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Cornet F, Blanchais C, Dusfour-Castan R, Meunier A, Quebre V, Sekkouri Alaoui H, Boudsoq F, Campos M, Crozat E, Guynet C, Pasta F, Rousseau P, Ton Hoang B, Bouet JY. DNA Segregation in Enterobacteria. EcoSal Plus 2023; 11:eesp00382020. [PMID: 37220081 PMCID: PMC10729935 DOI: 10.1128/ecosalplus.esp-0038-2020] [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: 11/24/2022] [Accepted: 04/13/2023] [Indexed: 01/28/2024]
Abstract
DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.
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Affiliation(s)
- François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Corentin Blanchais
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Romane Dusfour-Castan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Alix Meunier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Valentin Quebre
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hicham Sekkouri Alaoui
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - François Boudsoq
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Manuel Campos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Franck Pasta
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Bao Ton Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
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2
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Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids. mSphere 2022; 7:e0018422. [PMID: 36416553 PMCID: PMC9769657 DOI: 10.1128/msphere.00184-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is one of the major threats to public health worldwide. The mechanisms involved in the plasmid/host coadaptation are still poorly characterized, and their understanding is crucial to comprehend the genesis and evolution of multidrug-resistant bacteria. With this purpose, we designed an experimental evolution using Haemophilus influenzae RdKW20 as the model strain carrying the ColE1-like plasmid pB1000. Five H. influenzae populations adapted previously to the culture conditions were transformed with pB1000 and subsequently evolved to compensate for the plasmid-associated fitness cost. Afterward, we performed an integrative multiomic analysis combining genomics, transcriptomics, and metabolomics to explore the molecular mechanisms involved in the compensatory evolution of the plasmid. Our results demonstrate that minimal modifications in the host are responsible for plasmid adaptation. Among all of them, the most enriched process was amino acid metabolism, especially those pathways related to serine, tryptophan, and arginine, eventually related to the genesis and resolution of plasmid dimers. Additional rearrangements occurred during the plasmid adaptation, such as an overexpression of the ribonucleotide reductases and metabolic modifications within specific membrane phospholipids. All these findings demonstrate that the plasmid compensation occurs through the combination of diverse host-mediated mechanisms, of which some are beyond genomic and transcriptomic modifications. IMPORTANCE The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis. It is generally accepted that the acquisition and maintenance of mobile genetic elements entail a fitness cost to its host, which is susceptible to be alleviated through a coadaptation process or compensatory evolution. Notwithstanding, despite recent major efforts, the underlying mechanisms involved in this adaptation remain poorly characterized. Analyzing the plasmid/host coadaptation from a multiomic perspective sheds light on the physiological processes involved in the compensation, providing a new understanding on the genesis and evolution of plasmid-mediated antimicrobial-resistant bacteria.
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Hagbø M, Ravi A, Angell IL, Sunde M, Ludvigsen J, Diep DB, Foley SL, Vento M, Collado MC, Perez-Martinez G, Rudi K. Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota. Pediatr Res 2020; 88:57-65. [PMID: 31261372 DOI: 10.1038/s41390-019-0491-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/11/2019] [Accepted: 06/16/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND There is currently a lack of experimental evidence for horizontal gene transfer (HGT) mechanisms in the human gut microbiota. The aim of this study was therefore to experimentally determine the HGT potential in the microbiota of a healthy preterm infant twin pair and to evaluate the global occurrence of the mobilized elements. METHODS Stool samples were collected. Both shotgun metagenome sequencing and bacterial culturing were done for the same samples. A range of experimental conditions were used to test DNA transfer for the cultured isolates. Searches for global distribution of transferable elements were done for the ~120,000 metagenomic samples in the Sequence Read Archive (SRA) database. RESULTS DNA transfer experiments demonstrated frequent transmission of an ESBL encoding IncI1 plasmid, a high copy number ColEI plasmid, and bacteriophage P1. Both IncI1 and ColE1 were abundant in the stool samples. In vitro competition experiments showed that transconjugants containing IncI1 plasmids outcompeted the recipient strain in the absence of antibiotic selection. The SRA searches indicated a global distribution of the mobilizable elements, with chicken identified as a possible reservoir for the IncI1 ESBL encoding plasmid. CONCLUSION Our results experimentally support a major horizontal transmission and persistence potential of the preterm infant gut microbiota mobilome involving genes encoding ESBL.
