense. Nucleotide-binding domain leucine-rich repeat (NLR) proteins function as cytosolic innate immune sensors in plants and animals. However, the structural basis for ligand-induced NLR activation has so far remained unknown. NAIP5 (NLR family, apoptosis inhibitory protein 5) binds the bacterial protein flagellin and assembles with NLRC4 to form a multiprotein complex called an inflammasome. Here we report the cryo-electron microscopy structure of the assembled ~1.4-megadalton flagellin-NAIP5-NLRC4 inflammasome, revealing how a ligand activates an NLR. Six distinct NAIP5 domains contact multiple conserved regions of flagellin, prying NAIP5 into an open and active conformation. We show that innate immune recognition of multiple ligand surfaces is a generalizable strategy that limits pathogen evolution and immune escape.
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Affiliation(s)
- Jeannette L Tenthorey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicole Haloupek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - José Ramón López-Blanco
- Departamento de Química Física Biológica, Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Patricia Grob
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Elise Adamson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicholas A Lind
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Natasha M Bourgeois
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Pablo Chacón
- Departamento de Química Física Biológica, Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Russell E Vance
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Cancer Research Laboratory and Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, CA 94720, USA
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Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Wecko R, Simon S, Scherer S, Neuhaus K. A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. BMC Evol Biol 2018; 18:21. [PMID: 29433444 PMCID: PMC5810103 DOI: 10.1186/s12862-018-1134-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
Background Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few overlapping gene pairs have been described in bacteria. In contrast, transcriptome and translatome sequencing reveals many signals originated from the antisense strand of annotated genes, of which we analyzed an example gene pair in more detail. Results A small open reading frame of Escherichia coli O157:H7 strain Sakai (EHEC), designated laoB (L-arginine responsive overlapping gene), is embedded in reading frame −2 in the antisense strand of ECs5115, encoding a CadC-like transcriptional regulator. This overlapping gene shows evidence of transcription and translation in Luria-Bertani (LB) and brain-heart infusion (BHI) medium based on RNA sequencing (RNAseq) and ribosomal-footprint sequencing (RIBOseq). The transcriptional start site is 289 base pairs (bp) upstream of the start codon and transcription termination is 155 bp downstream of the stop codon. Overexpression of LaoB fused to an enhanced green fluorescent protein (EGFP) reporter was possible. The sequence upstream of the transcriptional start site displayed strong promoter activity under different conditions, whereas promoter activity was significantly decreased in the presence of L-arginine. A strand-specific translationally arrested mutant of laoB provided a significant growth advantage in competitive growth experiments in the presence of L-arginine compared to the wild type, which returned to wild type level after complementation of laoB in trans. A phylostratigraphic analysis indicated that the novel gene is restricted to the Escherichia/Shigella clade and might have originated recently by overprinting leading to the expression of part of the antisense strand of ECs5115. Conclusions Here, we present evidence of a novel small protein-coding gene laoB encoded in the antisense frame −2 of the annotated gene ECs5115. Clearly, laoB is evolutionarily young and it originated in the Escherichia/Shigella clade by overprinting, a process which may cause the de novo evolution of bacterial genes like laoB. Electronic supplementary material The online version of this article (10.1186/s12862-018-1134-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah M Hücker
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,Fraunhofer ITEM-R, Am Biopark 9, 93053, Regensburg, Germany
| | - Sonja Vanderhaeghen
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Isabel Abellan-Schneyder
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Romy Wecko
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Svenja Simon
- Department of Computer and Information Science, University of Konstanz, Box 78, 78457, Konstanz, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Klaus Neuhaus
- Chair for Microbial Ecology, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,Core Facility Microbiome/NGS, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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Abstract
AcrAB-TolC is the paradigm resistance-nodulation-division (RND) multidrug resistance efflux system in Gram-negative bacteria, with AcrB being the pump protein in this complex. We constructed a nonfunctional AcrB mutant by replacing D408, a highly conserved residue essential for proton translocation. Western blotting confirmed that the AcrB D408A mutant had the same native level of expression of AcrB as the parental strain. The mutant had no growth deficiencies in rich or minimal medium. However, compared with wild-type SL1344, the mutant had increased accumulation of Hoechst 33342 dye and decreased efflux of ethidium bromide and was multidrug hypersusceptible. The D408A mutant was attenuated in vivo in mouse and Galleria mellonella models and showed significantly reduced invasion into intestinal epithelial cells and macrophages in vitro A dose-dependent inhibition of invasion was also observed when two different efflux pump inhibitors were added to the wild-type strain during infection of epithelial cells. RNA sequencing (RNA-seq) revealed downregulation of bacterial factors necessary for infection, including those in the Salmonella pathogenicity islands 1, 2, and 4; quorum sensing genes; and phoPQ Several general stress response genes were upregulated, probably due to retention of noxious molecules inside the bacterium. Unlike loss of AcrB protein, loss of efflux function did not induce overexpression of other RND efflux pumps. Our data suggest that gene deletion mutants are unsuitable for studying membrane transporters and, importantly, that inhibitors of AcrB efflux function will not induce expression of other RND pumps.IMPORTANCE Antibiotic resistance is a major public health concern. In Gram-negative bacteria, overexpression of the AcrAB-TolC multidrug efflux system confers resistance to clinically useful drugs. Here, we show that loss of AcrB efflux function causes loss of virulence in Salmonella enterica serovar Typhimurium. This is due to the reduction of bacterial factors necessary for infection, which is likely to be caused by the retention of noxious molecules inside the bacterium. We also show that, in contrast to loss of AcrB protein, loss of efflux does not induce overexpression of other efflux pumps from the same family. This indicates that there are differences between loss of efflux protein and loss of efflux that make gene deletion mutants unsuitable for studying the biological function of membrane transporters. Understanding the biological role of AcrB will help to assess the risks of targeting efflux pumps as a strategy to combat antibiotic resistance.
