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Blesa A, Sánchez-Costa M, Berenguer J. The PulE ATPase is required for twitching motility and DNA donation during Thermus thermophilus transjugation. Int Microbiol 2024:10.1007/s10123-024-00598-4. [PMID: 39325340 DOI: 10.1007/s10123-024-00598-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 08/28/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
Thermus thermophilus can acquire DNA through natural competence and through transjugation, a mechanism that involves a two-step process of DNA secretion (push) and DNA internalization (pull) between mating cells of related species. The natural competence apparatus (NCA) is required in the recipient mate for the pull step. However, how the DNA exits of the donor cell is only partially known. The putative DNA translocase TdtA, encoded in mobile genetic element ICETh1 of T. thermophilus HB27, was shown to be required for DNA donation as reported by (Blesa et al. 2017a). This ring-shaped hexameric ATPase binds to the membrane and likely interacts with yet unknown secretory components that allow the extrusion of DNA through the membrane; thus, a genetic screening to identify additional putative secretory components was performed. Here, we describe that mutants in gene TT_C1844, which encodes a putative AAA-ATPase named PulE, do not synthesize the recently described "narrow" type 4 pili required for twitching motility and made up of the major PilA5 pilin. Concomitantly, pulE mutants also exhibited DNA donation defects during transjugation, suggesting a role of narrow pili in the donation process. However, single pilA5 null mutants still function as DNA donors in transjugation experiments, so we conclude that the need for PulE in transjugation is independent of its role in narrow pili synthesis and twitching motility.
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Affiliation(s)
- Alba Blesa
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal S/N, 28040, Madrid, Spain.
| | - Mercedes Sánchez-Costa
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
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Sánchez‐Costa M, Gola S, Rodríguez‐Sáiz M, Barredo J, Hidalgo A, Berenguer J. From accurate genome sequence to biotechnological application: The thermophile Mycolicibacterium hassiacum as experimental model. Microb Biotechnol 2024; 17:e14290. [PMID: 37498289 PMCID: PMC10832570 DOI: 10.1111/1751-7915.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/28/2023] Open
Abstract
Mycobacteria constitute a large group of microorganisms belonging to the phylum Actinobacteria encompassing some of the most relevant pathogenic bacteria and many saprophytic isolates that share a unique and complex cell envelope. Also unique to this group is the extensive capability to use and synthesize sterols, a class of molecules that include active signalling compounds of pharmaceutical use. However, few mycobacterial species and strains have been established as laboratory models to date, Mycolicibacterium smegmatis mc2 155 being the most common one. In this work, we focus on the use of a thermophilic mycobacterium, Mycolicibacterium hassiacum, which grows optimally above 50°C, as an emerging experimental model valid to extend our general knowledge of mycobacterial biology as well as for application purposes. To that end, accurate genomic sequences are key for gene mining, the study of pathogenicity or lack thereof and the potential for gene transfer. The combination of long- and short-massive sequencing technologies is strictly necessary to remove biases caused by errors specific to long-reads technology. By doing so in M. hassiacum, we obtained from the curated genome clues regarding the genetic manipulation potential of this microorganism from the presence of insertion sequences, CRISPR-Cas, type VII ESX secretion systems, as well as lack of plasmids. Finally, as a proof of concept of the applicability of M. hassiacum as a laboratory and industrial model, we used this high-quality genome of M. hassiacum to successfully knockout a gene involved in the use of phytosterols as source of carbon and energy, using an improved gene cassette for thermostable selection and a transformation protocol at high temperature.
