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Zahradka K, Zahradka D, Repar J. Structural Differences between the Genomes of Deinococcus radiodurans Strains from Different Laboratories. Genes (Basel) 2024; 15:847. [PMID: 39062626 PMCID: PMC11276467 DOI: 10.3390/genes15070847] [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: 05/24/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
The bacterium Deinococcus radiodurans is known to efficiently and accurately reassemble its genome after hundreds of DNA double-strand breaks (DSBs). Only at very large amounts of radiation-induced DSBs is this accuracy affected in the wild-type D. radiodurans, causing rearrangements in its genome structure. However, changes in its genome structure may also be possible during the propagation and storage of cell cultures. We investigate this possibility by listing structural differences between three completely sequenced genomes of D. radiodurans strains with a recent common ancestor-the type strain stored and sequenced in two different laboratories (of the ATCC 13939 lineage) and the first sequenced strain historically used as the reference (ATCC BAA-816). We detected a number of structural differences and found the most likely mechanisms behind them: (i) transposition/copy number change in mobile interspersed repeats-insertion sequences and small non-coding repeats, (ii) variable number of monomers within tandem repeats, (iii) deletions between long direct DNA repeats, and (iv) deletions between short (4-10 bp) direct DNA repeats. The most surprising finding was the deletions between short repeats because it indicates the utilization of a less accurate DSB repair mechanism in conditions in which a more accurate one should be both available and preferred. The detected structural differences, as well as SNPs and short indels, while being important footprints of deinococcal DNA metabolism and repair, are also a valuable resource for researchers using these D. radiodurans strains.
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Affiliation(s)
| | | | - Jelena Repar
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (K.Z.); (D.Z.)
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2
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A 16 th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 2022; 5:599. [PMID: 35710940 PMCID: PMC9203756 DOI: 10.1038/s42003-022-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past. Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
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3
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Reduced chlorhexidine susceptibility is associated with tetracycline resistance tet genes in clinical isolates of Escherichia coli. Antimicrob Agents Chemother 2022; 66:e0197221. [PMID: 35225650 DOI: 10.1128/aac.01972-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlorhexidine is a widely used antiseptic in hospital and community healthcare. Decreased susceptibility to this compound has been recently described in Klebsiella pneumoniae and Pseudomonas aeruginosa, together with cross-resistance to colistin. Surprisingly, few data are available for Escherichia coli, the main species responsible for community and healthcare-associated infections. In order to decipher chlorhexidine resistance mechanisms in E. coli, we studied both in vitro derived and clinical isolates through whole-genome sequence analysis. Comparison of strains grown in vitro under chlorhexidine pressure identified mutations in the gene mlaA coding for a phospholipid transport system. Phenotypic analyses of single-gene mutant from the Keio collection confirmed the role of this mutation in the decreased susceptibility to chlorhexidine. However, mutations in mlaA were not found in isolates from large clinical collections. In contrast, genome wide association studies (GWAS) showed that, in clinical strains, chlorhexidine reduced susceptibility was associated with the presence of tetA genes of class B coding for efflux pumps and located in a Tn10 transposon. Construction of recombinant strains in E. coli K-12 confirmed the role of tetA determinant in acquired resistance to both chlorhexidine and tetracycline. Our results reveal two different evolutionary paths leading to chlorhexidine decreased susceptibility: one restricted to in vitro evolution conditions and involving a retrograde phospholipid transport system; the other observed in clinical isolates associated with efflux pump TetA. None of these mechanisms provides cross-resistance to colistin. This work demonstrates the GWAS power to identify new resistance mechanisms in bacterial species.
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4
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Wu K, Cheng ZH, Williams E, Turner NT, Ran D, Li H, Zhou X, Guo H, Sung W, Liu DF, Lynch M, Long H. Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. Genome Biol Evol 2021; 13:evab148. [PMID: 34180992 PMCID: PMC8350357 DOI: 10.1093/gbe/evab148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.
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Affiliation(s)
- Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhou-Hua Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dapeng Ran
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Haichao Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Huilin Guo
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Dorman MJ, Thomson NR. 'Community evolution' - laboratory strains and pedigrees in the age of genomics. MICROBIOLOGY-SGM 2020; 166:233-238. [PMID: 31958052 PMCID: PMC7376263 DOI: 10.1099/mic.0.000869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular microbiologists depend heavily on laboratory strains of bacteria, which are ubiquitous across the community of research groups working on a common organism. However, this presumes that strains present in different laboratories are in fact identical. Work on a culture of Vibrio cholerae preserved from 1916 provoked us to consider recent studies, which have used both classical genetics and next-generation sequencing to study the heterogeneity of laboratory strains. Here, we review and discuss mutations and phenotypic variation in supposedlyisogenic reference strains of V. cholerae and Escherichia coli, and we propose that by virtue of the dissemination of laboratory strains across the world, a large ‘community evolution’ experiment is currently ongoing.