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Affiliation(s)
- Mari Hagbø
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway
| | - Anuradha Ravi
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway
| | - Inga Leena Angell
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway
| | - Marianne Sunde
- Norwegian Veterinary Institute, Section of Food safety and Emerging Health Threats, Oslo, Norway
| | - Jane Ludvigsen
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway
| | - Dzung B Diep
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Maximo Vento
- Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Maria Carmen Collado
- Unit of Lactic Acid Bacteria and Probiotics, Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Gaspar Perez-Martinez
- Unit of Lactic Acid Bacteria and Probiotics, Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Knut Rudi
- Norwegian University of Life Sciences, Faculty of Chemistry, Biotechnology and Food Science (KBM), Campus Ås, 1433 Ås, Norway.
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Fournes F, Val ME, Skovgaard O, Mazel D. Replicate Once Per Cell Cycle: Replication Control of Secondary Chromosomes. Front Microbiol 2018; 9:1833. [PMID: 30131796 PMCID: PMC6090056 DOI: 10.3389/fmicb.2018.01833] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022] Open
Abstract
Faithful vertical transmission of genetic information, especially of essential core genes, is a prerequisite for bacterial survival. Hence, replication of all the replicons is tightly controlled to ensure that all daughter cells get the same genome copy as their mother cell. Essential core genes are very often carried by the main chromosome. However they can occasionally be found on secondary chromosomes, recently renamed chromids. Chromids have evolved from non-essential megaplasmids, and further acquired essential core genes and a genomic signature closed to that of the main chromosome. All chromids carry a plasmidic replication origin, belonging so far to either the iterons or repABC type. Based on these differences, two categories of chromids have been distinguished. In this review, we focus on the replication initiation controls of these two types of chromids. We show that the sophisticated mechanisms controlling their replication evolved from their plasmid counterparts to allow a timely controlled replication, occurring once per cell cycle.
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Affiliation(s)
- Florian Fournes
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Eve Val
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
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5
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Feizollahzadeh S, Kouhpayeh S, Rahimmansh I, Khanahmad H, Sabzehei F, Ganjalikhani-Hakemi M, Andalib A, Hejazi Z, Rezaei A. The Increase in Protein and Plasmid Yields of E. coli with Optimized Concentration of Ampicillin as Selection Marker. IRANIAN JOURNAL OF BIOTECHNOLOGY 2018; 15:128-134. [PMID: 29845060 DOI: 10.15171/ijb.1467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 10/10/2016] [Accepted: 06/19/2016] [Indexed: 02/05/2023]
Abstract
Background:Escherichia coli is still the common host for ing and heterologous protein expression. Various strategies have been employed to increase protein expression in E. coli, but, it seems that external factors such as selection marker concentration can drastically affect the yield of protein and plasmid. Objectives: Alterations of protein expression and plasmid yields of E. coli in different concentrations of ampicillin, as selection marker, will be determined. In order to improve heterologous expression, the system will be redesigned and optimized. Materials and Methods: The expression cassette of codon optimized EGFP for E. coli was synthesized in pUC57. The pUC57-GFP was transformed into E. coli Top10F'. The expression of GFP was verified by SDS-PAGE and flow cytometry after induction by IPTG (0.5 mM) and incubation with 0, 100, 200 and 300 μg.mL-1 ampicillin. Plasmid copy numbers of samples were determined by Real-Time PCR on AMP gene using regression line of diluted standard curve. Results: GFP expressing clones formed fair green colonies on LB agar supplemented with 0.5 mM IPTG and showed fluorescence in FL1 filter of flow cytometry and an extra protein band on SDS-PAGE gel. The fluorescent intensity of GFP in 0, 100, 200 and 300 μg.mL-1 ampicillin in medium were 549.83, 549.78, 1443.52, 684.87, and plasmid copy numbers were 6.07×109 , 3.21×109 , 2.32×1010 , 8.11×108 , respectively. The plasmid yields were 55 ng.μL-1, 69 ng.μL-1, 164 ng.μL-1 and 41 ng.μL-1, respectively. Conclusion: Protein and plasmid yields of E. coli are variable in different concentrations of ampicillin and need to be optimized in newly designed expression systems. Protein and plasmid yield in the optimized concentration (200 μg.mL-1) was significantly (p < 0.01) higher than other doses.