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Affiliation(s)
- Mercedes Sánchez‐Costa
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
| | - Susanne Gola
- Department of Medical Technology and BiotechnologyErnst‐Abbe‐Hochschule Jena, University of Applied SciencesJenaGermany
| | | | - José‐Luis Barredo
- Department of BiotechnologyCuria, Parque Tecnológico de LeónLeónSpain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
| | - José Berenguer
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
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3
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Lahiri D, Nag M, Dey A, Sarkar T, Pati S, Nirmal NP, Ray RR, Upadhye VJ, Pandit S, Moovendhan M, Kavisri M. Marine bioactive compounds as antibiofilm agent: a metabolomic approach. Arch Microbiol 2023; 205:54. [PMID: 36602609 DOI: 10.1007/s00203-022-03391-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023]
Abstract
The ocean is a treasure trove of both living and nonliving creatures, harboring incredibly diverse group of organisms. A plethora of marine sourced bioactive compounds are discovered over the past few decades, many of which are found to show antibiofilm activity. These are of immense clinical significance since the formation of microbial biofilm is associated with the development of high antibiotic resistance. Biofilms are also responsible to bring about problems associated with industries. In fact, the toilets and wash-basins also show degradation due to development of biofilm on their surfaces. Antimicrobial resistance exhibited by the biofilm can be a potent threat not only for the health care unit along with industries and daily utilities. Various recent studies have shown that the marine members of various kingdom are capable of producing antibiofilm compounds. Many such compounds are with unique structural features and metabolomics approaches are essential to study such large sets of metabolites. Associating holobiome metabolomics with analysis of their chemical attribute may bring new insights on their antibiofilm effect and their applicability as a substitute for conventional antibiotics. The application of computer-aided drug design/discovery (CADD) techniques including neural network approaches and structured-based virtual screening, ligand-based virtual screening in combination with experimental validation techniques may help in the identification of these molecules and evaluation of their drug like properties.
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Affiliation(s)
- Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, 700160, West Bengal, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, 700160, West Bengal, India
| | - Ankita Dey
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, 732102, West Bengal, India
| | - Siddhartha Pati
- Nat Nov Bioscience Private Limited, Balasore, 756001, Odisha, India
| | - Nilesh P Nirmal
- Institute of Nutrition, Mahidol University, 999 Phutthamonthon 4 Road, Salaya, 73170, Nakhon Pathom, Thailand.
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India.
| | - Vijay Jagdish Upadhye
- Center of Research for Development (CR4D), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, Gujarat, India
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201306, India
| | - M Moovendhan
- Centre for Ocean Research (DST-FIST Sponsored Centre) MoES-Earth Science & Technology Cell, Col. Dr. Jeppiaar Research Park, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - M Kavisri
- Department of Civil Engineering, School of Building and Environment, Sathyabama Institute of Science and Technology, Chennai, 600119, India
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Coluzzi C, Garcillán-Barcia MP, de la Cruz F, Rocha EPC. Evolution of plasmid mobility: origin and fate of conjugative and non-conjugative plasmids. Mol Biol Evol 2022; 39:6593704. [PMID: 35639760 PMCID: PMC9185392 DOI: 10.1093/molbev/msac115] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
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Dawood A, Algharib SA, Zhao G, Zhu T, Qi M, Delai K, Hao Z, Marawan MA, Shirani I, Guo A. Mycoplasmas as Host Pantropic and Specific Pathogens: Clinical Implications, Gene Transfer, Virulence Factors, and Future Perspectives. Front Cell Infect Microbiol 2022; 12:855731. [PMID: 35646746 PMCID: PMC9137434 DOI: 10.3389/fcimb.2022.855731] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/04/2022] [Indexed: 12/28/2022] Open
Abstract
Mycoplasmas as economically important and pantropic pathogens can cause similar clinical diseases in different hosts by eluding host defense and establishing their niches despite their limited metabolic capacities. Besides, enormous undiscovered virulence has a fundamental role in the pathogenesis of pathogenic mycoplasmas. On the other hand, they are host-specific pathogens with some highly pathogenic members that can colonize a vast number of habitats. Reshuffling mycoplasmas genetic information and evolving rapidly is a way to avoid their host's immune system. However, currently, only a few control measures exist against some mycoplasmosis which are far from satisfaction. This review aimed to provide an updated insight into the state of mycoplasmas as pathogens by summarizing and analyzing the comprehensive progress, current challenge, and future perspectives of mycoplasmas. It covers clinical implications of mycoplasmas in humans and domestic and wild animals, virulence-related factors, the process of gene transfer and its crucial prospects, the current application and future perspectives of nanotechnology for diagnosing and curing mycoplasmosis, Mycoplasma vaccination, and protective immunity. Several questions remain unanswered and are recommended to pay close attention to. The findings would be helpful to develop new strategies for basic and applied research on mycoplasmas and facilitate the control of mycoplasmosis for humans and various species of animals.