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Ryu YS, Chandran SP, Kim K, Lee SK. Oligo- and dsDNA-mediated genome editing using a tetA dual selection system in Escherichia coli. PLoS One 2017; 12:e0181501. [PMID: 28719630 PMCID: PMC5515457 DOI: 10.1371/journal.pone.0181501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
The ability to precisely and seamlessly modify a target genome is needed for metabolic engineering and synthetic biology techniques aimed at creating potent biosystems. Herein, we report on a promising method in Escherichia coli that relies on the insertion of an optimized tetA dual selection cassette followed by replacement of the same cassette with short, single-stranded DNA (oligos) or long, double-stranded DNA and the isolation of recombinant strains by negative selection using NiCl2. This method could be rapidly and successfully used for genome engineering, including deletions, insertions, replacements, and point mutations, without inactivation of the methyl-directed mismatch repair (MMR) system and plasmid cloning. The method we describe here facilitates positive genome-edited recombinants with selection efficiencies ranging from 57 to 92%. Using our method, we increased lycopene production (3.4-fold) by replacing the ribosome binding site (RBS) of the rate-limiting gene (dxs) in the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway with a strong RBS. Thus, this method could be used to achieve scarless, proficient, and targeted genome editing for engineering E. coli strains.
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Affiliation(s)
- Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sathesh-Prabu Chandran
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Kyungchul Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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Tikh IB, Samuelson JC. Leveraging modern DNA assembly techniques for rapid, markerless genome modification. Biol Methods Protoc 2016; 1:bpw004. [PMID: 32368618 PMCID: PMC7189271 DOI: 10.1093/biomethods/bpw004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
Abstract
The ability to alter the genomic material of a prokaryotic cell is necessary for experiments designed to define the biology of the organism. In addition, the production of biomolecules may be significantly improved by application of engineered prokaryotic host cells. Furthermore, in the age of synthetic biology, speed and efficiency are key factors when choosing a method for genome alteration. To address these needs, we have developed a method for modification of the Escherichia coli genome named FAST-GE for Fast Assembly-mediated Scarless Targeted Genome Editing. Traditional cloning steps such as plasmid transformation, propagation and isolation were eliminated. Instead, we developed a DNA assembly-based approach for generating scarless strain modifications, which may include point mutations, deletions and gene replacements, within 48 h after the receipt of polymerase chain reaction primers. The protocol uses established, but optimized, genome modification components such as I-SceI endonuclease to improve recombination efficiency and SacB as a counter-selection mechanism. All DNA-encoded components are assembled into a single allele-exchange vector named pDEL. We were able to rapidly modify the genomes of both E. coli B and K-12 strains with high efficiency. In principle, the method may be applied to other prokaryotic organisms capable of circular dsDNA uptake and homologous recombination.
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Affiliation(s)
- Ilya B Tikh
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
| | - James C Samuelson
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
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A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J Bacteriol 2016; 198:2853-63. [PMID: 27501982 DOI: 10.1128/jb.00262-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED When microbes are faced with an environmental challenge or opportunity, preexisting enzymes with promiscuous secondary activities can be recruited to provide newly important functions. Mutations that increase the efficiency of a new activity often compromise the original activity, resulting in an inefficient bifunctional enzyme. We have investigated the mechanisms by which growth of Escherichia coli can be improved when fitness is limited by such an enzyme, E383A ProA (ProA*). ProA* can serve the functions of both ProA (required for synthesis of proline) and ArgC (required for synthesis of arginine), albeit poorly. We identified four genetic changes that improve the growth rate by up to 6.2-fold. Two point mutations in the promoter of the proBA* operon increase expression of the entire operon. Massive amplification of a genomic segment around the proBA* operon also increases expression of the entire operon. Finally, a synonymous point mutation in the coding region of proB creates a new promoter for proA* This synonymous mutation increases the level of ProA* by 2-fold but increases the growth rate by 5-fold, an ultrasensitive response likely arising from competition between two substrates for the active site of the inefficient bifunctional ProA*. IMPORTANCE The high-impact synonymous mutation we discovered in proB is remarkable for two reasons. First, most polar effects documented in the literature are detrimental. This finding demonstrates that polar effect mutations can have strongly beneficial effects, especially when an organism is facing a difficult environmental challenge for which it is poorly adapted. Furthermore, the consequence of the synonymous mutation in proB is a 2-fold increase in the level of ProA* but a disproportionately large 5.1-fold increase in growth rate. While ultrasensitive responses are often found in signaling networks and genetic circuits, an ultrasensitive response to an adaptive mutation has not been previously reported.