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Affiliation(s)
- Sadegh Feizollahzadeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Shirin Kouhpayeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Ilnaz Rahimmansh
- Department of Molecular Biology and Genetics, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Hossein Khanahmad
- Department of Molecular Biology and Genetics, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Faezeh Sabzehei
- Department of Molecular Biology and Genetics, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Mazdak Ganjalikhani-Hakemi
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Alireza Andalib
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Zahra Hejazi
- Department of Molecular Biology and Genetics, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
| | - Abbas Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461 Iran
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6
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Zharikova NV, Iasakov TR, Bumazhkin BK, Patutina EO, Zhurenko EI, Korobov VV, Sagitova AI, Kuznetsov BB, Markusheva TV. Isolation and sequence analysis of pCS36-4CPA, a small plasmid from Citrobacter sp. 36-4CPA. Saudi J Biol Sci 2018; 25:660-671. [PMID: 29736141 PMCID: PMC5935869 DOI: 10.1016/j.sjbs.2016.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/07/2015] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
A small plasmid designated pCS36-4CPA with a size of 5217 base pairs and G-C content of 50.74% was isolated from Citrobacter sp. 36-4CPA. The origin of replication (ori) of the plasmid was identified as a region of about 800 bp in length with an identity of 67.1% to the ColE1 plasmid at the nucleotide level. The replication region contained typical elements of ColE1-like plasmids: RNA I and RNA II with their corresponding -10 and -35 boxes, a single-strand initiation site (ssi), and a lagging-strand termination site (terH). As seen in other ColE1-like plasmids, pCS36-4CPA carried mobilisation machinery that include mobABCD genes but it did not possess the rom gene. Analysis of the multimer resolution site (mrs) was performed and XerC and XerD binding sites were identified. Also, the 70-nt transcript Rcd of pCS36-4CPA was predicted and similarity of the transcript's secondary structure with those of the ColE1-family was shown. The cargo module of pCS36-4CPA contained three open reading frames (ORFs). Two of them (ORF5 and ORF6) showed no significant homology to any known gene sequences but contained putative THAP DNA-binding (DBD) and type II restriction endonuclease EcoO109I domains. The seventh open reading frame (ORF7) encodes YhdJ-like DNA modification methylase. The region highly homologous to pCS36-4CPA was found in the Salmonella phage SE2 genome.
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7
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Cousin FJ, Lynch DB, Chuat V, Bourin MJB, Casey PG, Dalmasso M, Harris HMB, McCann A, O'Toole PW. A long and abundant non-coding RNA in Lactobacillus salivarius. Microb Genom 2017; 3:e000126. [PMID: 29114404 PMCID: PMC5643018 DOI: 10.1099/mgen.0.000126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/21/2017] [Indexed: 01/12/2023] Open
Abstract
Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq)transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.
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Affiliation(s)
- Fabien J Cousin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Denise B Lynch
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Victoria Chuat
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maxence J B Bourin
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Pat G Casey
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hugh M B Harris
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Angela McCann
- 1School of Microbiology, University College Cork, Cork, Ireland.,2APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- 2APC Microbiome Institute, University College Cork, Cork, Ireland.,1School of Microbiology, University College Cork, Cork, Ireland
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Burenina OY, Elkina DA, Hartmann RK, Oretskaya TS, Kubareva EA. Small noncoding 6S RNAs of bacteria. BIOCHEMISTRY (MOSCOW) 2015; 80:1429-46. [DOI: 10.1134/s0006297915110048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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