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Affiliation(s)
- Ali Dawood
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
- Hubei Hongshan Laboratory, Wuhan, China
| | - Samah Attia Algharib
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, HZAU, Wuhan, China
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Tingting Zhu
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Mingpu Qi
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Kong Delai
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Marawan A. Marawan
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Infectious Diseases, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Ihsanullah Shirani
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Para-Clinic Department, Faculty of Veterinary Medicine, Jalalabad, Afghanistan
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
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A Hyperthermoactive-Cas9 Editing Tool Reveals the Role of a Unique Arsenite Methyltransferase in the Arsenic Resistance System of Thermus thermophilus HB27. mBio 2021; 12:e0281321. [PMID: 34872358 PMCID: PMC8649762 DOI: 10.1128/mbio.02813-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Arsenic detoxification systems can be found in a wide range of organisms, from bacteria to humans. In a previous study, we discovered an arsenic-responsive transcriptional regulator in the thermophilic bacterium Thermus thermophilus HB27 (TtSmtB). Here, we characterize the arsenic resistance system of T. thermophilus in more detail. We employed TtSmtB-based pulldown assays with protein extracts from cultures treated with arsenate and arsenite to obtain an S-adenosyl-l-methionine (SAM)-dependent arsenite methyltransferase (TtArsM). In vivo and in vitro analyses were performed to shed light on this new component of the arsenic resistance network and its peculiar catalytic mechanism. Heterologous expression of TtarsM in Escherichia coli resulted in arsenite detoxification at mesophilic temperatures. Although TtArsM does not contain a canonical arsenite binding site, the purified protein does catalyze SAM-dependent arsenite methylation with formation of monomethylarsenites (MMAs) and dimethylarsenites (DMAs). In addition, in vitro analyses confirmed the unique interaction between TtArsM and TtSmtB. Next, a highly efficient ThermoCas9-based genome-editing tool was developed to delete the TtArsM-encoding gene on the T. thermophilus genome and to confirm its involvement in the arsenite detoxification system. Finally, the TtarsX efflux pump gene in the T. thermophilus ΔTtarsM genome was substituted by a gene encoding a stabilized yellow fluorescent protein (sYFP) to create a sensitive genome-based bioreporter system for the detection of arsenic ions.
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Khare T, Anand U, Dey A, Assaraf YG, Chen ZS, Liu Z, Kumar V. Exploring Phytochemicals for Combating Antibiotic Resistance in Microbial Pathogens. Front Pharmacol 2021; 12:720726. [PMID: 34366872 PMCID: PMC8334005 DOI: 10.3389/fphar.2021.720726] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance or microbial drug resistance is emerging as a serious threat to human healthcare globally, and the multidrug-resistant (MDR) strains are imposing major hurdles to the progression of drug discovery programs. Newer antibiotic-resistance mechanisms in microbes contribute to the inefficacy of the existing drugs along with the prolonged illness and escalating expenditures. The injudicious usage of the conventional and commonly available antibiotics in human health, hygiene, veterinary and agricultural practices is proving to be a major driver for evolution, persistence and spread of antibiotic-resistance at a frightening rate. The drying pipeline of new and potent antibiotics is adding to the severity. Therefore, novel and effective new drugs and innovative therapies to treat MDR infections are urgently needed. Apart from the different natural and synthetic drugs being tested, plant secondary metabolites or phytochemicals are proving efficient in combating the drug-resistant strains. Various phytochemicals from classes including alkaloids, phenols, coumarins, terpenes have been successfully demonstrated their inhibitory potential against the drug-resistant pathogens. Several phytochemicals have proved effective against the molecular determinants responsible for attaining the drug resistance in pathogens like membrane proteins, biofilms, efflux pumps and bacterial cell communications. However, translational success rate needs to be improved, but the trends are encouraging. This review highlights current knowledge and developments associated challenges and future prospects for the successful application of phytochemicals in combating antibiotic resistance and the resistant microbial pathogens.