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Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Sci Rep 2015; 5:17874. [PMID: 26643270 PMCID: PMC4672327 DOI: 10.1038/srep17874] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Generation of multiple genomic alterations is currently a time consuming process. Here, a method was established that enables highly efficient and simultaneous deletion of multiple genes in Escherichia coli. A temperature sensitive plasmid containing arabinose inducible lambda Red recombineering genes and a rhamnose inducible flippase recombinase was constructed to facilitate fast marker-free deletions. To further speed up the procedure, we integrated the arabinose inducible lambda Red recombineering genes and the rhamnose inducible FLP into the genome of E. coli K-12 MG1655. This system enables growth at 37 °C, thereby facilitating removal of integrated antibiotic cassettes and deletion of additional genes in the same day. Phosphorothioated primers were demonstrated to enable simultaneous deletions during one round of electroporation. Utilizing these methods, we constructed strains in which four to seven genes were deleted in E. coli W and E. coli K-12. The growth rate of an E. coli K-12 quintuple deletion strain was significantly improved in the presence of high concentrations of acetate and NaCl. In conclusion, we have generated a method that enables efficient and simultaneous deletion of multiple genes in several E. coli variants. The method enables deletion of up to seven genes in as little as seven days.
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Silva-Herzog E, McDonald EM, Crooks AL, Detweiler CS. Physiologic Stresses Reveal a Salmonella Persister State and TA Family Toxins Modulate Tolerance to These Stresses. PLoS One 2015; 10:e0141343. [PMID: 26633172 PMCID: PMC4669091 DOI: 10.1371/journal.pone.0141343] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/07/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial persister cells are considered a basis for chronic infections and relapse caused by bacterial pathogens. Persisters are phenotypic variants characterized by low metabolic activity and slow or no replication. This low metabolic state increases pathogen tolerance to antibiotics and host immune defenses that target actively growing cells. In this study we demonstrate that within a population of Salmonella enterica serotype Typhimurium, a small percentage of bacteria are reversibly tolerant to specific stressors that mimic the macrophage host environment. Numerous studies show that Toxin-Antitoxin (TA) systems contribute to persister states, based on toxin inhibition of bacterial metabolism or growth. To identify toxins that may promote a persister state in response to host-associated stressors, we analyzed the six TA loci specific to S. enterica serotypes that cause systemic infection in mammals, including five RelBE family members and one VapBC member. Deletion of TA loci increased or decreased tolerance depending on the stress conditions. Similarly, exogenous expression of toxins had mixed effects on bacterial survival in response to stress. In macrophages, S. Typhimurium induced expression of three of the toxins examined. These observations indicate that distinct toxin family members have protective capabilities for specific stressors but also suggest that TA loci have both positive and negative effects on tolerance.
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Affiliation(s)
- Eugenia Silva-Herzog
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Erin M. McDonald
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Amy L. Crooks
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Corrella S. Detweiler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. Sci Rep 2015; 5:15096. [PMID: 26463009 PMCID: PMC4604488 DOI: 10.1038/srep15096] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/15/2015] [Indexed: 02/02/2023] Open
Abstract
Genome engineering methods in E. coli allow for easy to perform manipulations of the chromosome in vivo with the assistance of the λ-Red recombinase system. These methods generally rely on the insertion of an antibiotic resistance cassette followed by removal of the same cassette, resulting in a two-step procedure for genomic manipulations. Here we describe a method and plasmid system that can edit the genome of E. coli without chromosomal markers. This system, known as Scarless Cas9 Assisted Recombineering (no-SCAR), uses λ-Red to facilitate genomic integration of donor DNA and double stranded DNA cleavage by Cas9 to counterselect against wild-type cells. We show that point mutations, gene deletions, and short sequence insertions were efficiently performed in several genomic loci in a single-step with regards to the chromosome and did not leave behind scar sites. The single-guide RNA encoding plasmid can be easily cured due to its temperature sensitive origin of replication, allowing for iterative chromosomal manipulations of the same strain, as is often required in metabolic engineering. In addition, we demonstrate the ability to efficiently cure the second plasmid in the system by targeting with Cas9, leaving the cells plasmid-free.
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