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Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK
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6
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Charpentier C, Kouby F, Hua C, Sbidian E, Darty M, Bosc R, De Prost N, Gomart C, Woerther PL, Tazi A, Decousser JW, Chosidow O. Group B streptococcal necrotizing soft-tissue infection: role of pharyngeal and perineal carriage. J Eur Acad Dermatol Venereol 2020; 35:e227-e228. [PMID: 32931041 DOI: 10.1111/jdv.16943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C Charpentier
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - F Kouby
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - C Hua
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - E Sbidian
- Department of Dermatology, Henri Mondor Hospital, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques), UPEC, Créteil, France
| | - M Darty
- Sequencing platform NGS, University Hospital Henri Mondor, Créteil, France
| | - R Bosc
- Department of Plastic, Reconstructive and Aesthetic Surgery, Henri Mondor Hospital, Créteil, France
| | - N De Prost
- Department of Medical Intensive Care Unit, Henri Mondor Hospital, Créteil, France
| | - C Gomart
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France
| | - P-L Woerther
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France.,EA 7380 Dynamyc, Paris Est Créteil University, Créteil, France
| | - A Tazi
- CNR Streptococci, Cochin Hospital, Paris, France.,Descartes University, Sorbonne, Paris, France.,INSERM U 1016, Cochin, Paris, France
| | - J-W Decousser
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France.,EA 7380 Dynamyc, Paris Est Créteil University, Créteil, France
| | - O Chosidow
- Department of Dermatology, Henri Mondor Hospital, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques), UPEC, Créteil, France.,INSERM CIC 1430, Créteil, France.,UPEC Université Paris-Est Créteil, Créteil, France
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7
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Advantage of the F2:A1:B- IncF Pandemic Plasmid over IncC Plasmids in In Vitro Acquisition and Evolution of bla CTX-M Gene-Bearing Plasmids in Escherichia coli. Antimicrob Agents Chemother 2019; 63:AAC.01130-19. [PMID: 31332067 PMCID: PMC6761558 DOI: 10.1128/aac.01130-19] [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] [Received: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022] Open
Abstract
Despite a fitness cost imposed on bacterial hosts, large conjugative plasmids play a key role in the diffusion of resistance determinants, such as CTX-M extended-spectrum β-lactamases. Among the large conjugative plasmids, IncF plasmids are the most predominant group, and an F2:A1:B- IncF-type plasmid encoding a CTX-M-15 variant was recently described as being strongly associated with the emerging worldwide Escherichia coli sequence type 131 (ST131)-O25b:H4 H30Rx/C2 sublineage. Despite a fitness cost imposed on bacterial hosts, large conjugative plasmids play a key role in the diffusion of resistance determinants, such as CTX-M extended-spectrum β-lactamases. Among the large conjugative plasmids, IncF plasmids are the most predominant group, and an F2:A1:B- IncF-type plasmid encoding a CTX-M-15 variant was recently described as being strongly associated with the emerging worldwide Escherichia coli sequence type 131 (ST131)-O25b:H4 H30Rx/C2 sublineage. In this context, we investigated the fitness cost of narrow-range F-type plasmids, including the F2:A1:B- IncF-type CTX-M-15 plasmid, and of broad-range C-type plasmids in the K-12-like J53-2 E. coli strain. Although all plasmids imposed a significant fitness cost to the bacterial host immediately after conjugation, we show, using an experimental-evolution approach, that a negative impact on the fitness of the host strain was maintained throughout 1,120 generations with the IncC-IncR plasmid, regardless of the presence or absence of cefotaxime, in contrast to the F2:A1:B- IncF plasmid, whose cost was alleviated. Many chromosomal and plasmid rearrangements were detected after conjugation in transconjugants carrying the IncC plasmids but not in transconjugants carrying the F2:A1:B- IncF plasmid, except for insertion sequence (IS) mobilization from the fliM gene leading to the restoration of motility of the recipient strains. Only a few mutations occurred on the chromosome of each transconjugant throughout the experimental-evolution assay. Our findings indicate that the F2:A1:B- IncF CTX-M-15 plasmid is well adapted to the E. coli strain studied, contrary to the IncC-IncR CTX-M-15 plasmid, and that such plasmid-host adaptation could participate in the evolutionary success of the CTX-M-15-producing pandemic E. coli ST131-O25b:H4 lineage.