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Affiliation(s)
- Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
| | - Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Abhijit Dey
- Ethnopharmacology and Natural Product Research Laboratory, Department of Life Sciences, Presidency University, Kolkata, India
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Zhijun Liu
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
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Gallo G, Puopolo R, Carbonaro M, Maresca E, Fiorentino G. Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5228. [PMID: 34069056 PMCID: PMC8157027 DOI: 10.3390/ijerph18105228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/13/2022]
Abstract
Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.
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Affiliation(s)
- Giovanni Gallo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Rosanna Puopolo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Miriam Carbonaro
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Emanuela Maresca
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Gabriella Fiorentino
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
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Blesa A, Baquedano I, González-de la Fuente S, Mencía M, Berenguer J. Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus. Microorganisms 2020; 8:microorganisms8122051. [PMID: 33371442 PMCID: PMC7767461 DOI: 10.3390/microorganisms8122051] [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: 11/27/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022] Open
Abstract
Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended “donor” strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain
- Correspondence: (A.B.); (J.B.); Tel.: +34-91194498 (J.B.)
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - Mario Mencía
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (I.B.); (S.G.-d.l.F.); (M.M.)
- Correspondence: (A.B.); (J.B.); Tel.: +34-91194498 (J.B.)
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11
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Chernova OA, Chernov VM, Mouzykantov AA, Baranova NB, Edelstein IA, Aminov RI. Antimicrobial drug resistance mechanisms among Mollicutes. Int J Antimicrob Agents 2020; 57:106253. [PMID: 33264670 DOI: 10.1016/j.ijantimicag.2020.106253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 07/08/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022]
Abstract
Representatives of the Mollicutes class are the smallest, wall-less bacteria capable of independent reproduction. They are widespread in nature, most are commensals, and some are pathogens of humans, animals and plants. They are also the main contaminants of cell cultures and vaccine preparations. Despite limited biosynthetic capabilities, they are highly adaptable and capable of surviving under various stress and extreme conditions, including antimicrobial selective pressure. This review describes current understanding of antibiotic resistance (ABR) mechanisms in Mollicutes. Protective mechanisms in these bacteria include point mutations, which may include non-target genes, and unique gene exchange mechanisms, contributing to transfer of ABR genes. Better understanding of the mechanisms of emergence and dissemination of ABR in Mollicutes is crucial to control these hypermutable bacteria and prevent the occurrence of highly ABR strains.
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Affiliation(s)
- Olga A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Vladislav M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Alexey A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Natalya B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Centre of RAS, Kazan, Russian Federation
| | - Inna A Edelstein
- Smolensk State Medical University, Ministry of Health of Russian Federation, Smolensk, Russian Federation
| | - Rustam I Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation.
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12
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García‐Quintans N, Baquedano I, Blesa A, Verdú C, Berenguer J, Mencía M. A thermostable DNA primase-polymerase from a mobile genetic element involved in defence against environmental DNA. Environ Microbiol 2020; 22:4647-4657. [PMID: 32830367 PMCID: PMC7693054 DOI: 10.1111/1462-2920.15207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/21/2022]
Abstract
Primase-polymerases (Ppol) are one of the few enzymes able to start DNA synthesis on ssDNA templates. The role of Thermus thermophilus HB27 Ppol, encoded along a putative helicase (Hel) within a mobile genetic element (ICETh2), has been studied. A mutant lacking Ppol showed no effects on the replication of the element. Also, no apparent differences in the sensitivity to DNA damaging agents and other stressors or morphological changes in the mutant cells were detected. However, the mutants lacking Ppol showed an increase in two to three orders of magnitude in their transformation efficiency with plasmids and genomic DNA acquired from the environment (eDNA), independently of its origin and G + C content. In contrast, no significant differences with the wild type were detected when the cells received the DNA from other T. thermophilus partners in conjugation-like mating experiments. The similarities of this behaviour with that shown by mutants lacking the Argonaute (ThAgo) protein suggests a putative partnership Ppol-ThAgo in the DNA-DNA interference mechanism of defence, although other eDNA defence mechanisms independent of ThAgo cannot be discarded.
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Affiliation(s)
- Nieves García‐Quintans
- Centro de Biología Molecular Severo Ochoa (CBMSO)Universidad Autónoma de Madrid‐Consejo Superior de Investigaciones CientíficasMadrid28049Spain
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa (CBMSO)Universidad Autónoma de Madrid‐Consejo Superior de Investigaciones CientíficasMadrid28049Spain
| | - Alba Blesa
- Department of Biotechnology, Faculty of Experimental SciencesUniversidad Francisco de VitoriaMadrid28223Spain
| | - Carlos Verdú
- Centro de Biología Molecular Severo Ochoa (CBMSO)Universidad Autónoma de Madrid‐Consejo Superior de Investigaciones CientíficasMadrid28049Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO)Universidad Autónoma de Madrid‐Consejo Superior de Investigaciones CientíficasMadrid28049Spain
| | - Mario Mencía
- Centro de Biología Molecular Severo Ochoa (CBMSO)Universidad Autónoma de Madrid‐Consejo Superior de Investigaciones CientíficasMadrid28049Spain
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13
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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14
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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries. Trends Microbiol 2020; 28:372-386. [DOI: 10.1016/j.tim.2020.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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15
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Baquedano I, Mencía M, Blesa A, Burrus V, Berenguerfi J. ICETh1 and ICETh2, two interdependent mobile genetic elements in Thermus thermophilus transjugation. Environ Microbiol 2019; 22:158-169. [PMID: 31715642 DOI: 10.1111/1462-2920.14833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 11/27/2022]
Abstract
Cell to cell DNA transfer between Thermus thermophilus, or transjugation, requires the natural competence apparatus (NCA) of the recipient cell and a DNA donation machinery in the donor. In T. thermophilus HB27, two mobile genetic elements with functional similarities to Integrative and Conjugative Elements (ICEs) coexist, ICETh1 encoding the DNA transfer apparatus and ICETh2, encoding a putative replication module. Here, we demonstrate that excision and integration of both elements depend on a single tyrosine recombinase encoded by ICETh2, and that excision is not required but improves the transfer of these elements to a recipient cell. These findings along with previous results suggest that ICETh1 and ICETh2 depend on each other for spreading among T. thermophilus by transjugation.
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Affiliation(s)
- Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
| | - Mario Mencía
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
| | - Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, 28223, Spain
| | - Vincent Burrus
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - José Berenguerfi
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
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16
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Dordet-Frisoni E, Faucher M, Sagné E, Baranowski E, Tardy F, Nouvel LX, Citti C. Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes. Front Microbiol 2019; 10:2441. [PMID: 31708906 PMCID: PMC6819513 DOI: 10.3389/fmicb.2019.02441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The capacity of Mycoplasmas to engage in horizontal gene transfers has recently been highlighted. Despite their small genome, some of these wall-less bacteria are able to exchange multiple, large portions of their chromosome via a conjugative mechanism that does not conform to canonical Hfr/oriT models. To understand the exact features underlying mycoplasma chromosomal transfer (MCT), extensive genomic analyses were performed at the nucleotide level, using individual mating progenies derived from our model organism, Mycoplasma agalactiae. Genome reconstruction showed that MCT resulted in the distributive transfer of multiple chromosomal DNA fragments and generated progenies composed of a variety of mosaic genomes, each being unique. Analyses of macro- and micro-events resulting from MCT revealed that the vast majority of the acquired fragments were unrelated and co-transferred independently from the selection marker, these resulted in up to 17% of the genome being exchanged. Housekeeping and accessory genes were equally affected by MCT, with up to 35 CDSs being gained or lost. This efficient HGT process also created a number of chimeric genes and genetic micro-variations that may impact gene regulation and/or expression. Our study unraveled the tremendous plasticity of M. agalactiae genome and point toward MCT as a major player in diversification and adaptation to changing environments, offering a significant advantage to this minimal pathogen.