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8
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Petronella N, Kundra P, Auclair O, Hébert K, Rao M, Kingsley K, De Bruyne K, Banerjee S, Gill A, Pagotto F, Tamber S, Ronholm J. Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing. Can J Microbiol 2019; 65:842-850. [PMID: 31356758 DOI: 10.1139/cjm-2019-0235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing Escherichia coli, Salmonella enterica, Listeria monocytogenes, and Vibrio parahaemolyticus were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.
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Affiliation(s)
- Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Palni Kundra
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Olivia Auclair
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Karine Hébert
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada.,Listeriosis Reference Service, Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Mary Rao
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Kyle Kingsley
- Applied Maths, Data Analytics Unit, bioMérieux, Austin, Texas, USA
| | | | - Swapan Banerjee
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Alexander Gill
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada.,Listeriosis Reference Service, Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada.,Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, Canada
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9
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Bourrel AS, Poirel L, Royer G, Darty M, Vuillemin X, Kieffer N, Clermont O, Denamur E, Nordmann P, Decousser JW, LAFAURIE M, BERCOT B, WALEWSKI V, LESCAT M, CARBONNELLE E, OUSSER F, IDRI N, RICARD JD, LANDRAUD L, LE DORZE M, JACQUIER H, CAMBAU E, LEPEULE R, GOMART C. Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways. J Antimicrob Chemother 2019; 74:1521-1530. [DOI: 10.1093/jac/dkz090] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/04/2023] Open
Affiliation(s)
- Anne Sophie Bourrel
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Laurent Poirel
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Guilhem Royer
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mélanie Darty
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Xavier Vuillemin
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Nicolas Kieffer
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Olivier Clermont
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
| | - Erick Denamur
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Patrice Nordmann
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Jean-Winoc Decousser
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
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10
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A Defective Undecaprenyl Pyrophosphate Synthase Induces Growth and Morphological Defects That Are Suppressed by Mutations in the Isoprenoid Pathway of Escherichia coli. J Bacteriol 2018; 200:JB.00255-18. [PMID: 29986944 DOI: 10.1128/jb.00255-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan exoskeleton shapes bacteria and protects them against osmotic forces, making its synthesis the target of many current antibiotics. Peptidoglycan precursors are attached to a lipid carrier and flipped from the cytoplasm into the periplasm to be incorporated into the cell wall. In Escherichia coli, this carrier is undecaprenyl phosphate (Und-P), which is synthesized as a diphosphate by the enzyme undecaprenyl pyrophosphate synthase (UppS). E. coli MG1655 exhibits wild-type morphology at all temperatures, but one of our laboratory strains (CS109) was highly aberrant when grown at 42°C. This strain contained mutations affecting the Und-P synthetic pathway genes uppS, ispH, and idi Normal morphology was restored by overexpressing uppS or by replacing the mutant (uppS31) with the wild-type allele. Importantly, moving uppS31 into MG1655 was lethal even at 30°C, indicating that the altered enzyme was highly deleterious, but growth was restored by adding the CS109 versions of ispH and idi Purified UppSW31R was enzymatically defective at all temperatures, suggesting that it could not supply enough Und-P during rapid growth unless suppressor mutations were present. We conclude that cell wall synthesis is profoundly sensitive to changes in the pool of polyisoprenoids and that isoprenoid homeostasis exerts a particularly strong evolutionary pressure.IMPORTANCE Bacterial morphology is determined primarily by the overall structure of the semirigid macromolecule peptidoglycan. Not only does peptidoglycan contribute to cell shape, but it also protects cells against lysis caused by excess osmotic pressure. Because it is critical for bacterial survival, it is no surprise that many antibiotics target peptidoglycan biosynthesis. However, important gaps remain in our understanding about how this process is affected by peptidoglycan precursor availability. Here, we report that a mutation altering the enzyme that synthesizes Und-P prevents cells from growing at high temperatures and that compensatory mutations in enzymes functioning upstream of uppS can reverse this phenotype. The results highlight the importance of Und-P metabolism for maintaining normal cell wall synthesis and shape.
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