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Affiliation(s)
| | - Marion Faucher
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | - Eveline Sagné
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Florence Tardy
- UMR Mycoplasmoses des Ruminants, VetAgro Sup, Laboratoire de Lyon, ANSES, Université de Lyon, Marcy-l'Étoile, France
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17
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Verdú C, Sanchez E, Ortega C, Hidalgo A, Berenguer J, Mencía M. A Modular Vector Toolkit with a Tailored Set of Thermosensors To Regulate Gene Expression in Thermus thermophilus. ACS OMEGA 2019; 4:14626-14632. [PMID: 31528818 PMCID: PMC6740178 DOI: 10.1021/acsomega.9b02107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/14/2019] [Indexed: 05/02/2023]
Abstract
Modular plasmid architectures have shown to be a very useful resource to standardize, build, share, and compare biological parts and functional vectors, and are being applied in an increasing number of microorganisms. Here, we present a modular plasmid toolkit for Thermus thermophilus, a species considered as a workhorse for biotechnology and a model for high-temperature biology. Apart from integrating improved versions of already existing parts, we have characterized specific promoters and developed a thermosensor-based palette that restricts the expression to Thermus and, at the same time, controls protein expression in this organism in a temperature-dependent manner.
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Affiliation(s)
| | | | | | | | - José Berenguer
- E-mail: . Tel.: +34 911964498. Fax: +34 911964420 (J.B.)
| | - Mario Mencía
- E-mail: . Tel.: +34 911964664.
Fax: +34 911964420 (M.M.)
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18
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Faucher M, Nouvel LX, Dordet-Frisoni E, Sagné E, Baranowski E, Hygonenq MC, Marenda MS, Tardy F, Citti C. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer. PLoS Genet 2019; 15:e1007910. [PMID: 30668569 PMCID: PMC6358093 DOI: 10.1371/journal.pgen.1007910] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/01/2019] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.
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Affiliation(s)
- Marion Faucher
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | | | | | - Eveline Sagné
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | | | | | - Marc-Serge Marenda
- Asia-Pacific Centre for Animal Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Florence Tardy
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | - Christine Citti
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- * E-mail: (LXN); (CC)
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19
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Blesa A, Sánchez M, Sacristán-Horcajada E, González-de la Fuente S, Peiró R, Berenguer J. Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 2019; 7:microorganisms7010025. [PMID: 30669685 PMCID: PMC6352166 DOI: 10.3390/microorganisms7010025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 11/28/2022] Open
Abstract
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain.
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Eva Sacristán-Horcajada
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
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20
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Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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21
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Alvarez L, Quintáns NG, Blesa A, Baquedano I, Mencía M, Bricio C, Berenguer J. Hierarchical Control of Nitrite Respiration by Transcription Factors Encoded within Mobile Gene Clusters of Thermus thermophilus. Genes (Basel) 2017; 8:genes8120361. [PMID: 29194386 PMCID: PMC5748679 DOI: 10.3390/genes8120361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 11/16/2022] Open
Abstract
Denitrification in Thermus thermophilus is encoded by the nitrate respiration conjugative element (NCE) and nitrite and nitric oxide respiration (nic) gene clusters. A tight coordination of each cluster’s expression is required to maximize anaerobic growth, and to avoid toxicity by intermediates, especially nitric oxides (NO). Here, we study the control of the nitrite reductases (Nir) and NO reductases (Nor) upon horizontal acquisition of the NCE and nic clusters by a formerly aerobic host. Expression of the nic promoters PnirS, PnirJ, and PnorC, depends on the oxygen sensor DnrS and on the DnrT protein, both NCE-encoded. NsrR, a nic-encoded transcription factor with an iron–sulfur cluster, is also involved in Nir and Nor control. Deletion of nsrR decreased PnorC and PnirJ transcription, and activated PnirS under denitrification conditions, exhibiting a dual regulatory role never described before for members of the NsrR family. On the basis of these results, a regulatory hierarchy is proposed, in which under anoxia, there is a pre-activation of the nic promoters by DnrS and DnrT, and then NsrR leads to Nor induction and Nir repression, likely as a second stage of regulation that would require NO detection, thus avoiding accumulation of toxic levels of NO. The whole system appears to work in remarkable coordination to function only when the relevant nitrogen species are present inside the cell.
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Affiliation(s)
- Laura Alvarez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
- Current Address: Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.
| | - Nieves G Quintáns
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Alba Blesa
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Mario Mencía
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Carlos Bricio
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
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22
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Antonucci I, Gallo G, Limauro D, Contursi P, Ribeiro AL, Blesa A, Berenguer J, Bartolucci S, Fiorentino G. An ArsR/SmtB family member regulates arsenic resistance genes unusually arranged in Thermus thermophilus HB27. Microb Biotechnol 2017; 10:1690-1701. [PMID: 28696001 PMCID: PMC5658604 DOI: 10.1111/1751-7915.12761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/01/2023] Open
Abstract
Arsenic resistance is commonly clustered in ars operons in bacteria; main ars operon components encode an arsenate reductase, a membrane extrusion protein, and an As‐sensitive transcription factor. In the As‐resistant thermophile Thermus thermophilus HB27, genes encoding homologues of these proteins are interspersed in the chromosome. In this article, we show that two adjacent genes, TtsmtB, encoding an ArsR/SmtB transcriptional repressor and, TTC0354, encoding a Zn2+/Cd2+‐dependent membrane ATPase are involved in As resistance; differently from characterized ars operons, the two genes are transcribed from dedicated promoters upstream of their respective genes, whose expression is differentially regulated at transcriptional level. Mutants defective in TtsmtB or TTC0354 are more sensitive to As than the wild type, proving their role in arsenic resistance. Recombinant dimeric TtSmtB binds in vitro to both promoters, but its binding capability decreases upon interaction with arsenate and, less efficiently, with arsenite. In vivo and in vitro experiments also demonstrate that the arsenate reductase (TtArsC) is subjected to regulation by TtSmtB. We propose a model for the regulation of As resistance in T. thermophilus in which TtSmtB is the arsenate sensor responsible for the induction of TtArsC which generates arsenite exported by TTC0354 efflux protein to detoxify cells.
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Affiliation(s)
- Immacolata Antonucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
| | - Giovanni Gallo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
| | - Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
| | - Ana Luisa Ribeiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Alba Blesa
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, 80126, Naples, Italy
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23
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Blesa A, Quintans NG, Baquedano I, Mata CP, Castón JR, Berenguer J. Role of Archaeal HerA Protein in the Biology of the Bacterium Thermus thermophilus. Genes (Basel) 2017; 8:genes8050130. [PMID: 28448436 PMCID: PMC5448004 DOI: 10.3390/genes8050130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 11/16/2022] Open
Abstract
Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å. A central pore was detected in the structure that ranges from 13 Å at one extreme, to 30 Å at the other. Mutants lacking HepA show defective natural competence and DNA donation capability in a conjugation-like process termed "transjugation", and also high sensitivity to UV and dramatic sensitivity to high temperatures. These data support that acquisition of an ancestral archaeal HerA has been fundamental for the adaptation of Thermus spp. to high temperatures.
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Affiliation(s)
- Alba Blesa
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Nieves G Quintans
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Ignacio Baquedano
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
| | - Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid 28049, Spain.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Calle Nicolás Cabrera 1, Madrid 28049, Spain.
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